Table of Contents

In memoriam

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Sydney Brenner—a personal perspective
- Byrappa Venkatesh
Genome Res. June 2019 29: vii-ix; doi:10.1101/gr.251918.119
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Research

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4q-D4Z4 chromatin architecture regulates the transcription of muscle atrophic genes in facioscapulohumeral muscular dystrophy
- Alice Cortesi,
- Matthieu Pesant,
- Shruti Sinha,
- Federica Marasca,
- Eleonora Sala,
- Francesco Gregoretti,
- Laura Antonelli,
- Gennaro Oliva,
- Chiara Chiereghin,
- Giulia Soldà,
- and Beatrice Bodega
Genome Res. June 2019 29: 883-895; Published in Advance May 16, 2019, doi:10.1101/gr.233288.117
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A massively parallel 3′ UTR reporter assay reveals relationships between nucleotide content, sequence conservation, and mRNA destabilization
- Adam J. Litterman,
- Robin Kageyama,
- Olivier Le Tonqueze,
- Wenxue Zhao,
- John D. Gagnon,
- Hani Goodarzi,
- David J. Erle,
- and K. Mark Ansel
Genome Res. June 2019 29: 896-906; Published in Advance May 31, 2019, doi:10.1101/gr.242552.118
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Systems analysis reveals complex biological processes during virus infection fate decisions
- Jordi Argilaguet,
- Mireia Pedragosa,
- Anna Esteve-Codina,
- Graciela Riera,
- Enric Vidal,
- Cristina Peligero-Cruz,
- Valentina Casella,
- David Andreu,
- Tsuneyasu Kaisho,
- Gennady Bocharov,
- Burkhard Ludewig,
- Simon Heath,
- and Andreas Meyerhans
Genome Res. June 2019 29: 907-919; Published in Advance May 28, 2019, doi:10.1101/gr.241372.118
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Diversification and collapse of a telomere elongation mechanism
- Bastien Saint-Leandre,
- Son C. Nguyen,
- and Mia T. Levine
Genome Res. June 2019 29: 920-931; Published in Advance May 28, 2019, doi:10.1101/gr.245001.118
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Turnover of ribosome-associated transcripts from de novo ORFs produces gene-like characteristics available for de novo gene emergence in wild yeast populations
- Éléonore Durand,
- Isabelle Gagnon-Arsenault,
- Johan Hallin,
- Isabelle Hatin,
- Alexandre K. Dubé,
- Lou Nielly-Thibault,
- Olivier Namy,
- and Christian R. Landry
Genome Res. June 2019 29: 932-943; Published in Advance May 31, 2019, doi:10.1101/gr.239822.118
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Convergent recombination cessation between mating-type genes and centromeres in selfing anther-smut fungi
- Fantin Carpentier,
- Ricardo C. Rodríguez de la Vega,
- Sara Branco,
- Alodie Snirc,
- Marco A. Coelho,
- Michael E. Hood,
- and Tatiana Giraud
Genome Res. June 2019 29: 944-953; Published in Advance May 1, 2019, doi:10.1101/gr.242578.118
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Human contamination in bacterial genomes has created thousands of spurious proteins
- Florian P. Breitwieser,
- Mihaela Pertea,
- Aleksey V. Zimin,
- and Steven L. Salzberg
Genome Res. June 2019 29: 954-960; Published in Advance May 7, 2019, doi:10.1101/gr.245373.118

