bioRxiv Channel: RNA Therapeutics Institute at UMass Chan Med School
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This feed contains articles for bioRxiv Channel "RNA Therapeutics Institute at UMass Chan Med School"
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In extracto cryo-EM reveals eEF2 as a major hibernation factor on 60S and 80S particles
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https://biorxiv.org/cgi/content/short/2025.11.25.690450v1?rss=1"
95% of ribosomes and, unexpectedly, to 60S subunits. eEF2*GDP is stabilized by interactions with the sarcin-ricin loop and protein uL14. Hibernating ribosomes also feature LARP1 involved in initiation and mTOR signaling; eIF5A implicated in elongation and termination; and other factors, exposing the variety of hibernation scenarios. Our work underscores the efficiency and potential of in extracto cryo-EM to discover native cellular complexes and mechanisms at near-atomic resolution.
]]>Seraj, Z.Zottig, X.Huang, C.Loveland, A. B.Diggs, S.Sholi, E.Grigorieff, N.Korostelev, A. A.2025-11-25doi:10.1101/2025.11.25.690450Cold Spring Harbor Laboratory Press2025-11-25
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High-throughput quantification of huntingtin mRNA expression and aggregation in mouse brain using automated RNAscope imaging.
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https://biorxiv.org/cgi/content/short/2026.02.09.704866v1?rss=1"
0.90) reflects variable probe binding along transcripts; for clusters, the linear scaling between cluster volume and mRNA content (R2 > 0.98) confirms uniform probe accessibility and enables quantitative conversion of fluorescence intensity to absolute mRNA counts. Applied to HttQ111+/- knock-in mice across multiple ages, we analyzed thousands of fields of view (FOVs), detecting >900,000 single mRNA molecules and segmenting >1.9 million mRNA clusters using two probes targeting mouse huntingtin (Htt): one detecting the spliced transcript that uses early cryptic polyadenylation sites in intron 1 (HTT1a), and one detecting full-length Htt (fl-HTT). Our analysis reveals considerable heterogeneity in mRNA accumulation: 16-63% of Q111 FOVs are classified as "extreme" (exceeding the 95th percentile of wildtype clustered mRNA levels), with striatum showing higher prevalence than cortex for both probes (HTT1a: 63% striatum, 31% cortex; fl-HTT: 44% striatum, 16%cortex). Extreme FOVs are characterized by elevated cluster numbers (2-6x more clusters per nucleus) and higher cluster density (1.3-1.7x more mRNA per {micro}m3). Cluster localization shows nuclear bias ([~]68%) in normal FOVs, but extreme FOVs exhibit a shift toward cytoplasmic localization, particularly for fl-HTT (48% nuclear vs 68% in normal FOVs), though the interpretation of this shift requires further investigation. Despite the large dataset at the cellular level, our study included only 11 mice (9 Q111, 2 wildtype), and this limited sample size precluded robust statistical inference at the animal level. Nevertheless, these quantitative metrics provide a framework for investigating disease mechanisms and evaluating therapeutic interventions using RNAscope in future studies with larger cohorts.
]]>van Velde, P.Tran, B.Allen, S.Luu, E.Furgal, R.Summers, A.Belgrad, J.Knox, E.Khvorova, A.Grunwald, D.2026-02-11doi:10.64898/2026.02.09.704866Cold Spring Harbor Laboratory Press2026-02-11
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Cryo-EM Structure of HRSL Domain Reveals Activating Crossed Helices at the Core of GCN2
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https://biorxiv.org/cgi/content/short/2024.04.24.591037v1?rss=1"
Solorio - Kirpichyan, K.Golovenko, D.Korostelev, A.Yan, N.Korennykh, A.2024-04-25doi:10.1101/2024.04.24.591037Cold Spring Harbor Laboratory Press2024-04-25
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mRNA nuclear clustering leads to a difference in mutant huntingtin mRNA and protein silencing by siRNAs in vivo
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https://biorxiv.org/cgi/content/short/2024.04.24.590997v1?rss=1"
Allen, S. J.O'Reilly, D.Miller, R.Sapp, E.Summers, A.Paquette, J.Moreno, D. E.Bramato, B.McHugh, N.Yamada, K.Aronin, N.DiFiglia, M.Khvorova, A.2024-04-28doi:10.1101/2024.04.24.590997Cold Spring Harbor Laboratory Press2024-04-28
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Preventing acute neurotoxicity of CNS therapeutic oligonucleotides with the addition of Ca2+ and Mg2+ in the formulation
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https://biorxiv.org/cgi/content/short/2024.06.06.597639v1?rss=1"
Miller, R.Paquette, J.Barker, A.Sapp, E.McHugh, N.Bramato, B.Yamada, N.Alterman, J.Echeveria, D.Yamada, K.Watts, J. K.Anaclet, C.DiFiglia, M.Khvorova, A.Aronin, N.2024-06-08doi:10.1101/2024.06.06.597639Cold Spring Harbor Laboratory Press2024-06-08
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RNAi-mediated silencing of SOD1 profoundly extends survival and functional outcomes in ALS mice
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https://biorxiv.org/cgi/content/short/2024.06.20.599943v1?rss=1"
Weiss, A.Gilbert, J. W.Flores, I. V. R.Belgrad, J.Ferguson, C.Dogan, E. O.Wightman, N.Mocarski, K.Echeverria, D.Summers, A.Bramato, B.McHugh, N.Furgal, R.Yamada, N.Cooper, D.Monopoli, K.Godinho, B. M. D. C.Hassler, M. R.Yamada, K.Greer, P. L.Henninger, N.Brown, R. H.Khvorova, A.2024-06-25doi:10.1101/2024.06.20.599943Cold Spring Harbor Laboratory Press2024-06-25
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PRC1.6 localizes on chromatin with the human silencing hub (HUSH) complex for promoter-specific silencing
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https://biorxiv.org/cgi/content/short/2024.07.12.603173v1?rss=1"
Rodriguez, T. C.Yurkovetskiy, L.Nagalekshmi, K.Lam, C. H. O.Jazbec, E.Maitland, S. A.Wolfe, S.Sontheimer, E. J.Luban, J.2024-07-12doi:10.1101/2024.07.12.603173Cold Spring Harbor Laboratory Press2024-07-12
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Amortized template-matching of molecular conformations from cryo-electron microscopy images using simulation-based inference
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https://biorxiv.org/cgi/content/short/2024.07.23.604154v1?rss=1"
Dingeldein, L.Silva-Sanchez, D.Evans, L.D'Imprima, E.Grigorieff, N.Covino, R.Cossio, P.2024-07-24doi:10.1101/2024.07.23.604154Cold Spring Harbor Laboratory Press2024-07-24
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Next generation APOBEC3 inhibitors: Optimally designed for potency and nuclease stability
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https://biorxiv.org/cgi/content/short/2024.09.05.611238v1?rss=1"
Hedger, A. K.Myint, W.Lee, J. M.Suchenski-Loustaunau, D.Balachandran, V.Shaqra, A. M.Kurt Yilmaz, N.Watts, J.Matsuo, H.Schiffer, C. A.2024-09-06doi:10.1101/2024.09.05.611238Cold Spring Harbor Laboratory Press2024-09-06
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Allelopathic effect of Anogeissus pendula Edgew. and Grewia flavescens A.Juss on Desmodium species in Alwar district of Rajasthan
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https://biorxiv.org/cgi/content/short/582023v1?rss=1"
Prasad, R.Yadav, A. S.2019-03-20doi:10.1101/582023Cold Spring Harbor Laboratory Press2019-03-20
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Antisense oligonucleotide targeting pathogenic sense repeat RNA in C9ORF72 suppresses production of antisense-dependent dipeptide repeat proteins implicated in ALS/FTD
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https://biorxiv.org/cgi/content/short/2024.10.04.616663v1?rss=1"
Gu, Y.Kankel, M. W.Watts, J.Jafar-nejad, P.Almeida, S.2024-10-05doi:10.1101/2024.10.04.616663Cold Spring Harbor Laboratory Press2024-10-05
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Virion-associated influenza hemagglutinin clusters upon sialic acid binding visualized by cryo-electron tomography
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https://biorxiv.org/cgi/content/short/2024.10.15.618557v1?rss=1"
