Papers, preprints, methods, and reviews.

Nature Communications

Telomerase RNA structural heterogeneity in living human cells detected by DMS-MaPseq

Forino NM, Woo JZ, Zaug AJ, Jimenez AG, Edelson E, Cech TR, Rouskin S, Stone MD. Nat Commun 16(1):925.

PubMed 39843442 PMC11754830

Science

The human mitochondrial mRNA structurome reveals mechanisms of gene expression

Moran JC, Brivanlou A, Brischigliaro M, Fontanesi F, Rouskin S, Barrientos A. Science 385(6706):eadm9238.

PubMed 39024447 PMC11510358

bioRxiv preprint

Discovery and quantification of long-range RNA base pairs in coronavirus genomes with SEARCH-MaP and SEISMIC-RNA

Allan MF, Aruda J, Plung JS, Grote SL, Martin des Taillades YJ, de Lajarte AA, Bathe M, Rouskin S. bioRxiv 2024.07.28.

PubMed 38746332 PMC11092567

Research Square preprint

Discovery and quantification of long-range RNA base pairs in coronavirus genomes with SEARCH-MaP and SEISMIC-RNA

Allan MF, Aruda J, Plung JS, Grote SL, des Taillades YJM, de Lajarte AA, Bathe M, Rouskin S. Research Square.

PubMed 39149495 PMC11326378

Current Opinion in Structural Biology

Untangling the pseudoknots of SARS-CoV-2: insights into structural heterogeneity and plasticity

Aruda J, Grote SL, Rouskin S. Curr Opin Struct Biol 88:102912.

PubMed 39168046

bioRxiv preprint

The folding of germ-granule mRNAs controls intermolecular base pairing in germ granules and maintains normal fly development

Tian S, Nguyen H, Ye Z, Rouskin S, Thirumalai D, Trcek T. bioRxiv 2024.05.31.

PubMed 38853845 PMC11160705

bioRxiv preprint

SEISMICgraph: a web-based tool for RNA structure data visualization

Wightman FF, Yang G, Martin des Taillades YJ, L'Esperance-Kerckhoff C, Grote S, Allan MF, Herschlag D, Rouskin S, Hagler LD. bioRxiv 2024.09.26.

PubMed 39386640 PMC11463429

bioRxiv preprint

Telomerase RNA structural heterogeneity in living human cells detected by DMS-MaPseq

Forino NM, Woo JZ, Zaug AJ, Jimenez AG, Edelson E, Cech TR, Rouskin S, Stone MD. bioRxiv 2024.08.29.

PubMed 37873413 PMC10592977

Nucleic Acids Research

Nucleic Acids Research

KREH2 helicase represses ND7 mRNA editing in procyclic-stage Trypanosoma brucei by opposite modulation of canonical and "moonlighting" gRNA utilization

Meehan J, Ivens A, Grote S, Rodshagen T, Chen Z, Goode C, Sharma SK, Kumar V, Frese A, Goodall Z, McCleskey L, Sechrist R, Zeng L, Savill NJ, Rouskin S, Schnaufer A, McDermott SM, Cruz-Reyes J. NAR 52(19):11940–11959.

PubMed 39149912 PMC11514453

Viruses

Viruses

Viral RNA interactome: the ultimate researcher's guide to RNA–protein interactions

Hanson WA, Romero Agosto GA, Rouskin S. Viruses 16(11):1485.

PubMed 39599817 PMC11599142

Current Protocols

Current Protocols

DMS-MapSeq analysis of antisense-oligonucleotide binding to lncRNA PANDA

Romero Agosto GA, Cox E, Rouskin S. Curr Protoc 4(11):e70038.

PubMed 39589322

bioRxiv

bioRxiv preprint

Structure-informed mutagenesis identifies a conserved region critical for mouse insulin-receptor 5′UTR IRES function

Dahl WB, Lan TCT, Rouskin S, Marr MT. bioRxiv 2024.11.05.

PubMed 39574669 PMC11580878

Nature Structural & Molecular Biology

Nature Struct Mol Biol

Pre-mRNA splicing order is predetermined and maintains splicing fidelity across multi-intronic transcripts

Choquet K, Koenigs A, Dülk SLJ, Smalec BM, Rouskin S, Churchman LS.

Trends in Biochemical Sciences

Trends Biochem Sci

RNA levers and switches controlling viral gene expression

Allan MF, Brivanlou A, Rouskin S.

Nature Communications

Nature Communications

3D RNA-scaffolded wireframe origami

Parsons MF, Allan MF, Li S, Shepherd TR, Ratanalert S, Zhang K, Pullen KM, Chiu W, Rouskin S, Bathe M. Nat Commun 14:1.

bioRxiv

bioRxiv preprint

Structure of pre-miR-31 reveals an active role in Dicer processing

Ma S, Kotar A, Grote S, Rouskin S, Keane SC.

Nature Communications

Secondary structural ensembles of the SARS-CoV-2 RNA genome in infected cells

Lan TCT, Allan MF, Malsick LE, Woo JZ, Zhu C, Zhang F, Khandwala S, Nyeo SYS, Sun Y, Guo JU, Bathe M, Näär AM, Griffiths A, Rouskin S. Nat Commun 13:1128.

PNAS

Recurrent emergence of Klebsiella pneumoniae carbapenem resistance mediated by an inhibitory ompK36 mRNA secondary structure

Wong JLC, David S, Sanchez-Garrido J, Woo JZ, Low WW, Morrechiato F, Giani T, Rossolini GM, Beis K, Brett SJ, Clements A, Aanensen DM, Rouskin S, Frankel G. PNAS 119(38):e2203593119.