Methods

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Plasmid detection and assembly in genomic and metagenomic data sets
- Dmitry Antipov,
- Mikhail Raiko,
- Alla Lapidus,
- and Pavel A. Pevzner
Genome Res. June 2019 29: 961-968; Published in Advance May 2, 2019, doi:10.1101/gr.241299.118
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methyl-ATAC-seq measures DNA methylation at accessible chromatin
- Roman Spektor,
- Nathaniel D. Tippens,
- Claudia A. Mimoso,
- and Paul D. Soloway
Genome Res. June 2019 29: 969-977; Published in Advance June 3, 2019, doi:10.1101/gr.245399.118
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One minute analysis of 200 histone posttranslational modifications by direct injection mass spectrometry
- Simone Sidoli,
- Yekaterina Kori,
- Mariana Lopes,
- Zuo-Fei Yuan,
- Hee Jong Kim,
- Katarzyna Kulej,
- Kevin A. Janssen,
- Laura M. Agosto,
- Julia Pinheiro Chagas da Cunha,
- Andrew J. Andrews,
- and Benjamin A. Garcia
Genome Res. June 2019 29: 978-987; Published in Advance May 23, 2019, doi:10.1101/gr.247353.118
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Genome-wide reconstitution of chromatin transactions reveals that RSC preferentially disrupts H2AZ-containing nucleosomes
- Aylin Cakiroglu,
- Cedric R. Clapier,
- Andreas H. Ehrensberger,
- Elodie Darbo,
- Bradley R. Cairns,
- Nicholas M. Luscombe,
- and Jesper Q. Svejstrup
Genome Res. June 2019 29: 988-998; Published in Advance May 16, 2019, doi:10.1101/gr.243139.118
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Beta-binomial modeling of CRISPR pooled screen data identifies target genes with greater sensitivity and fewer false negatives
- Hyun-Hwan Jeong,
- Seon Young Kim,
- Maxime W.C. Rousseaux,
- Huda Y. Zoghbi,
- and Zhandong Liu
Genome Res. June 2019 29: 999-1008; Published in Advance April 23, 2019, doi:10.1101/gr.245571.118
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Resources

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Recompleting the Caenorhabditis elegans genome
- Jun Yoshimura,
- Kazuki Ichikawa,
- Massa J. Shoura,
- Karen L. Artiles,
- Idan Gabdank,
- Lamia Wahba,
- Cheryl L. Smith,
- Mark L. Edgley,
- Ann E. Rougvie,
- Andrew Z. Fire,
- Shinichi Morishita,
- and Erich M. Schwarz
Genome Res. June 2019 29: 1009-1022; Published in Advance May 23, 2019, doi:10.1101/gr.244830.118
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Long-read sequencing reveals intra-species tolerance of substantial structural variations and new subtelomere formation in C. elegans
- Chuna Kim,
- Jun Kim,
- Sunghyun Kim,
- Daniel E. Cook,
- Kathryn S. Evans,
- Erik C. Andersen,
- and Junho Lee
Genome Res. June 2019 29: 1023-1035; Published in Advance May 23, 2019, doi:10.1101/gr.246082.118
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The C. elegans embryonic transcriptome with tissue, time, and alternative splicing resolution
- Adam D. Warner,
- Louis Gevirtzman,
- LaDeana W. Hillier,
- Brent Ewing,
- and Robert H. Waterston
Genome Res. June 2019 29: 1036-1045; Published in Advance May 23, 2019, doi:10.1101/gr.243394.118
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In memoriam

Sydney Brenner—a personal perspective

Research

4q-D4Z4 chromatin architecture regulates the transcription of muscle atrophic genes in facioscapulohumeral muscular dystrophy

A massively parallel 3′ UTR reporter assay reveals relationships between nucleotide content, sequence conservation, and mRNA destabilization

Systems analysis reveals complex biological processes during virus infection fate decisions

Diversification and collapse of a telomere elongation mechanism

Turnover of ribosome-associated transcripts from de novo ORFs produces gene-like characteristics available for de novo gene emergence in wild yeast populations

Convergent recombination cessation between mating-type genes and centromeres in selfing anther-smut fungi

Human contamination in bacterial genomes has created thousands of spurious proteins

Methods

Plasmid detection and assembly in genomic and metagenomic data sets

methyl-ATAC-seq measures DNA methylation at accessible chromatin

One minute analysis of 200 histone posttranslational modifications by direct injection mass spectrometry

Genome-wide reconstitution of chromatin transactions reveals that RSC preferentially disrupts H2AZ-containing nucleosomes

Beta-binomial modeling of CRISPR pooled screen data identifies target genes with greater sensitivity and fewer false negatives

Resources

Recompleting the Caenorhabditis elegans genome

Long-read sequencing reveals intra-species tolerance of substantial structural variations and new subtelomere formation in C. elegans

The C. elegans embryonic transcriptome with tissue, time, and alternative splicing resolution

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