Huang, Q. Y.Kim, R.Song, K.Grigorieff, N.Munro, J.Schiffer, C. A.Somasundaran, M.2024-10-18doi:10.1101/2024.10.15.618557Cold Spring Harbor Laboratory Press2024-10-18
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Mouse Pachytene piRNAs Cleave Hundreds of Transcripts,But Alter the Steady-State Abundance of Only a Minority of Targets
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https://biorxiv.org/cgi/content/short/2024.11.02.621675v1?rss=1"
Cecchini, K.Ajaykumar, N.Bagci, A.Zamore, P.Gainetdinov, I.2024-11-03doi:10.1101/2024.11.02.621675Cold Spring Harbor Laboratory Press2024-11-03
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Rational Design of Enhanced Nme2Cas9 and Nme2SmuCas9 Nucleases and Base Editors
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https://biorxiv.org/cgi/content/short/2024.10.30.620986v1?rss=1"
Bamidele, N.Andosoria, A.Chen, Z.Cheng, H.Panwala, R.Jazbec, E.Sontheimer, E. J.2024-10-30doi:10.1101/2024.10.30.620986Cold Spring Harbor Laboratory Press2024-10-30
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Dynamic cytoplasmic fluidity during morphogenesis in a human fungal pathogen
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https://biorxiv.org/cgi/content/short/2024.11.16.623909v1?rss=1"
Serrano, A.Puerner, C.Plumb, E.Chevalier, L.Elferich, J.Sinn, L. R.Grigorieff, N.Ralser, M.Delarue, M.Bassilana, M.Arkowitz, R. A.2024-11-17doi:10.1101/2024.11.16.623909Cold Spring Harbor Laboratory Press2024-11-17
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Raver1 links Ripk1 RNA splicing to caspase-8-mediated pyroptotic cell death, inflammation, and pathogen resistance
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https://biorxiv.org/cgi/content/short/2024.11.27.625707v1?rss=1"
Zhang, B.Orning, P.Lehman, J. W.Dinis, A.Torres-Ulloa, L.Elling, R.Kelliher, M. A.Bertin, J.Proulx, M. K.Ryan, L.Kandasamy, R. K.Espevik, T.Pai, A. A.Fitzgerald, K. A.Lien, E.2024-11-29doi:10.1101/2024.11.27.625707Cold Spring Harbor Laboratory Press2024-11-29
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Pol II degradation activates cell death independently from the loss of transcription
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https://biorxiv.org/cgi/content/short/2024.12.09.627542v1?rss=1"
Harper, N. W.Birdsall, G. A.Honeywell, M. E.Pai, A. A.Lee, M. J.2024-12-10doi:10.1101/2024.12.09.627542Cold Spring Harbor Laboratory Press2024-12-10
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Divalent siRNA for prion disease
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https://biorxiv.org/cgi/content/short/2024.12.05.627039v1?rss=1"
Gentile, J. E.Corridon, T. L.Serack, F. E.Echeverria, D.Kennedy, Z. E.Gallant-Behm, C. L.Hassler, M. R.Kinberger, G.Kamath, N. G.Lian, Y.Gross, K. Y.Miller, R.DeSouza-Lenz, K.Howard, M.Guzman, K.Chan, N.Curtis, D. T.Fettes, K.Lemaitre, M.Cappon, G.Jackson, A. L.Yamada, K.Alterman, J. F.Coffey, A. A.Minikel, E. V.Khvorova, A.Vallabh, S. M.2024-12-09doi:10.1101/2024.12.05.627039Cold Spring Harbor Laboratory Press2024-12-09
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Loss of the Integrator and Nuclear Exosome Targeting complexes disrupts oogenesis and causes the emergenceof atypical transcripts in Drosophila
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https://biorxiv.org/cgi/content/short/2025.03.05.641556v1?rss=1"
Lee, Y.Biasini, A.Tipping, C.Hong, S. H.Zamore, P.2025-03-11doi:10.1101/2025.03.05.641556Cold Spring Harbor Laboratory Press2025-03-11
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In-Situ High-Resolution Cryo-EM Reconstructions from CEMOVIS
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https://biorxiv.org/cgi/content/short/2025.03.29.646093v1?rss=1"
Elferich, J.Kaminek, M.Kong, L.Odriozola, A.Kukulski, W.Zuber, B.Grigorieff, N.2025-03-31doi:10.1101/2025.03.29.646093Cold Spring Harbor Laboratory Press2025-03-31
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Piwi and piRNAs repress transcription of aberrant rRNA genes containing retrotransposon fragments
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https://biorxiv.org/cgi/content/short/2025.04.30.651568v1?rss=1"
Fefelova, E. A.Shatskikh, A. S.Mikhaleva, E. A.Abramov, Y. A.Lavrov, S. A.Pirogov, S. A.Poltorachenko, V. A.Ilin, A. A.Zamore, P. D.Klenov, M. S.2025-04-30doi:10.1101/2025.04.30.651568Cold Spring Harbor Laboratory Press2025-04-30
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Single-dose administration of therapeutic divalent siRNA targeting MECP2 prevents lethality for one year in an MECP2 duplication mouse model
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https://biorxiv.org/cgi/content/short/2025.03.26.645328v1?rss=1"
Hariharan, V. N.Summers, A.Caiazzi, J.Hildebrand, S.OReilly, D.Tang, Q.Kennedy, Z.Echeverria, D.McHugh, N.Cooper, D.Sousa, J.Ferguson, C.Clipperton-Allen, A.Bogdanik, L.Coenraads, M.Khvorova, A.2025-03-29doi:10.1101/2025.03.26.645328Cold Spring Harbor Laboratory Press2025-03-29
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A Compact Base Editor Rescues AATD-associated Liver and Lung Disease in Mouse Models
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https://biorxiv.org/cgi/content/short/2025.05.07.652636v1?rss=1"
Gao, J.Bamidele, N.Pires-Ferreira, D.Destefano, A.Tang, Q.Cao, Y.Xie, J.Gao, G.Gruntman, A.Sontheimer, E.Flotte, T.Xue, W. J.2025-05-09doi:10.1101/2025.05.07.652636Cold Spring Harbor Laboratory Press2025-05-09
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Detection of HTTex1p by western blot and immunostaining of HD human and mouse brain using neo-epitope antibody P90 highlights impact of CAG repeat expansion on its size, solubility, and response to MSH3 silencing
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https://biorxiv.org/cgi/content/short/2024.12.31.630891v1?rss=1"
Sapp, E.Boudi, A.Iwanowicz, A.Belgrad, J.Miller, R.O'Reilly, D.Yamada, K.Deng, Y.Joni, M.Li, X.Kegel-Gleason, K.Khvorova, A.Reiner, A.Aronin, N.DiFiglia, M.2025-01-01doi:10.1101/2024.12.31.630891Cold Spring Harbor Laboratory Press2025-01-01
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Lowering the HTT1a transcript as an effective therapy for Huntingtons disease
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https://biorxiv.org/cgi/content/short/2025.06.10.658804v1?rss=1"
Papadopoulou, A. S.Alterman, J.Landles, C.Smith, E. J.Conroy, F.Phillips, J.Canibano-Pico, M.Nita, I. M.Osborne, G. F.Iqbal, A.Aldous, S. G.Bondulich, M. K.Gomez-Paredes, C.Sathasivam, K.O'Reilly, D.Echeverria, D.Bobkov, K.Greene, J. R.Aronin, N.Khvorova, A.Bates, G. P.2025-06-11doi:10.1101/2025.06.10.658804Cold Spring Harbor Laboratory Press2025-06-11
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A single amino acid variant in the variable region I of AAV capsid confers liver detargeting
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https://biorxiv.org/cgi/content/short/2025.03.04.641478v1?rss=1"
Xing, R.Xu, M.Reil, D.Destefano, A.Cui, M.Liu, N.Liang, J.Xu, G.Luo, L.Xu, M.Zhang, F.Tai, P. W.Gruntman, A. M.Flotte, T. R.Gao, G.Wang, D.2025-03-05doi:10.1101/2025.03.04.641478Cold Spring Harbor Laboratory Press2025-03-05
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Blocking somatic repeat expansion and lowering huntingtin via RNA interference synergize to prevent Huntingtons disease pathogenesis in mice
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https://biorxiv.org/cgi/content/short/2025.06.24.661398v1?rss=1"
110 CAGs), which exhibit robust expansion, mHTT inclusions, and transcriptional dysregulation by 12 months, long-term MSH3 silencing blocked expansion, reduced inclusions, and reversed gene expression changes. HTT silencing alone had limited effect, but combined MSH3/HTT targeting synergistically eliminated inclusions and restored transcriptomic profiles. Parallel treatment in wild-type mice showed no toxicity, supporting the safety of long-term intervention. These findings position somatic expansion as a promising therapeutic target and demonstrate the potential of RNAi-based co-silencing of MSH3 and HTT as a disease-modifying strategy for HD.
