Table of Contents

BIOINFORMATICS

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Characterization of CRISPR RNA transcription by exploiting stranded metatranscriptomic data
- Yuzhen Ye and
- Quan Zhang
RNA July 2016 22: 945-956; Published in Advance May 17, 2016, doi:10.1261/rna.055988.116
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A systematic computational analysis of the rRNA–3′ UTR sequence complementarity suggests a regulatory mechanism influencing post-termination events in metazoan translation
- Josef Pánek,
- Michal Kolář,
- Anna Herrmannová,
- and Leoš Shivaya Valášek
RNA July 2016 22: 957-967; Published in Advance May 17, 2016, doi:10.1261/rna.056119.116

ARTICLES

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Comparative genomic analysis of upstream miRNA regulatory motifs in Caenorhabditis
- Richard Jovelin,
- Aldis Krizus,
- Bakhtiyar Taghizada,
- Jeremy C. Gray,
- Patrick C. Phillips,
- Julie M. Claycomb,
- and Asher D. Cutter
RNA July 2016 22: 968-978; Published in Advance May 2, 2016, doi:10.1261/rna.055392.115
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Hfq assists small RNAs in binding to the coding sequence of ompD mRNA and in rearranging its structure
- Zuzanna Wroblewska and
- Mikolaj Olejniczak
RNA July 2016 22: 979-994; Published in Advance May 6, 2016, doi:10.1261/rna.055251.115
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An RNA matchmaker protein regulates the activity of the long noncoding RNA HOTAIR
- Emily K. Meredith,
- Maggie M. Balas,
- Karla Sindy,
- Krystal Haislop,
- and Aaron M. Johnson
RNA July 2016 22: 995-1010; Published in Advance May 4, 2016, doi:10.1261/rna.055830.115
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Transcription of lncRNA prt, clustered prt RNA sites for Mmi1 binding, and RNA polymerase II CTD phospho-sites govern the repression of pho1 gene expression under phosphate-replete conditions in fission yeast
- Debashree Chatterjee,
- Ana M. Sanchez,
- Yehuda Goldgur,
- Stewart Shuman,
- and Beate Schwer
RNA July 2016 22: 1011-1025; Published in Advance May 10, 2016, doi:10.1261/rna.056515.116
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The PUF binding landscape in metazoan germ cells
- Aman Prasad,
- Douglas F. Porter,
- Peggy L. Kroll-Conner,
- Ipsita Mohanty,
- Anne R. Ryan,
- Sarah L. Crittenden,
- Marvin Wickens,
- and Judith Kimble
RNA July 2016 22: 1026-1043; Published in Advance May 10, 2016, doi:10.1261/rna.055871.116
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The piRNA pathway is developmentally regulated during spermatogenesis in Drosophila
- Emilie Quénerch'du,
- Amit Anand,
- and Toshie Kai
RNA July 2016 22: 1044-1054; Published in Advance May 20, 2016, doi:10.1261/rna.055996.116
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Time course of large ribosomal subunit assembly in E. coli cells overexpressing a helicase inactive DbpA protein
- Riley C. Gentry,
- Jared J. Childs,
- Jirair Gevorkyan,
- Yulia V. Gerasimova,
- and Eda Koculi
RNA July 2016 22: 1055-1064; Published in Advance May 18, 2016, doi:10.1261/rna.055137.115
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Activation of PKR by short stem–loop RNAs containing single-stranded arms
- Christopher B. Mayo,
- C. Jason Wong,
- Prisma E. Lopez,
- Jeffrey W. Lary,
- and James L. Cole
RNA July 2016 22: 1065-1075; Published in Advance May 20, 2016, doi:10.1261/rna.053348.115
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Modeling and gene knockdown to assess the contribution of nonsense-mediated decay, premature termination, and selenocysteine insertion to the selenoprotein hierarchy
- Anze Zupanic,
- Catherine Meplan,
- Grazielle V.B. Huguenin,
- John E. Hesketh,
- and Daryl P. Shanley
RNA July 2016 22: 1076-1084; Published in Advance May 20, 2016, doi:10.1261/rna.055749.115
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Stable association of RNAi machinery is conserved between the cytoplasm and nucleus of human cells
- Roya Kalantari,
- Jessica A. Hicks,
- Liande Li,
- Keith T. Gagnon,
- Viswanadham Sridhara,
- Andrew Lemoff,
- Hamid Mirzaei,
- and David R. Corey
RNA July 2016 22: 1085-1098; Published in Advance May 19, 2016, doi:10.1261/rna.056499.116
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METHOD

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A whole-mount in situ hybridization method for microRNA detection in Caenorhabditis elegans
- Yoshiki Andachi and
- Yuji Kohara
RNA July 2016 22: 1099-1106; Published in Advance May 6, 2016, doi:10.1261/rna.054239.115

BIOINFORMATICS

Characterization of CRISPR RNA transcription by exploiting stranded metatranscriptomic data

A systematic computational analysis of the rRNA–3′ UTR sequence complementarity suggests a regulatory mechanism influencing post-termination events in metazoan translation

ARTICLES

Comparative genomic analysis of upstream miRNA regulatory motifs in Caenorhabditis

Hfq assists small RNAs in binding to the coding sequence of ompD mRNA and in rearranging its structure

An RNA matchmaker protein regulates the activity of the long noncoding RNA HOTAIR

Transcription of lncRNA prt, clustered prt RNA sites for Mmi1 binding, and RNA polymerase II CTD phospho-sites govern the repression of pho1 gene expression under phosphate-replete conditions in fission yeast

The PUF binding landscape in metazoan germ cells

The piRNA pathway is developmentally regulated during spermatogenesis in Drosophila

Time course of large ribosomal subunit assembly in E. coli cells overexpressing a helicase inactive DbpA protein

Activation of PKR by short stem–loop RNAs containing single-stranded arms

Modeling and gene knockdown to assess the contribution of nonsense-mediated decay, premature termination, and selenocysteine insertion to the selenoprotein hierarchy

Stable association of RNAi machinery is conserved between the cytoplasm and nucleus of human cells

METHOD

A whole-mount in situ hybridization method for microRNA detection in Caenorhabditis elegans

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