Table of Contents

BIOINFORMATICS

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clipplotr—a comparative visualization and analysis tool for CLIP data
- Anob M. Chakrabarti,
- Charlotte Capitanchik,
- Jernej Ule,
- and Nicholas M. Luscombe
RNA June 2023 29: 715-723; Published in Advance March 9, 2023, doi:10.1261/rna.079326.122
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REPORTS

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Molecular basis for GIGYF–TNRC6 complex assembly
- Meghna Sobti,
- Benjamin J. Mead,
- Alastair G. Stewart,
- Cátia Igreja,
- and Mary Christie
RNA June 2023 29: 724-734; Published in Advance February 28, 2023, doi:10.1261/rna.079596.123
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Translation reinitiation after uORFs does not fully protect mRNAs from nonsense-mediated decay
- Paul J. Russell,
- Jacob A. Slivka,
- Elaina P. Boyle,
- Arthur H.M. Burghes,
- and Michael G. Kearse
RNA June 2023 29: 735-744; Published in Advance March 6, 2023, doi:10.1261/rna.079525.122
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Phosphorylation controls the oligomeric state of She2 and mRNA localization in yeast
- Nastaran Farajzadeh,
- Karen Shahbabian,
- Yani Bouaziz,
- Emmanuelle Querido,
- and Pascal Chartrand
RNA June 2023 29: 745-755; Published in Advance March 15, 2023, doi:10.1261/rna.079555.122
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No evidence for epitranscriptomic m⁵C modification of SARS-CoV-2, HIV and MLV viral RNA
- Anming Huang,
- Lydia Riepler,
- Dietmar Rieder,
- Janine Kimpel,
- and Alexandra Lusser
RNA June 2023 29: 756-763; Published in Advance March 8, 2023, doi:10.1261/rna.079549.122
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ARTICLES

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Computational design and experimental verification of pseudoknotted ribozymes
- Sabrine Najeh,
- Kasra Zandi,
- Nawwaf Kharma,
- and Jonathan Perreault
RNA June 2023 29: 764-776; Published in Advance March 3, 2023, doi:10.1261/rna.079148.122
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The importance of m⁶A topology in chicken embryo mRNA: a precise mapping of m⁶A at the conserved chicken β-actin zipcode
- Francis Baron,
- Mi Zhang,
- Nathan Archer,
- Eleanor Bellows,
- Helen M. Knight,
- Simon Welham,
- Catrin S. Rutland,
- Nigel P. Mongan,
- Christopher J. Hayes,
- Rupert G. Fray,
- and Zsuzsa Bodi
RNA June 2023 29: 777-789; Published in Advance February 21, 2023, doi:10.1261/rna.079615.123
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Structural and dynamic effects of pseudouridine modifications on noncanonical interactions in RNA
- Jennifer Vögele,
- Elke Duchardt-Ferner,
- Holger Kruse,
- Zhengyue Zhang,
- Jiri Sponer,
- Miroslav Krepl,
- and Jens Wöhnert
RNA June 2023 29: 790-807; Published in Advance March 3, 2023, doi:10.1261/rna.079506.122
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Duf89 abets lncRNA control of fission yeast phosphate homeostasis via its antagonism of precocious lncRNA transcription termination
- Ana M. Sanchez,
- Angad Garg,
- Beate Schwer,
- and Stewart Shuman
RNA June 2023 29: 808-825; Published in Advance March 7, 2023, doi:10.1261/rna.079595.123
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Exploring the targeting spectrum of rocaglates among eIF4A homologs
- Sai Kiran Naineni,
- Regina Cencic,
- Francis Robert,
- Lauren E. Brown,
- Minza Haque,
- Jordan Scott-Talib,
- Patrick Sénéchal,
- T. Martin Schmeing,
- John A. Porco, Jr.,
- and Jerry Pelletier
RNA June 2023 29: 826-835; Published in Advance March 7, 2023, doi:10.1261/rna.079318.122