]]>Belgrad, J.Summers, A.Landles, C.Greene, J. R.Hildebrand, S.Knox, E.Sapp, E.Yamada, N.Furgal, R.Miller, R.Osborne, G. F.Chase, K.Luu, E.Freedman, J.Bramato, B.McHugh, N.Benoit, V.OReilly, D.Greer, P.Bates, G. P.Vogt, T. F.Lee, R.Howland, D.DiFiglia, M.Aronin, N.Khvorova, A.2025-06-25doi:10.1101/2025.06.24.661398Cold Spring Harbor Laboratory Press2025-06-25
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Pervasive noise in human splice site selection
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https://biorxiv.org/cgi/content/short/2025.07.16.665169v1?rss=1"
Khokhar, E. S.Brokaw, K.Kartje, Z. J.Sanabria, V.Javeed, N.Kumar, A.Watts, J. K.Pai, A. A.2025-07-20doi:10.1101/2025.07.16.665169Cold Spring Harbor Laboratory Press2025-07-20
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The Inaugural Flatiron Institute Cryo-EM Conformational Heterogeneity Challenge
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https://biorxiv.org/cgi/content/short/2025.07.18.665582v1?rss=1"
Astore, M. A.Woollard, G.Silva-Sanchez, D.Zhou, W.Kopylov, M.Dao Duc, K.Lederman, R. R.Li, Y.Zhou, Y.Yuan, J.Ye, F.Gu, Q.Vuillemot, R.Jonic, S.Dang, L.Ludtke, S. J.Bridges, H.Liu, S.McLean, M.Peretroukhin, V.Schwab, J.Cruz-Chu, E. R.Schwander, P.Gilles, M. A.Singer, A.Herreros, D.Carazo, J. M.Sorzano, C. O. S.Feathers, J. R.Zhong, E. D.Grigorieff, N.Cossio, P.Hanson, S. M.2025-07-22doi:10.1101/2025.07.18.665582Cold Spring Harbor Laboratory Press2025-07-22
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Therapeutic delivery of albumin-binding siRNA targeting IRS2 to diverse cell types reduces mammary tumor growth
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https://biorxiv.org/cgi/content/short/2025.07.29.667434v1?rss=1"
Tocheny, C. M.Buchwald, J. E.Dahlke, C. D.Fakih, H. H.Morgan, J. S.Summers, A.Wisniewski, C. A.Jackson, S. O.Lee, J.-S.Card, M.-A.Echeverria, D.Peterson, C.Mercurio, A. M.Khvorova, A.Shaw, L. M.2025-08-01doi:10.1101/2025.07.29.667434Cold Spring Harbor Laboratory Press2025-08-01
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Unbend: Correction of local beam-induced sample motion in cryo-EM images using a 3D spline model
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https://biorxiv.org/cgi/content/short/2025.09.05.674398v1?rss=1"
Kong, L.Zottig, X.Elferich, J.Grigorieff, N.2025-09-06doi:10.1101/2025.09.05.674398Cold Spring Harbor Laboratory Press2025-09-06
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Improved cryo-EM reconstruction of sub-50 kDa complexes using 2D template matching
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https://biorxiv.org/cgi/content/short/2025.09.11.675606v1?rss=1"
Zhang, K.Grant, T.Grigorieff, N.2025-09-16doi:10.1101/2025.09.11.675606Cold Spring Harbor Laboratory Press2025-09-16
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Structural mechanism of mRNA decoding by mammalian GTPase GTPBP1
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https://biorxiv.org/cgi/content/short/2025.09.26.678779v1?rss=1"
Susorov, D.Miscicka, A.Golovenko, D.Loveland, A. B.Zinoviev, A.Pestova, T. V.Korostelev, A. A.2025-09-26doi:10.1101/2025.09.26.678779Cold Spring Harbor Laboratory Press2025-09-26
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SPARK: in silico simulations for benchmarking nascent RNA sequencing experiments
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https://biorxiv.org/cgi/content/short/2025.11.06.687082v1?rss=1"
Calvo-Roitberg, E.Lehman, J. W.Tam, E.Elhajjajy, S.Engelhardt, B. E.Pai, A. A.2025-11-08doi:10.1101/2025.11.06.687082Cold Spring Harbor Laboratory Press2025-11-08
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Albumin-binding dendrimer-conjugated siRNA enables safe and effective gene silencing throughout the central nervous system
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https://biorxiv.org/cgi/content/short/2025.12.16.694641v1?rss=1"
Fakih, H.Ohara, M.Summers, A.Sarli, S.Kelly, K.Maru, B.Bramato, B.Khvorova, A.Watts, J.2025-12-18doi:10.64898/2025.12.16.694641Cold Spring Harbor Laboratory Press2025-12-18
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Structural basis for non-AUG translation regulation by 5MPs
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https://biorxiv.org/cgi/content/short/2025.12.28.696766v1?rss=1"
Zottig, X.Huang, C.-Y.Seraj, Z.Grigorieff, N.Korostelev, A. A.2025-12-29doi:10.64898/2025.12.28.696766Cold Spring Harbor Laboratory Press2025-12-29
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Systematic Identification of Germ Granule Proteins Reveals Specialized Roles in RNAi and Small RNA Inheritance
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https://biorxiv.org/cgi/content/short/2026.01.26.701902v1?rss=1"
Chen, S.Prescott, L. H.Mello, C. C.Phillips, C. M.2026-01-28doi:10.64898/2026.01.26.701902Cold Spring Harbor Laboratory Press2026-01-28
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Control of gene output by intron RNA structure
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https://biorxiv.org/cgi/content/short/2025.11.08.687378v1?rss=1"
Schärfen, L.Bech, P.Podszywałow-Bartnicka, P.Neugebauer, K. M.2025-11-09doi:10.1101/2025.11.08.687378Cold Spring Harbor Laboratory Press2025-11-09
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Mechanism of ribosome rescue by ArfA and RF2
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https://biorxiv.org/cgi/content/short/091256v1?rss=1"
Demo, G.Svidritskiy, E.Madireddy, R.Diaz-Avalos, R.Grant, T.Grigorieff, N.Sousa, D.Korostelev, A.2016-12-02doi:10.1101/091256Cold Spring Harbor Laboratory Press2016-12-02
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Reconstructing Spatial Transport Distributions In The Nuclear Pore Complex From 2D Images -- How Reliable Is It?
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https://biorxiv.org/cgi/content/short/145110v1?rss=1"
Tu, L.-C.Huisman, M.Chung, Y.-C.Smith, C.Grunwald, D.2017-06-02doi:10.1101/145110Cold Spring Harbor Laboratory Press2017-06-02
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Single-molecule FISH in Drosophila muscle reveals location dependent mRNA composition of megaRNPs
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https://biorxiv.org/cgi/content/short/156091v1?rss=1"
Noma, A.Smith, C. S.Huisman, M.Martin, R. M.Moore, M. J.Grunwald, D.2017-06-26doi:10.1101/156091Cold Spring Harbor Laboratory Press2017-06-26
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CRISPR-Based DNA Imaging in Living Cells Reveals Cell Cycle-Dependent Chromosome Dynamics
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https://biorxiv.org/cgi/content/short/195966v1?rss=1"
Ma, H.Tu, L.-C.Naseri, A.Chung, Y.-C.Grunwald, D.Zhang, S.Pederson, T.2017-09-29doi:10.1101/195966Cold Spring Harbor Laboratory Press2017-09-29
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Pan-arthropod analysis reveals somatic piRNAs as an ancestral TE defence
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https://biorxiv.org/cgi/content/short/185694v1?rss=1"
Lewis, S. H.Quarles, K. A.Yang, Y.Tanguy, M.Frezal, L.Smith, S. A.Sharma, P. P.Cordaux, R.Gilbert, C.Giraud, I.Collins, D. H.Zamore, P. D.Miska, E. A.Sarkies, P.Jiggins, F. M.2017-09-07doi:10.1101/185694Cold Spring Harbor Laboratory Press2017-09-07
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Fluorescence polarization control for on-off switching of single molecules at cryogenic temperatures
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https://biorxiv.org/cgi/content/short/204776v1?rss=1"
Hulleman, C.Huisman, M.Moerland, R.Grunwald, D.Stallinga, S.Rieger, B.2017-10-17doi:10.1101/204776Cold Spring Harbor Laboratory Press2017-10-17
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Conformational control of translation termination on the 70S ribosome
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https://biorxiv.org/cgi/content/short/226837v1?rss=1"
Svidritskiy, E.Korostelev, A. A.2017-11-29doi:10.1101/226837Cold Spring Harbor Laboratory Press2017-11-29
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Elimination of PCR duplicates in RNA-seq and small RNA-seq using unique molecular identifiers
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https://biorxiv.org/cgi/content/short/251892v1?rss=1"
Fu, Y.Wu, P.-H.Beane, T.Zamore, P. D.Weng, Z.2018-01-22doi:10.1101/251892Cold Spring Harbor Laboratory Press2018-01-22
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C-BERST: Defining subnuclear proteomic landscapes at genomic elements with dCas9-APEX2
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https://biorxiv.org/cgi/content/short/171819v1?rss=1"
Gao, X. D.Tu, L.-C.Mir, A.Dekker, J.Shaffer, S. A.Zhu, L. J.Wolfe, S. A.Sontheimer, E. J.2017-08-02doi:10.1101/171819Cold Spring Harbor Laboratory Press2017-08-02
<![CDATA[
Identification of piRNA binding sites reveals the Argonaute regulatory landscape of the C. elegans germline
]]>
https://biorxiv.org/cgi/content/short/262113v1?rss=1"
Shen, E.-Z.Chen, H.Ozturk, A. R.Tu, S.Shirayama, M.Tang, W.Ding, Y.-H.Dai, S.-Y.Weng, Z.Mello, C. C.2018-02-07doi:10.1101/262113Cold Spring Harbor Laboratory Press2018-02-07
<![CDATA[
Higher-Order Organization Principles of Pre-translational mRNPs
]]>
https://biorxiv.org/cgi/content/short/278747v1?rss=1"
Metkar, M.Ozadam, H.Lajoie, B. R.Imakaev, M.Mirny, L. A.Dekker, J.Moore, M. J.2018-03-08doi:10.1101/278747Cold Spring Harbor Laboratory Press2018-03-08
<![CDATA[
Transcriptome-wide analysis of the functional intronome using spliceosome profiling
]]>
https://biorxiv.org/cgi/content/short/226894v1?rss=1"
Chen, W.Moore, J.Ozadam, H.Shulha, H. P.Rhind, N.Weng, Z.Moore, M. J.2017-11-29doi:10.1101/226894Cold Spring Harbor Laboratory Press2017-11-29
<![CDATA[
Hydrophobicity drives the systemic distribution of lipid-conjugated siRNAs via lipid transport pathways
]]>
https://biorxiv.org/cgi/content/short/288092v1?rss=1"
Osborn, M. F.Coles, A. H.Biscans, A.Haraszti, R. A.Roux, L.Davis, S.Ly, S.Echeverria, D.Hassler, M. R.Godinho, B. M. D. C.Nikan, M.Khvorova, A.2018-03-23doi:10.1101/288092Cold Spring Harbor Laboratory Press2018-03-23
<![CDATA[
Diverse lipid conjugates for functional extra-hepatic siRNA delivery in vivo
]]>
https://biorxiv.org/cgi/content/short/289439v1?rss=1"
Biscans, A.Coles, A.Haraszti, R.Echeverria, D.Hassler, M.Osborn, M.Khvorova, A.2018-03-26doi:10.1101/289439Cold Spring Harbor Laboratory Press2018-03-26
<![CDATA[
Heavily and Fully Modified RNAs Guide Efficient SpyCas9-Mediated Genome Editing
]]>
https://biorxiv.org/cgi/content/short/290999v1?rss=1"
Mir, A.Alterman, J. F.Hassler, M. R.Debacker, A. J.Hudgens, E.Echeverria, D.Brodsky, M. H.Khvorova, A.Watts, J. K.Sontheimer, E. J.2018-03-28doi:10.1101/290999Cold Spring Harbor Laboratory Press2018-03-28
<![CDATA[
An Automated Bayesian Pipeline for Rapid Analysis of Single-Molecule Binding Data
]]>
https://biorxiv.org/cgi/content/short/261917v1?rss=1"
Smith, C. S.Jouravleva, K.Huisman, M.Jolly, S. M.Zamore, P. D.Grunwald, D.2018-04-11doi:10.1101/261917Cold Spring Harbor Laboratory Press2018-04-11
<![CDATA[
PIWI Proteins Act at Multiple Steps in the Production of Their Own Guides
]]>
https://biorxiv.org/cgi/content/short/261545v1?rss=1"
Zamore, P.Gainetdinov, I.Coplan, C.Cecchini, K.2018-02-07doi:10.1101/261545Cold Spring Harbor Laboratory Press2018-02-07
<![CDATA[
NmeCas9 is an intrinsically high-fidelity genome editing platform
]]>
https://biorxiv.org/cgi/content/short/172650v1?rss=1"
Amrani, N.Gao, X. D.Liu, P.Gupta, A.Edraki, A.Ibraheim, R.Sasaki, K. E.Zhu, L. J.Wolfe, S. A.Sontheimer, E. J.2017-08-04doi:10.1101/172650Cold Spring Harbor Laboratory Press2017-08-04
<![CDATA[
All-in-One Adeno-associated Virus Delivery and Genome Editing by Neisseria meningitidis Cas9 in vivo
]]>
https://biorxiv.org/cgi/content/short/295055v1?rss=1"
35% gene modification after two weeks of vector administration, with minimal off-target cleavage in vivo. Our findings indicate that NmeCas9 can facilitate future efforts to correct disease-causing mutations by expanding the targeting scope of RNA-guided nucleases.
