Genome Research Vol 31 Issue 7

Volume 31, Issue 7 | July 2021

Research
- - The loss of heterochromatin is associated with multiscale three-dimensional genome reorganization and aberrant transcription during cellular senescence
    Xianglin Zhang
    Xuehui Liu
    Zhenhai Du
    Lei Wei
    Huan Fang
    Qiongye Dong Jing Niu Yanda Li
    ...[+3 authors]...,
    Juntao Gao
    Michael Q. Zhang
    Wei Xie
    Xiaowo Wang
    First Published June 17, 2021
  - Selection and thermostability suggest G-quadruplexes are novel functional elements of the human genome
    Wilfried M. Guiblet
    Michael DeGiorgio
    Xiaoheng Cheng
    Francesca Chiaromonte
    Kristin A. Eckert
    Yi-Fei Huang
    Kateryna D. Makova
    First Published June 29, 2021
  - Deep sequencing of 1320 genes reveals the landscape of protein-truncating variants and their contribution to psoriasis in 19,973 Chinese individuals
    Huixin Xu
    Qi Zhen
    Mingzhou Bai
    Lin Fang
    Yong Zhang
    Bao Li Huiyao Ge Sunjin Moon Weiwei Chen Wenqing Fu Qiongqiong Xu Yuwen Zhou Yafeng Yu Long Lin Liang Yong Tao Zhang Shirui Chen Siyang Liu Hui Zhang Ruoyan Chen Lu Cao Yuanwei Zhang Ruixue Zhang Huanjie Yang
    ...[+19 authors]...,
    Xia Hu
    Joshua M. Akey
    Xin Jin
    Liangdan Sun
    First Published June 21, 2021
  - A KMT2A-AFF1 gene regulatory network highlights the role of core transcription factors and reveals the regulatory logic of key downstream target genes
    Joe R. Harman
    Ross Thorne
    Max Jamilly
    Marta Tapia
    Nicholas T. Crump
    Siobhan Rice Ryan Beveridge Edward Morrissey Marella F.T.R. de Bruijn
    ...[+4 authors]...,
    Irene Roberts
    Anindita Roy
    Tudor A. Fulga
    Thomas A. Milne
    First Published June 4, 2021
  - Widespread formation of double-stranded RNAs in testis
    Andreas Werner
    James E. Clark
    Calum Samaranayake
    John Casement
    Hany S. Zinad
    Shaymaa Sadeq
    ...[+1 authors]...,
    Surar Al-Hashimi
    Martin Smith
    Noora Kotaja
    John S. Mattick
    First Published June 22, 2021
  - Genome-wide profiling reveals functional interplay of DNA sequence composition, transcriptional activity, and nucleosome positioning in driving DNA supercoiling and helix destabilization in C. elegans
    Kristina Krassovsky
    Rajarshi P. Ghosh
    Barbara J. Meyer
    First Published June 24, 2021
  - The genomic basis of evolutionary differentiation among honey bees
    Fouks Bertrand
    Brand Philipp
    Nguyen Hung N.
    Herman Jacob
    Camara Francisco
    Ence Daniel Hagen Darren E. Hoff Katharina J. Nachweide Stefanie Romoth Lars Walden Kimberly K.O. Guigo Roderic Stanke Mario Narzisi Giuseppe Yandell Mark Robertson Hugh M. Koeniger Nikolaus Chantawannakul Panuwan Schatz Michael C.
    ...[+14 authors]...,
    Worley Kim C.
    Robinson Gene E.
    Elsik Christine G.
    Rueppell Olav
    First Published May 4, 2021
  - Competition for DNA binding between paralogous transcription factors determines their genomic occupancy and regulatory functions
    Yuning Zhang
    Tiffany D. Ho
    Nicolas E. Buchler
    Raluca Gordân
    First Published May 11, 2021
  - Polycomb-dependent differential chromatin compartmentalization determines gene coregulation in Arabidopsis
    Ying Huang
    Sanchari Sicar
    Juan S. Ramirez-Prado
    Deborah Manza-Mianza
    Javier Antunez-Sanchez
    Rim Brik-Chaouche Natalia Y. Rodriguez-Granados Jing An Catherine Bergounioux Magdy M. Mahfouz Heribert Hirt Martin Crespi Lorenzo Concia Fredy Barneche Simon Amiard Aline V. Probst Jose Gutierrez-Marcos
    ...[+12 authors]...,
    Federico Ariel
    Cécile Raynaud
    David Latrasse
    Moussa Benhamed
    First Published June 3, 2021
  - Conserved noncoding sequences provide insights into regulatory sequence and loss of gene expression in maize
    Baoxing Song
    Edward S. Buckler
    Hai Wang
    Yaoyao Wu
    Evan Rees
    Elizabeth A. Kellogg Daniel J. Gates Merritt Khaipho-Burch
    ...[+3 authors]...,
    Peter J. Bradbury
    Jeffrey Ross-Ibarra
    Matthew B. Hufford
    M. Cinta Romay
    First Published May 27, 2021
  - The effect of recombination on the evolution of a population of Neisseria meningitidis
    Neil MacAlasdair
    Maiju Pesonen
    Ola Brynildsrud
    Vegard Eldholm
    Paul A. Kristiansen
    Jukka Corander
    Dominique A. Caugant
    Stephen D. Bentley
    First Published June 9, 2021
Methods
- - Haplotype diversity and sequence heterogeneity of human telomeres
    Kirill Grigorev
    Jonathan Foox
    Daniela Bezdan
    Daniel Butler
    Jared J. Luxton
    Jake Reed Miles J. McKenna Lynn Taylor
    ...[+3 authors]...,
    Kerry A. George
    Cem Meydan
    Susan M. Bailey
    Christopher E. Mason
    First Published June 23, 2021
  - Enzymatic methyl sequencing detects DNA methylation at single-base resolution from picograms of DNA
    Romualdas Vaisvila
    V.K. Chaithanya Ponnaluri
    Zhiyi Sun
    Bradley W. Langhorst
    Lana Saleh
    Shengxi Guan Nan Dai Matthew A. Campbell Brittany S. Sexton Katherine Marks Mala Samaranayake James C. Samuelson Heidi E. Church Esta Tamanaha Ivan R. Corrêa Sriharsa Pradhan
    ...[+11 authors]...,
    Eileen T. Dimalanta
    Thomas C. Evans
    Louise Williams
    Theodore B. Davis
    First Published June 17, 2021
  - Rapid and accurate alignment of nucleotide conversion sequencing reads with HISAT-3N
    Yun Zhang
    Chanhee Park
    Christopher Bennett
    Micah Thornton
    Daehwan Kim
    First Published June 8, 2021
  - A Bayesian inference transcription factor activity model for the analysis of single-cell transcriptomes
    Shang Gao
    Yang Dai
    Jalees Rehman
    First Published June 30, 2021

