Table of Contents

Perspective

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Decrypting noncoding RNA interactions, structures, and functional networks
- Muller Fabbri,
- Leonard Girnita,
- Gabriele Varani,
- and George A. Calin
Genome Res. September 2019 29: 1377-1388; Published in Advance August 21, 2019, doi:10.1101/gr.247239.118
OPEN ACCESS ARTICLE

Research

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The 22q11 low copy repeats are characterized by unprecedented size and structural variability
- Wolfram Demaerel,
- Yulia Mostovoy,
- Feyza Yilmaz,
- Lisanne Vervoort,
- Steven Pastor,
- Matthew S. Hestand,
- Ann Swillen,
- Elfi Vergaelen,
- Elizabeth A. Geiger,
- Curtis R. Coughlin,
- Stephen K. Chow,
- Donna McDonald-McGinn,
- Bernice Morrow,
- Pui-Yan Kwok,
- Ming Xiao,
- Beverly S. Emanuel,
- Tamim H. Shaikh,
- and Joris R. Vermeesch
Genome Res. September 2019 29: 1389-1401; doi:10.1101/gr.248682.119
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Genome-wide analysis of polymerase III–transcribed Alu elements suggests cell-type–specific enhancer function
- Xiao-Ou Zhang,
- Thomas R. Gingeras,
- and Zhiping Weng
Genome Res. September 2019 29: 1402-1414; Published in Advance August 14, 2019, doi:10.1101/gr.249789.119
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Replication timing networks reveal a link between transcription regulatory circuits and replication timing control
- Juan Carlos Rivera-Mulia,
- Sebo Kim,
- Haitham Gabr,
- Abhijit Chakraborty,
- Ferhat Ay,
- Tamer Kahveci,
- and David M. Gilbert
Genome Res. September 2019 29: 1415-1428; Published in Advance August 21, 2019, doi:10.1101/gr.247049.118
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Estrogen-independent molecular actions of mutant estrogen receptor 1 in endometrial cancer
- Zannel Blanchard,
- Jeffery M. Vahrenkamp,
- Kristofer C. Berrett,
- Spencer Arnesen,
- and Jason Gertz
Genome Res. September 2019 29: 1429-1441; Published in Advance July 30, 2019, doi:10.1101/gr.244780.118
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Targeted delivery of CRISPR interference system against Fabp4 to white adipocytes ameliorates obesity, inflammation, hepatic steatosis, and insulin resistance
- Jee Young Chung,
- Qurrat Ul Ain,
- Yoonsung Song,
- Seok-Beom Yong,
- and Yong-Hee Kim
Genome Res. September 2019 29: 1442-1452; Published in Advance August 29, 2019, doi:10.1101/gr.246900.118
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A high resolution A-to-I editing map in the mouse identifies editing events controlled by pre-mRNA splicing
- Konstantin Licht,
- Utkarsh Kapoor,
- Fabian Amman,
- Ernesto Picardi,
- David Martin,
- Prajakta Bajad,
- and Michael F. Jantsch
Genome Res. September 2019 29: 1453-1463; Published in Advance August 19, 2019, doi:10.1101/gr.242636.118
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Distinct types of short open reading frames are translated in plant cells
- Igor Fesenko,
- Ilya Kirov,
- Andrey Kniazev,
- Regina Khazigaleeva,
- Vassili Lazarev,
- Daria Kharlampieva,
- Ekaterina Grafskaia,
- Viktor Zgoda,
- Ivan Butenko,
- Georgy Arapidi,
- Anna Mamaeva,
- Vadim Ivanov,
- and Vadim Govorun
Genome Res. September 2019 29: 1464-1477; Published in Advance August 6, 2019, doi:10.1101/gr.253302.119
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Unique genetic basis of the distinct antibiotic potency of high acetic acid production in the probiotic yeast Saccharomyces cerevisiae var. boulardii
- Benjamin Offei,
- Paul Vandecruys,
- Stijn De Graeve,
- María R. Foulquié-Moreno,
- and Johan M. Thevelein
Genome Res. September 2019 29: 1478-1494; Published in Advance August 29, 2019, doi:10.1101/gr.243147.118
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Large-scale genome analysis of bovine commensal Escherichia coli reveals that bovine-adapted E. coli lineages are serving as evolutionary sources of the emergence of human intestinal pathogenic strains
- Yoko Arimizu,
- Yumi Kirino,
- Mitsuhiko P. Sato,
- Koichi Uno,
- Toshio Sato,
- Yasuhiro Gotoh,
- Frédéric Auvray,
- Hubert Brugere,
- Eric Oswald,
- Jacques G. Mainil,
- Kelly S. Anklam,
- Dörte Döpfer,
- Shuji Yoshino,
- Tadasuke Ooka,
- Yasuhiro Tanizawa,
- Yasukazu Nakamura,
- Atsushi Iguchi,
- Tomoko Morita-Ishihara,
- Makoto Ohnishi,
- Koichi Akashi,
- Tetsuya Hayashi,
- and Yoshitoshi Ogura
Genome Res. September 2019 29: 1495-1505; Published in Advance August 22, 2019, doi:10.1101/gr.249268.119
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Methods