Nature Communications

Nature Communications

An intranasal ASO therapeutic targeting SARS-CoV-2

Zhu C, Lee JY, Woo JZ, Xu L, Nguyenla X, Yamashiro LH, Ji F, Biering SB, Van Dis E, Gonzalez F, Fox D, Wehri E, Rustagi A, Pinsky BA, Schaletzky J, Blish CA, Chiu C, Harris E, Sadreyev RI, Stanley S, Kauppinen S, Rouskin S, Näär AM. Nat Commun 13:4503.

Nucleic Acids Research

Nucleic Acids Research

Web-based platform for analysis of RNA folding from high-throughput chemical probing data

Jurich CP, Brivanlou A, Rouskin S, Yesselman JD. NAR gkac435.

JoVE

JoVE

Probing RNA structures with dimethyl-sulfate mutational profiling with sequencing in vitro and in cells

Dülk SLJ, Rouskin S. J Vis Exp 190.

bioRxiv

bioRxiv preprint

Pre-mRNA splicing order is predetermined and maintains splicing fidelity across multi-intronic transcripts

Choquet K, Koenigs A, Dülk SLJ, Smalec BM, Rouskin S, Churchman LS.

RNA

RNA

Sigma-factor-dependent translational activation in Bacillus subtilis

McCormick DM, Lalanne J, Lan TCT, Rouskin S, Li G.

Nature

Determination of RNA structural diversity and its role in HIV-1 RNA splicing regulation

Tomezsko P, Corbin V, Gupta P, Swaminathan H, Glasgow M, Persad S, Edwards M, Mcintosh L, Papenfuss A, Emery A, Swanstrom R, Zang Z, Lan T, Bieniasz P, Kuritzkes D, Tsibris A, Rouskin S. Nature 582(7812):438–442.

Methods

Methods

Viral RNA structure analysis using DMS-MaPseq

Tomezsko P, Swaminathan H, Rouskin S.

Molecular Cell

Molecular Cell

A stress response that monitors and regulates mRNA structure is central to cold-shock adaptation

Zhang Y, Burkhardt DH, Rouskin S, Li G, Weissman JS, Gross CA. Mol Cell 70(2).

Nature Methods

DMS-MaPseq for genome-wide or targeted RNA structure probing in vivo

Zubradt M, Gupta P, Persad S, Lambowitz AM, Weissman JS, Rouskin S. Nat Methods 14(1):75–82.

eLife

eLife

Operon mRNAs are organized into ORF-centric structures that predict translation efficiency

Burkhardt DH, Rouskin S, Zhang Y, Li G, Weissman JS, Gross CA. eLife 6.

Nature

Genome-wide probing of RNA structure reveals active unfolding of mRNA structures in vivo

Rouskin S, Zubradt M, Washietl S, Kellis M, Weissman JS. Nature 505(7485):701–705.

Molecular Systems Biology

Mol Syst Biol

Causal signals between codon bias, mRNA structure, and the efficiency of translation and elongation

Pop C, Rouskin S, Ingolia NT, Han L, Phizicky EM, Weissman JS, Koller D. Mol Syst Biol 10:770.

Cell

Cell

A ribosome-bound quality-control complex triggers degradation of nascent peptides and signals translation stress

Brandman O, Stewart-Ornstein J, Wong D, Larson A, Williams CC, Li GW, Zhou S, King D, Shen PS, Weibezahn J, Dunn JG, Rouskin S, Inada T, Frost A, Weissman JS. Cell, 2012.

Nature Protocols

Nature Protocols

The ribosome-profiling strategy for monitoring translation in vivo by deep sequencing of ribosome-protected mRNA fragments

Ingolia NT, Brar GA, Rouskin S, McGeachy AM, Weissman JS. Nat Protoc, 2012.

Curr Protoc Mol Biol

Curr Protoc Mol Biol

Genome-wide annotation and quantitation of translation by ribosome profiling

Ingolia NT, Brar GA, Rouskin S, McGeachy AM, Weissman JS. Curr Protoc Mol Biol, 2013.

J Pediatr

J Pediatr

Utility of DNA microarrays for detection of viruses in acute respiratory-tract infections in children

Chiu CY, Urisman A, Greenhow TL, Rouskin S, Yagi S, Schnurr D, Wright C, Drew WL, Wang D, Weintrub PS, DeRisi JL, Ganem D. J Pediatr, 2008.

J Infect Dis

J Infect Dis

Pan-viral screening of respiratory tract infections in adults with and without asthma reveals unexpected human coronavirus and rhinovirus diversity

Kistler A, Avila PC, Rouskin S, Wang D, Ward T, Yagi S, Schnurr D, Ganem D, DeRisi JL, Boushey HA. J Infect Dis, 2007.

J Clin Microbiol

J Clin Microbiol

Diagnosis of a critical respiratory illness caused by human metapneumovirus using a pan-virus microarray

Chiu CY, Alizadeh AA, Rouskin S, Merker JD, Yeh E, Yagi S, Schnurr D, Patterson BK, Ganem D, DeRisi JL. J Clin Microbiol, 2007.

Virology Journal

Virology Journal

Genome-wide diversity and selective pressure in the human rhinovirus

Kistler AL, Webster DR, Rouskin S, Magrini V, Credle JJ, Schnurr DP, Boushey HA, Mardis ER, Li H, DeRisi JL. Virology J, 2007.

Clin Infect Dis

Clin Infect Dis

Microarray detection of human parainfluenzavirus-4 infection associated with respiratory failure in an immunocompetent adult

Chiu CY, Rouskin S, Koshy A, Urisman A, Fischer K, Yagi S, Schnurr D, Eckburg PB, Tompkins LS, Blackburn BG, Merker JD, Patterson BK, Ganem D, DeRisi JL. Clin Infect Dis, 2006.