]]>Ibraheim, R.Song, C.-Q.Mir, A.Amrani, N.Xue, W.Sontheimer, E. J.2018-04-04doi:10.1101/295055Cold Spring Harbor Laboratory Press2018-04-04
<![CDATA[
Maelstrom Represses Canonical Polymerase II Transcription within Bi-Directional piRNA Clusters in Drosophila melanogaster
]]>
https://biorxiv.org/cgi/content/short/344572v1?rss=1"
Chang, T. H.Mattei, E.Gainetdinov, I.Weng, Z.Zamore, P.2018-06-12doi:10.1101/344572Cold Spring Harbor Laboratory Press2018-06-12
<![CDATA[
Potent Cas9 inhibition in bacterial and human cells by new anti-CRISPR protein families
]]>
https://biorxiv.org/cgi/content/short/350504v1?rss=1"
Lee, J.Mir, A.Edraki, A.Garcia, B.Amrani, N.Lou, H. E.Gainetdinov, I.Pawluk, A.Ibraheim, R.Gao, X. D.Liu, P.Davidson, A. R.Maxwell, K. L.Sontheimer, E. J.2018-06-20doi:10.1101/350504Cold Spring Harbor Laboratory Press2018-06-20
<![CDATA[
Robust genome editing with short single-stranded and long, partially single-stranded DNA donors in C. elegans
]]>
https://biorxiv.org/cgi/content/short/352260v1?rss=1"
Mello, C.Dokshin, G. A.Ghanta, K. S.Piscopo, K. M.2018-06-20doi:10.1101/352260Cold Spring Harbor Laboratory Press2018-06-20
<![CDATA[
The Genetic Landscape of Diamond-Blackfan Anemia
]]>
https://biorxiv.org/cgi/content/short/365890v1?rss=1"
5% of DBA cases. Overall, this comprehensive report should not only inform clinical practice for DBA patients, but also the design and analysis of future rare variant studies for heterogeneous Mendelian disorders.
]]>Ulirsch, J. C.Verboon, J. M.Kazerounian, S.Guo, M. H.Yuan, D.Ludwig, L. S.Handsaker, R. E.Abdulhay, N. J.Fiorini, C.Genovese, G.Lim, E. T.Cheng, A.Cummings, B. B.Chao, K. R.Beggs, A. H.Genetti, C. A.Sieff, C. A.Newburger, P. E.Niewiadomska, E.Matysiak, M.Vlachos, A.Lipton, J. M.Atsidaftos, E.Glader, B.Narla, A.Gleizes, P.-E.O'Donohue, M.-F.Montel-Lehry, N.Amor, D. J.McCarroll, S. A.O'Donnell-Luria, A. H.Gupta, N.Gabriel, S. B.MacArthur, D. G.Lander, E. S.Lek, M.Da Costa, L.Nathan, D. G.Korostelev, A. K.Do, R.Sank2018-07-10doi:10.1101/365890Cold Spring Harbor Laboratory Press2018-07-10
<![CDATA[
Photon count estimation in single-molecule localization microscopy
]]>
https://biorxiv.org/cgi/content/short/396424v1?rss=1"
Rieger, B.Stallinga, S.Hulleman, C. N.Thorsen, R. O.Grunwald, D.Hammer, M.2018-08-20doi:10.1101/396424Cold Spring Harbor Laboratory Press2018-08-20
<![CDATA[
DEBrowser: Interactive Differential Expression Analysis and Visualization Tool for Count Data
]]>
https://biorxiv.org/cgi/content/short/399931v1?rss=1"
Kucukural, A.Yukselen, O.Ozata, D. M.Moore, M. J.Garber, M.2018-08-24doi:10.1101/399931Cold Spring Harbor Laboratory Press2018-08-24
<![CDATA[
The RNA-binding ATPase, Armitage, Couples piRNA Amplification in Nuage to Phased piRNA Production on Mitochondria
]]>
https://biorxiv.org/cgi/content/short/445825v1?rss=1"
Ge, D. T.Wang, W.Tipping, C.Gainetdinov, I.Weng, Z.Zamore, P. D.2018-10-17doi:10.1101/445825Cold Spring Harbor Laboratory Press2018-10-17
<![CDATA[
GCNA interacts with Spartan and Topoisomerase II to regulate genome stability.
]]>
https://biorxiv.org/cgi/content/short/570200v1?rss=1"
Davis, G. M.Dokshin, G.Sawle, A. D.Eldridge, M. D.Romer, K. A.Gourley, T. E.Molesworth, L. W.Tatnell, H. R.Ozturk, A. R.de Rooij, D. G.Hannon, G. J.Page, D. C.Mello, C. C.Carmell, M. A.2019-03-07doi:10.1101/570200Cold Spring Harbor Laboratory Press2019-03-07
<![CDATA[
High-resolution cryo-EM structures of outbreak strain human norovirus shells reveal size variations
]]>
https://biorxiv.org/cgi/content/short/580167v1?rss=1"
Jung, J.Grant, T.Thomas, D. R.Diehnelt, C. W.Grigorieff, N.Joshua-Tor, L.2019-03-16doi:10.1101/580167Cold Spring Harbor Laboratory Press2019-03-16
<![CDATA[
Extensive ribosome and RF2 rearrangements during translation termination
]]>
https://biorxiv.org/cgi/content/short/600445v1?rss=1"
Svidritskiy, E.Demo, G.Loveland, A. B.Xu, C.Korostelev, A. A.2019-04-05doi:10.1101/600445Cold Spring Harbor Laboratory Press2019-04-05
<![CDATA[
Free circular introns with an unusual branchpoint in neuronal projections
]]>
https://biorxiv.org/cgi/content/short/623447v1?rss=1"
Eddy, S. R.Saini, H.Moore, M. J.Bicknell, A. A.2019-04-30doi:10.1101/623447Cold Spring Harbor Laboratory Press2019-04-30
<![CDATA[
Structure of the Vesicular Stomatitis Virus L Protein in Complex with Its Phosphoprotein Cofactor
]]>
https://biorxiv.org/cgi/content/short/792960v1?rss=1"
Jenni, S.Bloyet, L.-M.Diaz-Avalos, R.Liang, B.Whelan, S. P. J.Grigorieff, N.Harrison, S. C.2019-10-03doi:10.1101/792960Cold Spring Harbor Laboratory Press2019-10-03
<![CDATA[
An Evolutionarily Conserved piRNA-producing Locus Required for Male Mouse Fertility
]]>
https://biorxiv.org/cgi/content/short/386201v1?rss=1"
80% of small RNAs in the adult mouse testis, have been proposed to bind and regulate target RNAs like miRNAs, cleave targets like siRNAs, or lack biological function altogether. Although piRNA pathway protein mutants are male sterile, no biological function has been identified for any mammalian piRNA-producing locus. Here, we report that males lacking piRNAs from a conserved mouse pachytene piRNA locus on chromosome 6 (pi6) produce sperm with defects in capacitation and egg fertilization. Moreover, heterozygous embryos sired by pi6-/- fathers show reduced viability in utero. Molecular analyses suggest that pi6 piRNAs repress gene expression by cleaving mRNAs encoding proteins required for sperm function. pi6 also participates in a network of piRNA-piRNA precursor interactions that initiate piRNA production from a second piRNA locus on chromosome 10 as well as pi6 itself. Our data establish a direct role for pachytene piRNAs in spermiogenesis and embryo viability.nnHighlightsO_LINormal male mouse fertility and spermiogenesis require piRNAs from the pi6 locusnC_LIO_LISperm capacitation and binding to the zona pellucida of the egg require pi6 piRNAsnC_LIO_LIHeterozygous embryos sired by pi6-/- fathers show reduced viability in uteronC_LIO_LIDefects in pi6 mutant sperm reflect changes in the abundance of specific mRNAs.nC_LI
]]>Wu, P.-H.Fu, Y.Cecchini, K.Ozata, D. M.Weng, Z.Zamore, P. D.2018-08-07doi:10.1101/386201Cold Spring Harbor Laboratory Press2018-08-07
<![CDATA[
Efficient Homology-directed Repair with Circular ssDNA Donors
]]>
https://biorxiv.org/cgi/content/short/864199v1?rss=1"
Iyer, S.Mir, A.Ibraheim, R.Lee, J.VegaBadillo, J.Roscoe, B.Zhu, L. J.Liu, P.Luk, K.Mintzer, E.de Brito, J. S.Zamore, P.Sontheimer, E. J.Wolfe, S.2019-12-05doi:10.1101/864199Cold Spring Harbor Laboratory Press2019-12-05
<![CDATA[
mRNA stem-loops can pause the ribosome by hindering A-site tRNA binding
]]>
https://biorxiv.org/cgi/content/short/2020.02.05.936120v1?rss=1"
Bao, C.Loerch, S.Ling, C.Korostelev, A. A.Grigorieff, N.Ermolenko, D.2020-02-06doi:10.1101/2020.02.05.936120Cold Spring Harbor Laboratory Press2020-02-06