Table of Contents

Volume 31, Issue 7 | July 2021

Research

The loss of heterochromatin is associated with multiscale three-dimensional genome reorganization and aberrant transcription during cellular senescence

Selection and thermostability suggest G-quadruplexes are novel functional elements of the human genome

Deep sequencing of 1320 genes reveals the landscape of protein-truncating variants and their contribution to psoriasis in 19,973 Chinese individuals

A KMT2A-AFF1 gene regulatory network highlights the role of core transcription factors and reveals the regulatory logic of key downstream target genes

Widespread formation of double-stranded RNAs in testis

Genome-wide profiling reveals functional interplay of DNA sequence composition, transcriptional activity, and nucleosome positioning in driving DNA supercoiling and helix destabilization in C. elegans

The genomic basis of evolutionary differentiation among honey bees

Competition for DNA binding between paralogous transcription factors determines their genomic occupancy and regulatory functions

Polycomb-dependent differential chromatin compartmentalization determines gene coregulation in Arabidopsis

Conserved noncoding sequences provide insights into regulatory sequence and loss of gene expression in maize

The effect of recombination on the evolution of a population of Neisseria meningitidis

Methods

Haplotype diversity and sequence heterogeneity of human telomeres

Enzymatic methyl sequencing detects DNA methylation at single-base resolution from picograms of DNA

Rapid and accurate alignment of nucleotide conversion sequencing reads with HISAT-3N

A Bayesian inference transcription factor activity model for the analysis of single-cell transcriptomes

Table of Contents

Volume 31, Issue 7 | July 2021

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Research

Methods