Table of Contents

July 2021; 31 (7)

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,
    • Juntao Gao,
    • Michael Q. Zhang,
    • Wei Xie,
    • and Xiaowo Wang
    Genome Res. July 2021 31: 1121-1135; Published in Advance June 17, 2021, doi:10.1101/gr.275235.121

  • 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,
    • and Kateryna D. Makova
    Genome Res. July 2021 31: 1136-1149; Published in Advance June 29, 2021, doi:10.1101/gr.269589.120
    OPEN ACCESS ARTICLE

  • 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,
    • Xia Hu,
    • Joshua M. Akey,
    • Xin Jin,
    • and Liangdan Sun
    Genome Res. July 2021 31: 1150-1158; Published in Advance June 21, 2021, doi:10.1101/gr.267963.120

  • 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,
    • Irene Roberts,
    • Anindita Roy,
    • Tudor A. Fulga,
    • and Thomas A. Milne
    Genome Res. July 2021 31: 1159-1173; Published in Advance June 4, 2021, doi:10.1101/gr.268490.120
    OPEN ACCESS ARTICLE

  • Widespread formation of double-stranded RNAs in testis

    • Andreas Werner,
    • James E. Clark,
    • Calum Samaranayake,
    • John Casement,
    • Hany S. Zinad,
    • Shaymaa Sadeq,
    • Surar Al-Hashimi,
    • Martin Smith,
    • Noora Kotaja,
    • and John S. Mattick
    Genome Res. July 2021 31: 1174-1186; Published in Advance June 22, 2021, doi:10.1101/gr.265603.120

  • 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,
    • and Barbara J. Meyer
    Genome Res. July 2021 31: 1187-1202; Published in Advance June 24, 2021, doi:10.1101/gr.270082.120

  • The genomic basis of evolutionary differentiation among honey bees

    • Bertrand Fouks,
    • Philipp Brand,
    • Hung N. Nguyen,
    • Jacob Herman,
    • Francisco Camara,
    • Daniel Ence,
    • Darren E. Hagen,
    • Katharina J. Hoff,
    • Stefanie Nachweide,
    • Lars Romoth,
    • Kimberly K.O. Walden,
    • Roderic Guigo,
    • Mario Stanke,
    • Giuseppe Narzisi,
    • Mark Yandell,
    • Hugh M. Robertson,
    • Nikolaus Koeniger,
    • Panuwan Chantawannakul,
    • Michael C. Schatz,
    • Kim C. Worley,
    • Gene E. Robinson,
    • Christine G. Elsik,
    • and Olav Rueppell
    Genome Res. July 2021 31: 1203-1215; Published in Advance May 4, 2021, doi:10.1101/gr.272310.120
    OPEN ACCESS ARTICLE

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

    • Yuning Zhang,
    • Tiffany D. Ho,
    • Nicolas E. Buchler,
    • and Raluca Gordân
    Genome Res. July 2021 31: 1216-1229; Published in Advance May 11, 2021, doi:10.1101/gr.275145.120
    OPEN ACCESS ARTICLE

  • 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,
    • Federico Ariel,
    • Cécile Raynaud,
    • David Latrasse,
    • and Moussa Benhamed
    Genome Res. July 2021 31: 1230-1244; Published in Advance June 3, 2021, doi:10.1101/gr.273771.120

  • 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,
    • Peter J. Bradbury,
    • Jeffrey Ross-Ibarra,
    • Matthew B. Hufford,
    • and M. Cinta Romay
    Genome Res. July 2021 31: 1245-1257; Published in Advance May 27, 2021, doi:10.1101/gr.266528.120

  • 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,
    • and Stephen D. Bentley
    Genome Res. July 2021 31: 1258-1268; Published in Advance June 9, 2021, doi:10.1101/gr.264465.120
    OPEN ACCESS ARTICLE

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,
    • Kerry A. George,
    • Cem Meydan,
    • Susan M. Bailey,
    • and Christopher E. Mason
    Genome Res. July 2021 31: 1269-1279; Published in Advance June 23, 2021, doi:10.1101/gr.274639.120
    OPEN ACCESS ARTICLE

  • 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, Jr.,
    • Sriharsa Pradhan,
    • Eileen T. Dimalanta,
    • Thomas C. Evans, Jr.,
    • Louise Williams,
    • and Theodore B. Davis
    Genome Res. July 2021 31: 1280-1289; Published in Advance June 17, 2021, doi:10.1101/gr.266551.120
    OPEN ACCESS ARTICLE

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

    • Yun Zhang,
    • Chanhee Park,
    • Christopher Bennett,
    • Micah Thornton,
    • and Daehwan Kim
    Genome Res. July 2021 31: 1290-1295; Published in Advance June 8, 2021, doi:10.1101/gr.275193.120

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

    • Shang Gao,
    • Yang Dai,
    • and Jalees Rehman
    Genome Res. July 2021 31: 1296-1311; Published in Advance June 30, 2021, doi:10.1101/gr.265595.120
    OPEN ACCESS ARTICLE
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July 2021; 31 (7)
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