Genome Res. Advance Online Articles for 28 Jun 2021

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Research
Allelic diversification after transposable element exaptation promoted Gsdf as the master sex determining gene of sablefish
Amaury HERPIN, Manfred Schartl, Alexandra Depince, Yann Guiguen, Julien Bobe, Aurelie Hua-Van, Edward S Hayman, Anna Octavera, Goro Yoshizaki, Krista M Nichols, Giles W Goetz and John A Luckenbach
Genome Res. published 28 June 2021; doi:10.1101/gr.274266.120

Evolution and genomic signatures of spontaneous somatic mutation in Drosophila intestinal stem cells
Nick Riddiford, Katarzyna Siudeja, Marius van den Beek, Benjamin Boumard and Allison J Bardin
Genome Res. published 24 June 2021; doi:10.1101/gr.268441.120 Open Access

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. published 4 June 2021; doi:10.1101/gr.268490.120 Open Access

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. published 24 June 2021; doi:10.1101/gr.270082.120

Dynamic of broad H3K4me3 domains uncover an epigenetic switch between cell identity and cancer-related genes
Mohamed Belhocine, Mathieu Simonin, José David Abad Flores, Agata Cieslak, Iris Manosalva, Lydie Pradel, Charlotte Smith, Eve-Lyne Mathieu, Guillaume Charbonnier, Joost H.A. Martens, Hendrik G. Stunnenberg, Muhammad Ahmad Maqbool, Aneta Mikulasova, Lisa J. Russell, Daniel Rico, Denis Puthier, Pierre Ferrier, Vahid Asnafi and Salvatore Spicuglia
Genome Res. published 23 June 2021; doi:10.1101/gr.266924.120

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. published 11 May 2021; doi:10.1101/gr.275145.120 Open Access

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. published 27 May 2021; doi:10.1101/gr.266528.120

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. published 3 June 2021; doi:10.1101/gr.273771.120

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. published 22 June 2021; doi:10.1101/gr.265603.120

Methods
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. published 8 June 2021; doi:10.1101/gr.275193.120

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. published 23 June 2021; doi:10.1101/gr.274639.120 Open Access

Resource
Transcriptional milestones in Dictyostelium development
Mariko Katoh-Kurasawa, Karin Hrovatin, Shigenori Hirose, Amanda Webb, Hsing-I Ho, Blaz Zupan and Gad Shaulsky
Genome Res. published 28 June 2021; doi:10.1101/gr.275496.121
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