Table of Contents

LETTER TO THE EDITOR

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Frame-shifted proteins of a given gene are unlikely to retain the same function
- Alexander S. Mankin
RNA October 2020 26: 1301-1302; Published in Advance June 5, 2020, doi:10.1261/rna.076398.120
OPEN ACCESS ARTICLE

BIOINFORMATIC

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A hybrid deep clustering approach for robust cell type profiling using single-cell RNA-seq data
- Suhas Srinivasan,
- Anastasia Leshchyk,
- Nathan T. Johnson,
- and Dmitry Korkin
RNA October 2020 26: 1303-1319; Published in Advance June 12, 2020, doi:10.1261/rna.074427.119
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Meta-analysis of transcriptomic variation in T-cell populations reveals both variable and consistent signatures of gene expression and splicing
- Caleb M. Radens,
- Davia Blake,
- Paul Jewell,
- Yoseph Barash,
- and Kristen W. Lynch
RNA October 2020 26: 1320-1333; Published in Advance June 17, 2020, doi:10.1261/rna.075929.120

REPORT

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Inactivation of fission yeast Erh1 de-represses pho1 expression: evidence that Erh1 is a negative regulator of prt lncRNA termination
- Beate Schwer,
- Ana M. Sanchez,
- and Stewart Shuman
RNA October 2020 26: 1334-1344; Published in Advance June 16, 2020, doi:10.1261/rna.076463.120

ARTICLES

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Studies with recombinant U7 snRNP demonstrate that CPSF73 is both an endonuclease and a 5′–3′ exonuclease
- Xiao-cui Yang,
- Yadong Sun,
- Wei Shen Aik,
- William F. Marzluff,
- Liang Tong,
- and Zbigniew Dominski
RNA October 2020 26: 1345-1359; Published in Advance June 17, 2020, doi:10.1261/rna.076273.120
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Prefoldin-like Bud27 influences the transcription of ribosomal components and ribosome biogenesis in Saccharomyces cerevisiae
- Verónica Martínez-Fernández,
- Abel Cuevas-Bermúdez,
- Francisco Gutiérrez-Santiago,
- Ana I. Garrido-Godino,
- Olga Rodríguez-Galán,
- Antonio Jordán-Pla,
- Sergio Lois,
- Juan C. Triviño,
- Jesús de la Cruz,
- and Francisco Navarro
RNA October 2020 26: 1360-1379; Published in Advance June 5, 2020, doi:10.1261/rna.075507.120
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Pdc2/Pat1 increases the range of decay factors and RNA bound by the Lsm1–7 complex
- Joseph H. Lobel and
- John D. Gross
RNA October 2020 26: 1380-1388; Published in Advance June 8, 2020, doi:10.1261/rna.075812.120
OPEN ACCESS ARTICLE
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Allosteric regulation of U1 snRNP by splicing regulatory proteins controls spliceosomal assembly
- Hossein Shenasa,
- Maliheh Movassat,
- Elmira Forouzmand,
- and Klemens J. Hertel
RNA October 2020 26: 1389-1399; Published in Advance June 10, 2020, doi:10.1261/rna.075135.120
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Molecular basis for the distinct cellular functions of the Lsm1–7 and Lsm2–8 complexes
- Eric J. Montemayor,
- Johanna M. Virta,
- Samuel M. Hayes,
- Yuichiro Nomura,
- David A. Brow,
- and Samuel E. Butcher
RNA October 2020 26: 1400-1413; Published in Advance June 9, 2020, doi:10.1261/rna.075879.120
OPEN ACCESS ARTICLE
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Elimination of Calm1 long 3′-UTR mRNA isoform by CRISPR–Cas9 gene editing impairs dorsal root ganglion development and hippocampal neuron activation in mice
- Bongmin Bae,
- Hannah N. Gruner,
- Maebh Lynch,
- Ting Feng,
- Kevin So,
- Daniel Oliver,
- Grant S. Mastick,
- Wei Yan,
- Simon Pieraut,
- and Pedro Miura
RNA October 2020 26: 1414-1430; Published in Advance June 10, 2020, doi:10.1261/rna.076430.120
OPEN ACCESS ARTICLE
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Structure-seq2 probing of RNA structure upon amino acid starvation reveals both known and novel RNA switches in Bacillus subtilis
- Laura E. Ritchey,
- David C. Tack,
- Helen Yakhnin,
- Elizabeth A. Jolley,
- Sarah M. Assmann,
- Philip C. Bevilacqua,
- and Paul Babitzke
RNA October 2020 26: 1431-1447; Published in Advance July 1, 2020, doi:10.1261/rna.075986.120
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Global discovery of bacterial RNA-binding proteins by RNase-sensitive gradient profiles reports a new FinO domain protein
- Milan Gerovac,
- Youssef El Mouali,
- Jochen Kuper,
- Caroline Kisker,
- Lars Barquist,
- and Jörg Vogel
RNA October 2020 26: 1448-1463; Published in Advance July 9, 2020, doi:10.1261/rna.076992.120
OPEN ACCESS ARTICLE
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Origin, conservation, and loss of alternative splicing events that diversify the proteome in Saccharomycotina budding yeasts
- Jennifer E. Hurtig,
- Minseon Kim,
- Luisa J. Orlando-Coronel,
- Jellisa Ewan,
- Michelle Foreman,
- Lee-Ann Notice,
- Michelle A. Steiger,
- and Ambro van Hoof
RNA October 2020 26: 1464-1480; Published in Advance July 6, 2020, doi:10.1261/rna.075655.120