<![CDATA[
Detecting chromatin interactions along and between sister chromatids with SisterC
]]>
https://biorxiv.org/cgi/content/short/2020.03.10.986208v1?rss=1"
Oomen, M. E.Hedger, A. K.Watts, J. K.Dekker, J.2020-03-11doi:10.1101/2020.03.10.986208Cold Spring Harbor Laboratory Press2020-03-11
<![CDATA[
The RNA phosphatase PIR-1 regulates endogenous small RNA pathways in C. elegans
]]>
https://biorxiv.org/cgi/content/short/2020.08.03.235143v1?rss=1"
Chaves, D. A.Hui, D.Li, L.Moresco, J. J.Oh, M. E.Conte, D.Yates, J. R.Mello, C. C.Gu, W.2020-08-04doi:10.1101/2020.08.03.235143Cold Spring Harbor Laboratory Press2020-08-04
<![CDATA[
Ribosome inhibition by C9ORF72-ALS/FTD-associated poly-PR and poly-GR proteins revealed by cryo-EM
]]>
https://biorxiv.org/cgi/content/short/2020.08.30.274597v1?rss=1"
Loveland, A. B.Svidritskiy, E.Susorov, D.Lee, S.Park, A.Demo, G.Gao, F.-B.Korostelev, A. A.2020-08-31doi:10.1101/2020.08.30.274597Cold Spring Harbor Laboratory Press2020-08-31
<![CDATA[
CASCADES, a novel SOX2 super-enhancer associated long noncoding RNA, regulates cancer stem cell specification and differentiation in glioblastoma multiforme
]]>
https://biorxiv.org/cgi/content/short/2020.09.05.284349v1?rss=1"
Shahzad, U.Li, C.Johnston, M.Wang, J. J.Sabha, N.Varn, F. S.Riemenschneider, A.Krumholtz, S.Meda, P.Smith, C.Karamchandani, J.Watts, J. K.Verhaak, R. G. W.Gallo, M.Rutka, J. T.Das, S.2020-09-06doi:10.1101/2020.09.05.284349Cold Spring Harbor Laboratory Press2020-09-06
<![CDATA[
Terminal Modification, Sequence, and Length Determine Small RNA Stability in Animals
]]>
https://biorxiv.org/cgi/content/short/2020.09.08.287979v1?rss=1"
Gainetdinov, I.Colpan, C.Cecchini, K.Albosta, P.Jouravleva, K.Vega-Badillo, J.Lee, Y.Ozata, D.Zamore, P. D.2020-09-08doi:10.1101/2020.09.08.287979Cold Spring Harbor Laboratory Press2020-09-08
<![CDATA[
PIE-1 promotes SUMOylation and activation of HDAC1 during the C. elegans oogenesis
]]>
https://biorxiv.org/cgi/content/short/2020.08.17.253955v1?rss=1"
Kim, H.Ding, Y.-H.Lu, S.Zuo, M.-Q.Conte, D.Dong, M.-Q.Mello, C.2020-08-17doi:10.1101/2020.08.17.253955Cold Spring Harbor Laboratory Press2020-08-17
<![CDATA[
HDAC1 SUMOylation promotes Argonaute directed transcriptional silencing in C. elegans
]]>
https://biorxiv.org/cgi/content/short/2020.08.17.254466v1?rss=1"
Kim, H.Ding, Y.-H.Zhang, G.Yan, Y.-H.Conte, D.Dong, M.-Q.Mello, C.2020-08-17doi:10.1101/2020.08.17.254466Cold Spring Harbor Laboratory Press2020-08-17
<![CDATA[
Precision Cas9 Genome Editing in vivo with All-in-one, Self-targeting AAV Vectors
]]>
https://biorxiv.org/cgi/content/short/2020.10.09.333997v1?rss=1"
Ibraheim, R.Tai, P. W. L.Mir, A.Javeed, N.Wang, J.Rodriguez, T. C.Nelson, S.Khokhar, E.Mintzer, E.Maitland, S.Cao, Y.Tsagkaraki, E.Wolfe, S. A.Wang, D.Pai, A. A.Xue, W.Gao, G.Sontheimer, E. J.2020-10-09doi:10.1101/2020.10.09.333997Cold Spring Harbor Laboratory Press2020-10-09
<![CDATA[
CRISPR-enhanced human adipocyte 'browning' as cell therapy for metabolic disease
]]>
https://biorxiv.org/cgi/content/short/2020.10.13.337923v1?rss=1"
Tsagkaraki, E.Nicoloro, S.De Souza, T.Solivan-Rivera, J.Desai, A.Shen, Y.Kelly, M.Guilherme, A.Henriques, F.Ibraheim, R.Amrani, N.Luk, K.Maitland, S.Friedline, R. H.Tauer, L.Hu, X.Kim, J. K.Wolfe, S. A.Sontheimer, E. J.Corvera, S.Czech, M. P.2020-10-13doi:10.1101/2020.10.13.337923Cold Spring Harbor Laboratory Press2020-10-13
<![CDATA[
Translation-dependent and independent mRNA decay occur through mutually exclusive pathways that are defined by ribosome density during T Cell activation.
]]>
https://biorxiv.org/cgi/content/short/2020.10.16.341222v1?rss=1"
Mercier, B. C.Labaronne, E.Cluet, D.Bicknell, A.Corbin, A.Guiguettaz, L.Aube, F.Modolo, L.Auboeuf, D.Moore, M. J.Ricci, E. P.2020-10-17doi:10.1101/2020.10.16.341222Cold Spring Harbor Laboratory Press2020-10-17
<![CDATA[
Deep sequencing of pre-translational mRNPs reveals hidden flux through evolutionarily conserved AS-NMD pathways
]]>
https://biorxiv.org/cgi/content/short/847004v1?rss=1"
Kovalak, C. A.Moore, M. J.Metkar, M.2019-11-19doi:10.1101/847004Cold Spring Harbor Laboratory Press2019-11-19
<![CDATA[
Structural basis for +1 ribosomal frameshifting during EF-G-catalyzed translocation
]]>
https://biorxiv.org/cgi/content/short/2020.12.29.424751v1?rss=1"
Demo, G.Loveland, A. B.Svidritskiy, E.Gamper, H. B.Hou, Y.-M.Korostelev, A. A.2020-12-29doi:10.1101/2020.12.29.424751Cold Spring Harbor Laboratory Press2020-12-29
<![CDATA[
5′ Modifications Improve Potency and Efficacy of DNA Donors for Precision Genome Editing
]]>
https://biorxiv.org/cgi/content/short/354480v1?rss=1"
Ghanta, K. S.Dokshin, G. A.Mir, A.Krishnamurthy, P. M.Gneid, H.Edraki, A.Watts, J. K.Sontheimer, E. J.Mello, C. C.2018-06-22doi:10.1101/354480Cold Spring Harbor Laboratory Press2018-06-22
<![CDATA[
Quantifying and Mitigating Motor Phenotypes Induced by Antisense Oligonucleotides in the Central Nervous System
]]>
https://biorxiv.org/cgi/content/short/2021.02.14.431096v1?rss=1"
Moazami, M. P.Rembetsy-Brown, J. M.Wang, F.Krishnamurthy, P. M.Weiss, A.Marosfoi, M.King, R. M.Motwani, M.Gray-Edwards, H.Fitzgerald, K. A.Brown, R. H.Watts, J. K.2021-02-15doi:10.1101/2021.02.14.431096Cold Spring Harbor Laboratory Press2021-02-15
<![CDATA[
Improved prime editors enable pathogenic allele correction and cancer modelling in adult mice
]]>
https://biorxiv.org/cgi/content/short/2020.12.15.422970v1?rss=1"
Liu, P.Liang, S.Zheng, C.Mintzer, E.Zhao, Y. G.Ponnienselvan, K.Mir, A.Sontheimer, E. J.Gao, G.Flotte, T. R.Wolfe, S.Xue, W.2020-12-16doi:10.1101/2020.12.15.422970Cold Spring Harbor Laboratory Press2020-12-16
<![CDATA[
The testis-specific transcription factor TCFL5 responds to A MYBto elaborate the male meiotic program in placental mammals
]]>
https://biorxiv.org/cgi/content/short/2021.04.04.438419v1?rss=1"
Ozata, D. M.Yu, T.Cecchini, K.Mou, H.Arif, A.Colpan, C.Adriano Biasini, A.Gainetdinov, I.de Rooij, D. G.Weng, Z.Zamore, P.2021-04-05doi:10.1101/2021.04.04.438419Cold Spring Harbor Laboratory Press2021-04-05
<![CDATA[
Locating Macromolecular Assemblies in Cells by 2D Template Matching with cisTEM
]]>
https://biorxiv.org/cgi/content/short/2021.04.20.440648v1?rss=1"
Lucas, B. A.Himes, B. A.Xue, L.Grant, T.Mahamid, J.Grigorieff, N.2021-04-21doi:10.1101/2021.04.20.440648Cold Spring Harbor Laboratory Press2021-04-21
<![CDATA[
The tiny, conserved zinc-finger protein GTSF1helps PIWI proteins achieve their full catalytic potential
]]>
https://biorxiv.org/cgi/content/short/2021.05.04.442675v1?rss=1"
Arif, A.Ozata, D. M.Andersson, C.Izumi, N.Tomari, Y.Zamore, P. D.2021-05-04doi:10.1101/2021.05.04.442675Cold Spring Harbor Laboratory Press2021-05-04
<![CDATA[
Cryo-TEM simulations of amorphous radiation-sensitive samples using multislice wave propagation.