METHODS

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Single-molecule RNA in situ detection in clinical FFPE tissue sections by vsmCISH
- Meng Jiang,
- Kaipeng Wei,
- Meiqing Li,
- Chen Lin,
- and Rongqin Ke
RNA June 2023 29: 836-846; Published in Advance February 22, 2023, doi:10.1261/rna.079482.122
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Nanopore sequencing of internal 2′-PO₄ modifications installed by RNA repair
- Laura K. White,
- Saylor M. Strugar,
- Andrea MacFadden,
- and Jay R. Hesselberth
RNA June 2023 29: 847-861; Published in Advance February 28, 2023, doi:10.1261/rna.079290.122

ERRATUM

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Erratum: Knockouts of TUT7 and 3′hExo show that they cooperate in histone mRNA maintenance and degradation
- Chris E. Holmquist,
- Wenxia He,
- Rita M. Meganck,
- and William F. Marzluff
RNA June 2023 29: 862; doi:10.1261/rna.079667.123
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CORRIGENDUM

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Corrigendum: Shortening of 3′ UTRs in most cell types composing tumor tissues implicates alternative polyadenylation in protein metabolism
- Dominik Burri and
- Mihaela Zavolan
RNA June 2023 29: 863; doi:10.1261/rna.079645.123
OPEN ACCESS ARTICLE

BIOINFORMATICS

clipplotr—a comparative visualization and analysis tool for CLIP data

REPORTS

Molecular basis for GIGYF–TNRC6 complex assembly

Translation reinitiation after uORFs does not fully protect mRNAs from nonsense-mediated decay

Phosphorylation controls the oligomeric state of She2 and mRNA localization in yeast

No evidence for epitranscriptomic m⁵C modification of SARS-CoV-2, HIV and MLV viral RNA

ARTICLES

Computational design and experimental verification of pseudoknotted ribozymes

The importance of m⁶A topology in chicken embryo mRNA: a precise mapping of m⁶A at the conserved chicken β-actin zipcode

Structural and dynamic effects of pseudouridine modifications on noncanonical interactions in RNA

Duf89 abets lncRNA control of fission yeast phosphate homeostasis via its antagonism of precocious lncRNA transcription termination

Exploring the targeting spectrum of rocaglates among eIF4A homologs

METHODS

Single-molecule RNA in situ detection in clinical FFPE tissue sections by vsmCISH

Nanopore sequencing of internal 2′-PO₄ modifications installed by RNA repair

ERRATUM

Erratum: Knockouts of TUT7 and 3′hExo show that they cooperate in histone mRNA maintenance and degradation

CORRIGENDUM

Corrigendum: Shortening of 3′ UTRs in most cell types composing tumor tissues implicates alternative polyadenylation in protein metabolism

This Issue

Current Issue

In This Issue

Table of Contents

BIOINFORMATICS

clipplotr—a comparative visualization and analysis tool for CLIP data

REPORTS

Molecular basis for GIGYF–TNRC6 complex assembly

Translation reinitiation after uORFs does not fully protect mRNAs from nonsense-mediated decay

Phosphorylation controls the oligomeric state of She2 and mRNA localization in yeast

No evidence for epitranscriptomic m5C modification of SARS-CoV-2, HIV and MLV viral RNA

ARTICLES

Computational design and experimental verification of pseudoknotted ribozymes

The importance of m6A topology in chicken embryo mRNA: a precise mapping of m6A at the conserved chicken β-actin zipcode

Structural and dynamic effects of pseudouridine modifications on noncanonical interactions in RNA

Duf89 abets lncRNA control of fission yeast phosphate homeostasis via its antagonism of precocious lncRNA transcription termination

Exploring the targeting spectrum of rocaglates among eIF4A homologs

METHODS

Single-molecule RNA in situ detection in clinical FFPE tissue sections by vsmCISH

Nanopore sequencing of internal 2′-PO4 modifications installed by RNA repair

ERRATUM

Erratum: Knockouts of TUT7 and 3′hExo show that they cooperate in histone mRNA maintenance and degradation

CORRIGENDUM

Corrigendum: Shortening of 3′ UTRs in most cell types composing tumor tissues implicates alternative polyadenylation in protein metabolism

This Issue

Current Issue

In This Issue

No evidence for epitranscriptomic m⁵C modification of SARS-CoV-2, HIV and MLV viral RNA

The importance of m⁶A topology in chicken embryo mRNA: a precise mapping of m⁶A at the conserved chicken β-actin zipcode

Nanopore sequencing of internal 2′-PO₄ modifications installed by RNA repair