METHODS

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Nuclease-mediated depletion biases in ribosome footprint profiling libraries
- Boris Zinshteyn,
- Jamie R. Wangen,
- Boyang Hua,
- and Rachel Green
RNA October 2020 26: 1481-1488; Published in Advance June 5, 2020, doi:10.1261/rna.075523.120
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Validation strategies for antibodies targeting modified ribonucleotides
- Franziska Weichmann,
- Robert Hett,
- Aloys Schepers,
- Taku Ito-Kureha,
- Andrew Flatley,
- Kaouthar Slama,
- Florian D. Hastert,
- Nicholas B. Angstman,
- M. Cristina Cardoso,
- Julian König,
- Stefan Hüttelmaier,
- Christoph Dieterich,
- Stefan Canzar,
- Mark Helm,
- Vigo Heissmeyer,
- Regina Feederle,
- and Gunter Meister
RNA October 2020 26: 1489-1506; Published in Advance July 7, 2020, doi:10.1261/rna.076026.120

LETTER TO THE EDITOR

Frame-shifted proteins of a given gene are unlikely to retain the same function

BIOINFORMATIC

A hybrid deep clustering approach for robust cell type profiling using single-cell RNA-seq data

Meta-analysis of transcriptomic variation in T-cell populations reveals both variable and consistent signatures of gene expression and splicing

REPORT

Inactivation of fission yeast Erh1 de-represses pho1 expression: evidence that Erh1 is a negative regulator of prt lncRNA termination

ARTICLES

Studies with recombinant U7 snRNP demonstrate that CPSF73 is both an endonuclease and a 5′–3′ exonuclease

Prefoldin-like Bud27 influences the transcription of ribosomal components and ribosome biogenesis in Saccharomyces cerevisiae

Pdc2/Pat1 increases the range of decay factors and RNA bound by the Lsm1–7 complex

Allosteric regulation of U1 snRNP by splicing regulatory proteins controls spliceosomal assembly

Molecular basis for the distinct cellular functions of the Lsm1–7 and Lsm2–8 complexes

Elimination of Calm1 long 3′-UTR mRNA isoform by CRISPR–Cas9 gene editing impairs dorsal root ganglion development and hippocampal neuron activation in mice

Structure-seq2 probing of RNA structure upon amino acid starvation reveals both known and novel RNA switches in Bacillus subtilis

Global discovery of bacterial RNA-binding proteins by RNase-sensitive gradient profiles reports a new FinO domain protein

Origin, conservation, and loss of alternative splicing events that diversify the proteome in Saccharomycotina budding yeasts

METHODS

Nuclease-mediated depletion biases in ribosome footprint profiling libraries

Validation strategies for antibodies targeting modified ribonucleotides

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