]]>
https://biorxiv.org/cgi/content/short/2021.02.19.431636v1?rss=1"
Himes, B. A.Grigorieff, N.2021-02-19doi:10.1101/2021.02.19.431636Cold Spring Harbor Laboratory Press2021-02-19
<![CDATA[
Programming large target genomic deletion and concurrent insertion via a prime editing-based method: PEDAR
]]>
https://biorxiv.org/cgi/content/short/2021.05.12.443800v1?rss=1"
100 bp). Thus, developing a method to accurately delete insertions/duplications and repair the deletion junction could improve the scope of gene therapies. Here, we engineer a novel gene editor, PE-Cas9, by conjugating Cas9 nuclease to reverse transcriptase. Combined with two prime editing guide RNAs (pegRNAs) targeting complementary DNA strands, PE-Cas9 can direct the replacement of a genomic fragment, ranging from to ~1-kb to >10-kb, with a desired sequence at the target site without requiring an exogenous DNA template. In a reporter cell line, this PE-Cas9-based deletion and repair (PEDAR) method restored mCherry expression through in-frame deletion of a disrupted GFP sequence. We further show that PEDAR efficiency could be enhanced by using pegRNAs with high cleavage activity or increasing transfection efficiency. In tyrosinemia mice, PEDAR removed a 1.38-kb pathogenic insertion within the Fah gene and precisely repaired the deletion junction to restore FAH expression in liver. This study highlights PEDAR as a tool for correcting pathogenic mutations.
]]>Jiang, T.Zhang, X.-O.Weng, Z.Xue, W.2021-05-13doi:10.1101/2021.05.12.443800Cold Spring Harbor Laboratory Press2021-05-13
<![CDATA[
Widespread occurrence of hybrid internal-terminal exons in human transcriptomes
]]>
https://biorxiv.org/cgi/content/short/2021.05.27.446076v1?rss=1"
Fiszbein, A.McGurk, M.Calvo-Roitberg, E.Kim, G.Burge, C.Pai, A. A.2021-05-29doi:10.1101/2021.05.27.446076Cold Spring Harbor Laboratory Press2021-05-29
<![CDATA[
Time-resolved cryo-EM visualizes ribosomal translocation with EF-G and GTP
]]>
https://biorxiv.org/cgi/content/short/2021.05.31.446434v1?rss=1"
Carbone, C. E.Loveland, A. B.Gamper, H.Hou, Y.-M.Demo, G.Korostelev, A. A.2021-05-31doi:10.1101/2021.05.31.446434Cold Spring Harbor Laboratory Press2021-05-31
<![CDATA[
Towards community-driven metadata standards for light microscopy: tiered specifications extending the OME model
]]>
https://biorxiv.org/cgi/content/short/2021.04.25.441198v1?rss=1"
Hammer, M.Huisman, M.Rigano, A.Boehm, U.Chambers, J. J.Gaudreault, N.North, A. J.Pimentel, J. A.Sudar, D.Bajcsy, P.Brown, C. M.Corbett, A. D.Faklaris, O.Lacoste, J.Laude, A.Nelson, G.Nitschke, R.Farzam, F.Smith, C.Grunwald, D.Strambio-De-Castillia, C.2021-04-26doi:10.1101/2021.04.25.441198Cold Spring Harbor Laboratory Press2021-04-26
<![CDATA[
Micro-Meta App: an interactive software tool to facilitate the collection of microscopy metadata based on community-driven specifications
]]>
https://biorxiv.org/cgi/content/short/2021.05.31.446382v1?rss=1"
Rigano, A.Ehmsen, S.Ozturk, S. U.Ryan, J.Balashov, A.Hammer, M.Kirli, K.Bellve, K.Boehm, U.Brown, C. M.Chambers, J. J.Coleman, R. A.Cosolo, A.Faklaris, O.Fogarty, K.Guilbert, T.Hamacher, A. B.Itano, M. S.Keeley, D. P.Kunis, S.Lacoste, J.Laude, A.Ma, W.Marcello, M.Montero-Llopis, P.Nelson, G.Nitschke, R.Pimentel, J. A.Weidtkamp-Peters, S.Park, P. J.Alver, B.Grunwald, D.Strambio-De-Castillia, C.2021-05-31doi:10.1101/2021.05.31.446382Cold Spring Harbor Laboratory Press2021-05-31
<![CDATA[
Quantification of Antisense Oligonucleotides by Splint Ligation and Quantitative Polymerase Chain Reaction
]]>
https://biorxiv.org/cgi/content/short/2021.06.05.447195v1?rss=1"
Shin, M.Krishnamurthy, P. M.Watts, J. K.2021-06-05doi:10.1101/2021.06.05.447195Cold Spring Harbor Laboratory Press2021-06-05
<![CDATA[
A cohesin traffic pattern genetically linked to gene regulation
]]>
https://biorxiv.org/cgi/content/short/2021.07.29.454218v1?rss=1"
Valton, A.-L.Venev, S. V.Mair, B.Khokhar, E.Tong, A. H.Usaj, M.Chan, K. S.Pai, A.Moffat, J.Dekker, J.2021-07-30doi:10.1101/2021.07.29.454218Cold Spring Harbor Laboratory Press2021-07-30
<![CDATA[
Development of a flexible split prime editor using truncated reverse transcriptase
]]>
https://biorxiv.org/cgi/content/short/2021.08.26.457801v1?rss=1"
6.3 kb) in vivo. Although PE can be split into two fragments and delivered using dual adeno-associated viruses (AAVs), choice of split sites within Cas9 - which affects editing efficiency - is limited due to the large size of PE. Furthermore, the potential effect of overexpressing RT in mammalian cells is largely unknown. Here, we developed a compact PE with complete deletion of the RNase H domain of reverse transcriptase (RT), which showed comparable editing to full-length PE. Using compact PE, we tested the effect of 4 different Cas9 split sites and found that the Glu 573 split site supports robust editing (up to 93% of full-length PE). The compact PE, but not PE2, abolished its binding to eRF1 and showed minimal effect on stop codon readthrough, which therefore might reduce the effects on protein biosynthesis. This study identifies a safe and efficient compact PE2 that enables flexible split-PE design to facilitate efficient delivery in vivo and advance the utility of prime editing.
]]>Xue, W.Zheng, C.LIANG, S.Liu, P.Liu, B.Kwan, S.Wolfe, S.2021-08-27doi:10.1101/2021.08.26.457801Cold Spring Harbor Laboratory Press2021-08-27
<![CDATA[
Orthogonal CRISPR-Cas genome editing and efficient inhibition with anti-CRISPRs in zebrafish embryos
]]>
https://biorxiv.org/cgi/content/short/2020.11.07.372151v1?rss=1"
Takasugi, P. R.Drage, E. P.Kanishka, S. N.Higbee, M. A.Gagnon, J. A.2020-11-08doi:10.1101/2020.11.07.372151Cold Spring Harbor Laboratory Press2020-11-08
<![CDATA[
RNA-silencing induces target gene relocalization toward a specialized nuage domain
]]>
https://biorxiv.org/cgi/content/short/2021.03.09.434681v1?rss=1"
Mello, C.Yang, Y.Grunwald, D.Priess, J.2021-03-11doi:10.1101/2021.03.09.434681Cold Spring Harbor Laboratory Press2021-03-11
<![CDATA[
High-throughput analysis of ANRIL circRNA isoforms in human pancreatic islets
]]>
https://biorxiv.org/cgi/content/short/2022.01.03.474854v1?rss=1"
MacMillan, H. J.Kong, Y.Calvo-Roitberg, E.Alonso, L. C.Pai, A. A.2022-01-04doi:10.1101/2022.01.03.474854Cold Spring Harbor Laboratory Press2022-01-04
<![CDATA[
A family of C. elegans VASA homologs control Argonaute pathway specificity and promote transgenerational silencing
]]>
https://biorxiv.org/cgi/content/short/2022.01.18.476504v1?rss=1"
Dai, S.Tang, X.Li, L.Ishidate, T.Ozturk, A. R.Chen, H.Yan, Y.-H.Dong, M.-Q.Shen, E.-Z.Mello, C. C.2022-01-18doi:10.1101/2022.01.18.476504Cold Spring Harbor Laboratory Press2022-01-18
<![CDATA[
In situ single particle classification reveals distinct 60S maturation intermediates in cells
]]>
https://biorxiv.org/cgi/content/short/2022.04.10.487797v1?rss=1"
Lucas, B. A.Zhang, K.Loerch, S.Grigorieff, N.2022-04-10doi:10.1101/2022.04.10.487797Cold Spring Harbor Laboratory Press2022-04-10
<![CDATA[
Structural Basis of MicroRNA Biogenesis by Dicer-1 and Its Partner Protein Loqs-PB
]]>
https://biorxiv.org/cgi/content/short/2022.04.19.488762v1?rss=1"
Jourevleva, K.Golovenko, D.Demo, G.Dutcher, R. C.Hall, T. M.Zamore, P. D.Korostelev, A. A.2022-04-20doi:10.1101/2022.04.19.488762Cold Spring Harbor Laboratory Press2022-04-20
<![CDATA[
Defocus Corrected Large Area Cryo-EM (DeCo-LACE) for Label-Free Detection of Molecules across Entire Cell Sections
]]>
https://biorxiv.org/cgi/content/short/2022.06.13.495969v1?rss=1"
Elferich, J.Schiroli, G.Scadden, D.Grigorieff, N.2022-06-14doi:10.1101/2022.06.13.495969Cold Spring Harbor Laboratory Press2022-06-14
<![CDATA[
Chemical engineering of therapeutic siRNAs for allele-specific gene silencing in vivo in CNS
]]>
https://biorxiv.org/cgi/content/short/2022.06.29.498088v1?rss=1"
50-fold selectivity for the mutant HD-causing allele, based on a single nucleotide difference. The optimized compound exhibits selective silencing of mutant huntingtin (HTT) protein in patient derived cells and throughout the HD mouse brain, providing a demonstration of SNP-based allele-specific RNAi silencing of gene expression in vivo in the CNS. The ability to target a disease-causing allele using RNAi-based therapies could be applied to a wide range of dominant CNS disorders, where maintenance of wild-type expression is essential.
