Table of Contents

March 2023; 33 (3)

Research

  • Global loss of cellular m6A RNA methylation following infection with different SARS-CoV-2 variants

    • Roshan Vaid,
    • Akram Mendez,
    • Ketan Thombare,
    • Rebeca Burgos-Panadero,
    • Rémy Robinot,
    • Barbara F. Fonseca,
    • Nikhil R. Gandasi,
    • Johan Ringlander,
    • Mohammad Hassan Baig,
    • Jae-June Dong,
    • Jae Yong Cho,
    • Björn Reinius,
    • Lisa A. Chakrabarti,
    • Kristina Nystrom,
    • and Tanmoy Mondal
    Genome Res. March 2023 33: 299-313; Published in Advance March 1, 2023, doi:10.1101/gr.276407.121
    OPEN ACCESS ARTICLE

  • Kinetic networks identify TWIST2 as a key regulatory node in adipogenesis

    • Arun B. Dutta,
    • Daniel S. Lank,
    • Roza K. Przanowska,
    • Piotr Przanowski,
    • Lixin Wang,
    • Bao Nguyen,
    • Ninad M. Walavalkar,
    • Fabiana M. Duarte,
    • and Michael J. Guertin
    Genome Res. March 2023 33: 314-331; Published in Advance February 21, 2023, doi:10.1101/gr.277559.122
    OPEN ACCESS ARTICLE

  • The impact of SWI/SNF and NuRD inactivation on gene expression is tightly coupled with levels of RNA polymerase II occupancy at promoters

    • Sachin Pundhir,
    • Jinyu Su,
    • Marta Tapia,
    • Anne Meldgaard Hansen,
    • James Seymour Haile,
    • Klaus Hansen,
    • and Bo Torben Porse
    Genome Res. March 2023 33: 332-345; Published in Advance March 16, 2023, doi:10.1101/gr.277089.122
    OPEN ACCESS ARTICLE

  • Enhancers display constrained sequence flexibility and context-specific modulation of motif function

    • Franziska Reiter,
    • Bernardo P. de Almeida,
    • and Alexander Stark
    Genome Res. March 2023 33: 346-358; Published in Advance March 20, 2023, doi:10.1101/gr.277246.122

  • Large haplotypes highlight a complex age structure within the maize pan-genome

    • Jianing Liu and
    • R. Kelly Dawe
    Genome Res. March 2023 33: 359-370; Published in Advance February 28, 2023, doi:10.1101/gr.276705.122

  • SWATH-MS-based proteogenomic analysis reveals the involvement of alternative splicing in poplar upon lead stress

    • Fu-Yuan Zhu,
    • Xin Chen,
    • Yu-Chen Song,
    • Lydia Pui Ying Lam,
    • Yuki Tobimatsu,
    • Bei Gao,
    • Mo-Xian Chen,
    • and Fu-Liang Cao
    Genome Res. March 2023 33: 371-385; Published in Advance March 24, 2023, doi:10.1101/gr.277473.122

Methods

  • Defining the separation landscape of topological domains for decoding consensus domain organization of the 3D genome

    • Dachang Dang,
    • Shao-Wu Zhang,
    • Ran Duan,
    • and Shihua Zhang
    Genome Res. March 2023 33: 386-400; Published in Advance March 9, 2023, doi:10.1101/gr.277187.122

  • Simultaneous profiling of host expression and microbial abundance by spatial metatranscriptome sequencing

    • Lin Lyu,
    • Xue Li,
    • Ru Feng,
    • Xin Zhou,
    • Tuhin K. Guha,
    • Xiaofei Yu,
    • Guo Qiang Chen,
    • Yufeng Yao,
    • Bing Su,
    • Duowu Zou,
    • Michael P. Snyder,
    • and Lei Chen
    Genome Res. March 2023 33: 401-411; Published in Advance March 27, 2023, doi:10.1101/gr.277178.122

  • Tn5 tagments and transposes oligos to single-stranded DNA for strand-specific RNA sequencing

    • Yanjun Zhang,
    • Yin Tang,
    • Zhongxing Sun,
    • Junqi Jia,
    • Yuan Fang,
    • Xinyi Wan,
    • and Dong Fang
    Genome Res. March 2023 33: 412-426; Published in Advance March 23, 2023, doi:10.1101/gr.277213.122

  • Evaluation of N6-methyldeoxyadenosine antibody-based genomic profiling in eukaryotes

    • Brian M. Debo,
    • Benjamin J. Mallory,
    • and Andrew B. Stergachis
    Genome Res. March 2023 33: 427-434; Published in Advance February 14, 2023, doi:10.1101/gr.276696.122

Resources

  • Genome-wide identification of tandem repeats associated with splicing variation across 49 tissues in humans

    • Kohei Hamanaka,
    • Daisuke Yamauchi,
    • Eriko Koshimizu,
    • Kei Watase,
    • Kaoru Mogushi,
    • Kinya Ishikawa,
    • Hidehiro Mizusawa,
    • Naomi Tsuchida,
    • Yuri Uchiyama,
    • Atsushi Fujita,
    • Kazuharu Misawa,
    • Takeshi Mizuguchi,
    • Satoko Miyatake,
    • and Naomichi Matsumoto
    Genome Res. March 2023 33: 435-447; Published in Advance March 27, 2023, doi:10.1101/gr.277335.122

  • Complete sequencing of a cynomolgus macaque major histocompatibility complex haplotype

    • Julie A. Karl,
    • Trent M. Prall,
    • Hailey E. Bussan,
    • Joshua M. Varghese,
    • Aparna Pal,
    • Roger W. Wiseman,
    • and David H. O'Connor
    Genome Res. March 2023 33: 448-462; Published in Advance February 28, 2023, doi:10.1101/gr.277429.122

  • A sheep pangenome reveals the spectrum of structural variations and their effects on tail phenotypes

    • Ran Li,
    • Mian Gong,
    • Xinmiao Zhang,
    • Fei Wang,
    • Zhenyu Liu,
    • Lei Zhang,
    • Qimeng Yang,
    • Yuan Xu,
    • Mengsi Xu,
    • Huanhuan Zhang,
    • Yunfeng Zhang,
    • Xuelei Dai,
    • Yuanpeng Gao,
    • Zhuangbiao Zhang,
    • Wenwen Fang,
    • Yuta Yang,
    • Weiwei Fu,
    • Chunna Cao,
    • Peng Yang,
    • Zeinab Amiri Ghanatsaman,
    • Niloufar Jafarpour Negari,
    • Hojjat Asadollahpour Nanaei,
    • Xiangpeng Yue,
    • Yuxuan Song,
    • Xianyong Lan,
    • Weidong Deng,
    • Xihong Wang,
    • Chuanying Pan,
    • Ruidong Xiang,
    • Eveline M. Ibeagha-Awemu,
    • Pat (J.S.) Heslop-Harrison,
    • Benjamin D. Rosen,
    • Johannes A. Lenstra,
    • Shangquan Gan,
    • and Yu Jiang
    Genome Res. March 2023 33: 463-477; Published in Advance April 3, 2023, doi:10.1101/gr.277372.12
    OPEN ACCESS ARTICLE
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This Issue

March 2023; 33 (3)
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