Volume 29, Issue 9 | September 2019

Perspective
- - Decrypting noncoding RNA interactions, structures, and functional networks
    Muller Fabbri
    Leonard Girnita
    Gabriele Varani
    George A. Calin
    First Published August 21, 2019
Research
- - 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
    ...[+9 authors]...,
    Ming Xiao
    Beverly S. Emanuel
    Tamim H. Shaikh
    Joris R. Vermeesch
    First Published September 3, 2019
  - Genome-wide analysis of polymerase III–transcribed Alu elements suggests cell-type–specific enhancer function
    Xiao-Ou Zhang
    Thomas R. Gingeras
    Zhiping Weng
    First Published August 14, 2019
  - 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
    First Published August 21, 2019
  - Estrogen-independent molecular actions of mutant estrogen receptor 1 in endometrial cancer
    Zannel Blanchard
    Jeffery M. Vahrenkamp
    Kristofer C. Berrett
    Spencer Arnesen
    Jason Gertz
    First Published July 30, 2019
  - 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
    Yong-Hee Kim
    First Published August 29, 2019
  - 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
    First Published August 19, 2019
  - 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
    ...[+4 authors]...,
    Georgy Arapidi
    Anna Mamaeva
    Vadim Ivanov
    Vadim Govorun
    First Published August 6, 2019
  - 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
    Johan M. Thevelein
    First Published August 29, 2019
  - 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
    ...[+13 authors]...,
    Makoto Ohnishi
    Koichi Akashi
    Tetsuya Hayashi
    Yoshitoshi Ogura
    First Published August 22, 2019
Methods
- - Identifying loci under positive selection in complex population histories
    Alba Refoyo-Martínez
    Rute R. da Fonseca
    Katrín Halldórsdóttir
    Einar Árnason
    Thomas Mailund
    First Published July 30, 2019
  - 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
    ...[+19 authors]...,
    Wei Li
    Andrew R. Hoffman
    Ji-Fan Hu
    Jiuwei Cui
    First Published July 17, 2019
  - 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
    First Published September 3, 2019
  - 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
    First Published August 22, 2019
Resource
- - 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
    ...[+12 authors]...,
    Kim E. Nichols
    Leslie L. Robison
    James R. Downing
    Jinghui Zhang
    First Published August 22, 2019
Corrigenda
- - 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
    ...[+3 authors]...,
    Qichang Fan
    Nicholas W. VanKuren
    Manyuan Long
    Liping Wei
    First Published September 3, 2019
  - 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
    First Published September 3, 2019

Table of Contents

Volume 29, Issue 9 | September 2019

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

Table of Contents

Volume 29, Issue 9 | September 2019

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Perspective

Research

Methods

Resource

Corrigenda