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Identifying loci under positive selection in complex population histories
- Alba Refoyo-Martínez,
- Rute R. da Fonseca,
- Katrín Halldórsdóttir,
- Einar Árnason,
- Thomas Mailund,
- and Fernando Racimo
Genome Res. September 2019 29: 1506-1520; Published in Advance July 30, 2019, doi:10.1101/gr.246777.118
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Profiling the long noncoding RNA interaction network in the regulatory elements of target genes by chromatin in situ reverse transcription sequencing
- Shilin Zhang,
- Yichen Wang,
- Lin Jia,
- Xue Wen,
- Zhonghua Du,
- Cong Wang,
- Yajing Hao,
- Dehai Yu,
- Lei Zhou,
- Naifei Chen,
- Jingcheng Chen,
- Huiling Chen,
- Hui Zhang,
- Ilkay Celik,
- Günhan Gülsoy,
- Jianjun Luo,
- Baoming Qin,
- Xueling Cui,
- Zhonghui Liu,
- Songling Zhang,
- Miguel A. Esteban,
- Ferhat Ay,
- Wei Xu,
- Runsheng Chen,
- Wei Li,
- Andrew R. Hoffman,
- Ji-Fan Hu,
- and Jiuwei Cui
Genome Res. September 2019 29: 1521-1532; Published in Advance July 17, 2019, doi:10.1101/gr.244996.118
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Discovering human transcription factor physical interactions with genetic variants, novel DNA motifs, and repetitive elements using enhanced yeast one-hybrid assays
- Shaleen Shrestha,
- Jared Allan Sewell,
- Clarissa Stephanie Santoso,
- Elena Forchielli,
- Sebastian Carrasco Pro,
- Melissa Martinez,
- and Juan Ignacio Fuxman Bass
Genome Res. September 2019 29: 1533-1544; doi:10.1101/gr.248823.119
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Direct RNA nanopore sequencing of full-length coronavirus genomes provides novel insights into structural variants and enables modification analysis
- Adrian Viehweger,
- Sebastian Krautwurst,
- Kevin Lamkiewicz,
- Ramakanth Madhugiri,
- John Ziebuhr,
- Martin Hölzer,
- and Manja Marz
Genome Res. September 2019 29: 1545-1554; Published in Advance August 22, 2019, doi:10.1101/gr.247064.118

Resource

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Pediatric Cancer Variant Pathogenicity Information Exchange (PeCanPIE): a cloud-based platform for curating and classifying germline variants
- Michael N. Edmonson,
- Aman N. Patel,
- Dale J. Hedges,
- Zhaoming Wang,
- Evadnie Rampersaud,
- Chimene A. Kesserwan,
- Xin Zhou,
- Yanling Liu,
- Scott Newman,
- Michael C. Rusch,
- Clay L. McLeod,
- Mark R. Wilkinson,
- Stephen V. Rice,
- Thierry Soussi,
- J. Paul Taylor,
- Michael Benatar,
- Jared B. Becksfort,
- Kim E. Nichols,
- Leslie L. Robison,
- James R. Downing,
- and Jinghui Zhang
Genome Res. September 2019 29: 1555-1565; Published in Advance August 22, 2019, doi:10.1101/gr.250357.119
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Corrigenda

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Corrigendum: A long-term demasculinization of X-linked intergenic noncoding RNAs in Drosophila melanogaster
- Ge Gao,
- Maria D. Vibranovski,
- Li Zhang,
- Zheng Li,
- Min Liu,
- Yong E. Zhang,
- Xinmin Li,
- Wenxia Zhang,
- Qichang Fan,
- Nicholas W. VanKuren,
- Manyuan Long,
- and Liping Wei
Genome Res. September 2019 29: 1566_1; doi:10.1101/gr.255315.119
OPEN ACCESS ARTICLE
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Corrigendum: Mutational signatures of DNA mismatch repair deficiency in C. elegans and human cancers
- Bettina Meier,
- Nadezda V. Volkova,
- Ye Hong,
- Pieta Schofield,
- Peter J. Campbell,
- Moritz Gerstung,
- and Anton Gartner
Genome Res. September 2019 29: 1566_2; doi:10.1101/gr.255596.119
OPEN ACCESS ARTICLE

Perspective

Decrypting noncoding RNA interactions, structures, and functional networks

Research

The 22q11 low copy repeats are characterized by unprecedented size and structural variability

Genome-wide analysis of polymerase III–transcribed Alu elements suggests cell-type–specific enhancer function

Replication timing networks reveal a link between transcription regulatory circuits and replication timing control

Estrogen-independent molecular actions of mutant estrogen receptor 1 in endometrial cancer

Targeted delivery of CRISPR interference system against Fabp4 to white adipocytes ameliorates obesity, inflammation, hepatic steatosis, and insulin resistance

A high resolution A-to-I editing map in the mouse identifies editing events controlled by pre-mRNA splicing

Distinct types of short open reading frames are translated in plant cells

Unique genetic basis of the distinct antibiotic potency of high acetic acid production in the probiotic yeast Saccharomyces cerevisiae var. boulardii

Large-scale genome analysis of bovine commensal Escherichia coli reveals that bovine-adapted E. coli lineages are serving as evolutionary sources of the emergence of human intestinal pathogenic strains

Methods

Identifying loci under positive selection in complex population histories

Profiling the long noncoding RNA interaction network in the regulatory elements of target genes by chromatin in situ reverse transcription sequencing

Discovering human transcription factor physical interactions with genetic variants, novel DNA motifs, and repetitive elements using enhanced yeast one-hybrid assays

Direct RNA nanopore sequencing of full-length coronavirus genomes provides novel insights into structural variants and enables modification analysis

Resource

Pediatric Cancer Variant Pathogenicity Information Exchange (PeCanPIE): a cloud-based platform for curating and classifying germline variants

Corrigenda

Corrigendum: A long-term demasculinization of X-linked intergenic noncoding RNAs in Drosophila melanogaster

Corrigendum: Mutational signatures of DNA mismatch repair deficiency in C. elegans and human cancers

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