]]>Conroy, F.Miller, R.Alterman, J. F.Hassler, M. R.Echeverria, D.Godinho, B. M. D. C.Knox, E. G.Sapp, E.Sousa, J.Yamada, K.Mahmood, F.Boudi, A.Kegel-Gleason, K.DiFiglia, M.Aronin, N.Khvorova, A.Pfister, E. L.2022-07-02doi:10.1101/2022.06.29.498088Cold Spring Harbor Laboratory Press2022-07-02
<![CDATA[
Silencing of ApoE with Divalent siRNAs Drives Activation of Immune Clearance Pathways and Improves Amyloid Pathology in Mouse Models of Alzheimer's Disease
]]>
https://biorxiv.org/cgi/content/short/2022.06.28.498012v1?rss=1"
Ferguson, C.Hildebrand, S.Godinho, B. M. D. C.Buchwald, J.Echeverria, D.Coles, A.Grigorenko, A.Vanjielli, L.Sousa, J.McHugh, N.Hassler, M.Santarelli, F.Heneka, M. T.Rogaev, E.Khvorova, A.2022-07-02doi:10.1101/2022.06.28.498012Cold Spring Harbor Laboratory Press2022-07-02
<![CDATA[
Asymmetric trichotomous data partitioning enables development of predictive machine learning models using limited siRNA efficacy datasets
]]>
https://biorxiv.org/cgi/content/short/2022.07.08.499317v1?rss=1"
Monopoli, K. R.Korkin, D.Khvorova, A.2022-07-10doi:10.1101/2022.07.08.499317Cold Spring Harbor Laboratory Press2022-07-10
<![CDATA[
Relaxed targeting rules allow PIWI-clade Argonaute proteins to silence ever-mutating transposons
]]>
https://biorxiv.org/cgi/content/short/2022.08.04.502788v1?rss=1"
Gainetdinov, I.Cecchini, K.Vega-Badillo, J.Bagci, A.Colpan, C.Arif, A.Wu, P.-H.Zamore, P. D.2022-08-05doi:10.1101/2022.08.04.502788Cold Spring Harbor Laboratory Press2022-08-05
<![CDATA[
Structure of the catalytically active APOBEC3G bound to a DNA oligonucleotide inhibitor reveals tetrahedral geometry of the transition state
]]>
https://biorxiv.org/cgi/content/short/2022.08.15.504001v1?rss=1"
Maiti, A.Hedger, A.Myint, W.Balachandran, V.Watts, J.Schiffer, C. A.Matsuo, H.2022-08-15doi:10.1101/2022.08.15.504001Cold Spring Harbor Laboratory Press2022-08-15
<![CDATA[
Di-valent siRNA Mediated Silencing of MSH3 Blocks Somatic Repeat Expansion in Mouse Models of Huntington's Disease
]]>
https://biorxiv.org/cgi/content/short/2022.09.06.506795v1?rss=1"
O'Reilly, D.Belgrad, J.Ferguson, C.Summers, A.Sapp, E.McHugh, C.Mathews, E.Buchwald, J.Ly, S.Echeverria Moreno, D.Kennedy, Z.Hariharan, V.Monopoli, K.Yang, X.Carroll, J.Difiglia, M.Aronin, N.Khvorova, A.2022-09-06doi:10.1101/2022.09.06.506795Cold Spring Harbor Laboratory Press2022-09-06
<![CDATA[
Drosophila Males Use 5'-to-3' Phased Biogenesis to Make Stellate-silencing piRNAs that Lack Homology to Maternally Deposited piRNA Guides
]]>
https://biorxiv.org/cgi/content/short/2022.09.12.507655v1?rss=1"
Venkei, Z. G.Gainetdinov, I.Starostik, M.Choi, C.Chen, P.Balsara, C.Whitfield, T.Bell, G. W.Feng, S.Jacobsen, S. E.Aravin, A.Kim, J. K.Zamore, P.Yamashita, Y. M.2022-09-13doi:10.1101/2022.09.12.507655Cold Spring Harbor Laboratory Press2022-09-13
<![CDATA[
The nuclear Argonaute HRDE-1 directs target gene re-localization and shuttles to nuage to promote small RNA mediated inherited silencing
]]>
https://biorxiv.org/cgi/content/short/2022.10.04.510877v1?rss=1"
Ding, Y.-H.Ochoa, H.Ishidate, T.Mello, C.2022-10-05doi:10.1101/2022.10.04.510877Cold Spring Harbor Laboratory Press2022-10-05
<![CDATA[
Career Self-Efficacy Disparities in Underrepresented Biomedical Scientist Trainees
]]>
https://biorxiv.org/cgi/content/short/2022.10.21.512368v1?rss=1"
Chatterjee, D.Jacob, G. A.Sturzenegger Varvayanis, S.Wefes, I.Chalkley, R.Nogueira, A. T.Fuhrmann, C.Varadarajan, J.Hubbard, N. M.Gaines, C. H.Layton, R. L.Chaudhary, S.2022-10-21doi:10.1101/2022.10.21.512368Cold Spring Harbor Laboratory Press2022-10-21
<![CDATA[
Formamide significantly enhances the efficiency of chemical adenylation of RNA sequencing ligation adaptors
]]>
https://biorxiv.org/cgi/content/short/2022.11.16.516815v1?rss=1"
90% yield. In standard conditions, with water as the solvent, hydrolysis of the starting material to adenosine monophosphate limits the yields. To our surprise, we find that rather than increasing adenylation yields by decreasing the rate of ImpA hydrolysis, formamide does so by increasing the reaction rate between ImpA and 5'-phosphorylated DNA by [~]10 fold. The method described here enables straightforward preparation of chemically adenylated adapters with higher than 90% yield, simplifying reagent preparation for NGS.
]]>Hildebrand, S.Hedger, A. K.Watts, J.Khvorova, A.2022-11-16doi:10.1101/2022.11.16.516815Cold Spring Harbor Laboratory Press2022-11-16
<![CDATA[
From primordial clocks to circadian oscillators
]]>
https://biorxiv.org/cgi/content/short/2022.11.28.518275v1?rss=1"
Pitsawong, W.Padua, R. A.Grant, T.Hoemberger, M.Otten, R.Bradshaw, N.Grigorieff, N.Kern, D.2022-11-29doi:10.1101/2022.11.28.518275Cold Spring Harbor Laboratory Press2022-11-29
<![CDATA[
Quantification of gallium cryo-FIB milling damage in biological lamella
]]>
https://biorxiv.org/cgi/content/short/2023.02.01.526705v1?rss=1"
Lucas, B. A.Grigorieff, N.2023-02-03doi:10.1101/2023.02.01.526705Cold Spring Harbor Laboratory Press2023-02-03
<![CDATA[
Epigenetic regulation of innate immune genes and enhanced interleukin-10 expression underlie chronic subclinical Plasmodium chabaudi infection
]]>
https://biorxiv.org/cgi/content/short/2023.02.23.529826v1?rss=1"
de Souza Silva, L.Nguyen, Y. A. H.Monks, B. G.Forconi, C. S.Crabtree, J. N.Rodriguez, T.Tamburro, N. D. P.Sontheimer, E. J.Horvath, G. L.Abdullah, Z.Latz, E.Caffrey, D. R.Kurt-Jones, E.Gazzinelli, R. T.Fitzgerald, K. A.Golenbock, D. T.2023-02-24doi:10.1101/2023.02.23.529826Cold Spring Harbor Laboratory Press2023-02-24
<![CDATA[
Broadly effective ACE2 decoy proteins protect mice from lethal SARS-CoV-2 infection
]]>
https://biorxiv.org/cgi/content/short/2023.02.22.529625v1?rss=1"
75% animals, and increased animal survival rate from 0% (untreated) to >87.5% (treated). These results demonstrate that both proteins are good drug candidates for protecting animals from severe COVID-19. In a head-to-head comparison of these two proteins with five previously-described ACE2-Ig constructs, we found that two of these constructs, each carrying five surface mutations in the ACE2 region, had partial loss of neutralization potency against three SARS-CoV-2 variants. These data suggest that extensively mutating ACE2 residues near the RBD-binding interface should be avoided or performed with extra caution. Further, we found that both ACE2-Ig-95 and ACE2-Ig-105/106 could be produced to gram/liter level, demonstrating the developability of them as biologic drug candidates. Stress-condition stability test of them further suggests that more studies are required in the future to improve the stability of these proteins. These studies provide useful insight into critical factors for engineering and preclinical development of ACE2 decoys as broadly effective therapeutics against diverse ACE2-utilizing coronaviruses.
Abstract ImportanceEngineering soluble ACE2 proteins that function as a receptor decoy to block SARS-CoV-2 infection is a very attractive approach to broadly effective and hard-to-escape anti-SARS-CoV-2 agents. This study here describes development of two antibody-like soluble ACE2 proteins that broadly block diverse SARS-CoV-2 variants including Omicron. In a stringent COVID-19 mouse model, both proteins successfully protected >87.5% animals from lethal SARS-CoV-2 infection. In addition, a head-to-head comparison of the two constructs developed in this study with five previously-described ACE2 decoy constructs were performed here. Two previously-described constructs with relatively more ACE2-surface mutations were found with less robust neutralization activities against diverse SARS-CoV-2 variants. Further, the developability of the two proteins as biologic drug candidates was also assessed here. This study provides two broadly anti-SARS-CoV-2 drug candidates and useful insight into critical factors for engineering and preclinical development of ACE2 decoy as broadly effective therapeutics against diverse ACE2-utilizing coronaviruses.
TweetTwo antibody-like ACE2 decoy proteins could block diverse SARS-CoV-2 variants and prevent animals from severe COVID-19.
]]>Lu, M.Yao, W.Li, Y.Ma, D.Zhang, Z.Wang, H.Tang, X.Wang, Y.Li, C.Cheng, D.Lin, H.Yin, Y.Zhao, J.Zhong, G.2023-02-23doi:10.1101/2023.02.22.529625Cold Spring Harbor Laboratory Press2023-02-23
<![CDATA[
Self-delivering CRISPR RNAs for AAV Co-delivery and Genome Editing in vivo
]]>
https://biorxiv.org/cgi/content/short/2023.03.20.533459v1?rss=1"
Zhang, H.Kelly, K.Lee, J.Echeverria, D.Cooper, D.Panwala, R.Chen, Z.Gaston, N.Newby, G. A.Xie, J.Liu, D. R.Gao, G.Wolfe, S. A.Khvorova, A.Watts, J. K.Sontheimer, E. J.2023-03-20doi:10.1101/2023.03.20.533459Cold Spring Harbor Laboratory Press2023-03-20
<![CDATA[
Engineering Nme2Cas9 Adenine Base Editors with Improved Activity and Targeting Scope
]]>
https://biorxiv.org/cgi/content/short/2023.04.14.536905v1?rss=1"
Bamidele, N.Zhang, H.Dong, X.Gaston, N.Cheng, H.Kelly, K.Watts, J. K.Xie, J.Gao, G.Sontheimer, E. J.2023-04-14doi:10.1101/2023.04.14.536905Cold Spring Harbor Laboratory Press2023-04-14
<![CDATA[
Genome-wide kinetic profiling of pre-mRNA 3' end cleavage
]]>
https://biorxiv.org/cgi/content/short/2023.06.21.545926v1?rss=1"
Torres-Ulloa, L.Calvo-Roitberg, E.Pai, A. A.2023-06-22doi:10.1101/2023.06.21.545926Cold Spring Harbor Laboratory Press2023-06-22
<![CDATA[
Dual targeting of hepatocyte DGAT2 and stellate cell FASN alleviates nonalcoholic steatohepatitis in mice.
]]>
https://biorxiv.org/cgi/content/short/2023.07.05.547848v1?rss=1"
Yenilmez, B.Harney, S. M.DiMarzio, C.Kelly, M.Min, K.Echeverria, D.Bramato, B. M.Jackson, S. O.Reddig, K.Kim, J. K.Khvorova, A.Czech, M. P.2023-07-05doi:10.1101/2023.07.05.547848Cold Spring Harbor Laboratory Press2023-07-05
<![CDATA[
Challenges in identifying mRNA transcript starts and ends from long-read sequencing data
]]>
https://biorxiv.org/cgi/content/short/2023.07.26.550536v1?rss=1"
Calvo-Roitberg, E.Daniels, R. F.Pai, A. A.2023-07-27doi:10.1101/2023.07.26.550536Cold Spring Harbor Laboratory Press2023-07-27
<![CDATA[
Casein kinase II promotes piRNA production through direct phosphorylation of USTC component TOFU-4
]]>
https://biorxiv.org/cgi/content/short/2023.08.09.552615v1?rss=1"
Mello, C.ZHANG, G.Zheng, C.ding, y.-h.2023-08-10doi:10.1101/2023.08.09.552615Cold Spring Harbor Laboratory Press2023-08-10
<![CDATA[
Single intravitreal administration of a tetravalent siRNA exhibits robust and efficient gene silencing in rodent and swine photoreceptors
]]>
https://biorxiv.org/cgi/content/short/2023.09.20.558641v1?rss=1"
Cheng, S.-Y.Caiazzi, J.Biscans, A.Alterman, J. F.Echeverria, D.McHugh, N.Hassler, M.Jolly, S.Giguere, D.Cipi, J.Khvorova, A.Punzo, C.2023-09-22doi:10.1101/2023.09.20.558641Cold Spring Harbor Laboratory Press2023-09-22
<![CDATA[
Baited reconstruction with 2D template matching for high-resolution structure determination in vitro and in vivo without template bias
]]>
https://biorxiv.org/cgi/content/short/2023.07.03.547552v1?rss=1"
Lucas, B. A.Himes, B. A.Grigorieff, N.2023-07-03doi:10.1101/2023.07.03.547552Cold Spring Harbor Laboratory Press2023-07-03
<![CDATA[
Condensation of a nuclear mRNA export factor regulates mRNA transport during stress
]]>
https://biorxiv.org/cgi/content/short/2022.01.30.478372v1?rss=1"
Heinrich, S.Hondele, M.Marchand, D.Derrer, C. P.Zedan, M.Oswald, A.Uliana, F.Mancini, R.Grunwald, D.Weis, K.2022-01-30doi:10.1101/2022.01.30.478372Cold Spring Harbor Laboratory Press2022-01-30
<![CDATA[
Lactate transporter MCT1 in hepatic stellate cells promotes fibrotic collagen expression in nonalcoholic steatohepatitis
]]>
https://biorxiv.org/cgi/content/short/2023.05.03.539244v1?rss=1"
Min, K.Yenilmez, B.Kelly, M.Echeverria, D.Elleby, M.Lifshitz, L. M.Raymond, N.Tsagkaraki, E.Harney, S. M.DiMarzio, C.McHugh, N.Bramato, B.Morrison, B.Rothstein, J. D.Khvorova, A.Czech, M. P.2023-05-03doi:10.1101/2023.05.03.539244Cold Spring Harbor Laboratory Press2023-05-03
<![CDATA[
Modular vector assembly enables rapid assessment of emerging CRISPR technologies
]]>
https://biorxiv.org/cgi/content/short/2023.10.25.564061v1?rss=1"
McGee, A. V.Liu, Y. V.Griffith, A. L.Szegletes, Z. M.Wen, B.Kraus, C.Miller, N. W.Steger, R. J.Escude Velasco, B.Bosch, J. A.Zirin, J. D.Viswanatha, R.Sontheimer, E. J.Goodale, A.Greene, M. A.Green, T. M.Doench, J. G.2023-10-27doi:10.1101/2023.10.25.564061Cold Spring Harbor Laboratory Press2023-10-27
<![CDATA[
Addressing the dNTP bottleneck restricting prime editing activity
]]>
https://biorxiv.org/cgi/content/short/2023.10.21.563443v1?rss=1"
Ponnienselvan, K.Liu, P.Nyalile, T.Oikemus, S.Joynt, A. T.Kelly, K.Guo, D.Chen, Z.Lee, J. M.Schiffer, C. A.Emerson, C. P.Lawson, N. D.Watts, J. K.Sontheimer, E. J.Luban, J. J.Wolfe, S. A.2023-10-21doi:10.1101/2023.10.21.563443Cold Spring Harbor Laboratory Press2023-10-21
<![CDATA[
Structural mechanism of angiogenin activation by the ribosome
]]>
https://biorxiv.org/cgi/content/short/2023.12.11.570495v1?rss=1"
Loveland, A. B.Koh, C. S.Ganesan, R.Jacobson, A.Korostelev, A. A.2023-12-11doi:10.1101/2023.12.11.570495Cold Spring Harbor Laboratory Press2023-12-11
<![CDATA[
A programmable dual-targeting di-valent siRNA scaffold supports potent multi-gene modulation in the central nervous system
]]>
https://biorxiv.org/cgi/content/short/2023.12.19.572404v1?rss=1"
Belgrad, J.Tang, Q.Hildebrand, S.Summers, A.Sapp, E.Echeverria, D.O'Reilly, D.Luu, E.Bramato, B.Allen, S.Cooper, D.Alterman, J.Yamada, K.Aronin, N.DiFiglia, M.Khvorova, A.2023-12-19doi:10.1101/2023.12.19.572404Cold Spring Harbor Laboratory Press2023-12-19
<![CDATA[
mRNA initiation and termination are spatially coordinated
]]>
https://biorxiv.org/cgi/content/short/2024.01.05.574404v1?rss=1"
Calvo-Roitberg, E.Carroll, C. L.Venev, S. V.Kim, G.Mick, S. T.Dekker, J.Fiszbein, A.Pai, A. A.2024-01-07doi:10.1101/2024.01.05.574404Cold Spring Harbor Laboratory Press2024-01-07
<![CDATA[
Traumatic injury causes selective degeneration and TDP-43 mislocalization in human iPSC-derived C9orf72-associated ALS/FTD motor neurons
]]>
https://biorxiv.org/cgi/content/short/2024.03.21.586073v1?rss=1"
Martin, E. J.Santacruz, C.Mitevska, A.Jones, I. E.Krishnan, G.Gao, F.-B.Finan, J. D.Kiskinis, E.2024-03-26doi:10.1101/2024.03.21.586073Cold Spring Harbor Laboratory Press2024-03-26
<![CDATA[
Germline Blastomeres transcriptomics in the presence or absence of PIE-1 during C. elegans early embryogenesis
]]>
https://biorxiv.org/cgi/content/short/2026.02.14.705883v1?rss=1"
Ponsard, P.Stubbe, F.-X.Tricquet, P.Mello, C.Hermand, D.2026-02-14doi:10.64898/2026.02.14.705883Cold Spring Harbor Laboratory Press2026-02-14