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Research: Adaptation of centromeres to breakage through local genomic and epigenomic remodeling in wheat
- Jingwei Zhou,
- Yuhong Huang,
- Huan Ma,
- Yiqian Chen,
- Chuanye Chen,
- Fangpu Han,
- and Handong Su
Genome Res. November 2025 35: 2461-2471; Published in Advance September 30, 2025, doi:10.1101/gr.280913.125
...Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China; 3State Key Laboratory of Seed Innovation, Institute of Genetics and Developmental Biology, Chinese Academy...
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Resource: Genetic features and genomic targets of human KRAB-zinc finger proteins
- Jonas de Tribolet-Hardy,
- Christian W. Thorball,
- Romain Forey,
- Evarist Planet,
- Julien Duc,
- Alexandre Coudray,
- Bara Khubieh,
- Sandra Offner,
- Cyril Pulver,
- Jacques Fellay,
- Michael Imbeault,
- Priscilla Turelli,
- and Didier Trono
Genome Res. August 2023 33: 1409-1423; Published in Advance September 20, 2023, doi:10.1101/gr.277722.123
.... The colors and their intensity represent the direction and strength of the correlations, with blue representing a positive and red a negative correlation. Only significant correlations after Bonferroni correction are shown. (D) Primate versus nonprimate KZFP constraint across indicated KZFP domains...
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Research: 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
...University, New York, New York 10065, USA; 5MU Institute for Data Science and Informatics, University of Missouri, Columbia, Missouri 65211, USA; 6Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, 08036 Barcelona, Spain; 7School of Forest Resources and Conservation...
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Research: 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
...corresponds to a 36-bp genomic region centered on a CACGTG site. Plot shows the fluorescence intensities from PBM assays, which are proportional to the level of bound TF at each genomic site. We note that fluorescence intensities are generally not directly comparable between PBM experiments for different...
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Method: Background-suppressed live visualization of genomic loci with an improved CRISPR system based on a split fluorophore
- Narendra Chaudhary,
- Si-Hyeong Nho,
- Hayoon Cho,
- Narangerel Gantumur,
- Jae Sun Ra,
- Kyungjae Myung,
- and Hajin Kim
Genome Res. September 2020 30: 1306-1316; Published in Advance September 4, 2020, doi:10.1101/gr.260018.119
...Narendra Chaudhary1, Si-Hyeong Nho1, Hayoon Cho1, Narangerel Gantumur1, Jae Sun Ra2, Kyungjae Myung1,2 and Hajin Kim1,2 1School of Life Sciences, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea; 2Center for Genomic Integrity, Institute for Basic Science...
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Research: Widespread roles of enhancer-like transposable elements in cell identity and long-range genomic interactions
- Yaqiang Cao,
- Guoyu Chen,
- Gang Wu,
- Xiaoli Zhang,
- Joseph McDermott,
- Xingwei Chen,
- Chi Xu,
- Quanlong Jiang,
- Zhaoxiong Chen,
- Yingying Zeng,
- Daosheng Ai,
- Yi Huang,
- and Jing-Dong J. Han
Genome Res. January 2019 29: 40-52; Published in Advance November 19, 2018, doi:10.1101/gr.235747.118
...activity of L2 elements. Our results reveal a previously unappreciated co-evolution and interaction between two TE families in shaping regulatory networks.Transposable elements (TEs) are widespread throughout the , covering more than 50% of the human (International Human Genome Sequencing Consortium 2001...
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Method: Massively parallel cis-regulatory analysis in the mammalian central nervous system
- Susan Q. Shen,
- Connie A. Myers,
- Andrew E.O. Hughes,
- Leah C. Byrne,
- John G. Flannery,
- and Joseph C. Corbo
Genome Res. February 2016 26: 238-255; Published in Advance November 17, 2015, doi:10.1101/gr.193789.115
..., California 94720, USA Cis-regulatory elements (CREs, e.g., promoters and enhancers) regulate gene expression, and variants within CREs can modulate disease risk. Next-generation sequencing has enabled the rapid generation of genomic data that predict the locations of CREs, but a bottleneck lies...
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Method: Predicting human genes susceptible to genomic instability associated with Alu/Alu-mediated rearrangements
- Xiaofei Song,
- Christine R. Beck,
- Renqian Du,
- Ian M. Campbell,
- Zeynep Coban-Akdemir,
- Shen Gu,
- Amy M. Breman,
- Pawel Stankiewicz,
- Grzegorz Ira,
- Chad A. Shaw,
- and James R. Lupski
Genome Res. August 2018 28: 1228-1242; Published in Advance June 15, 2018, doi:10.1101/gr.229401.117
...Baylor Genetics, Houston, Texas 77021, USA; 3Department of Pediatrics, Baylor College of Medicine, Houston, Texas 77030, USA; 4Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030, USA; 5Texas Children's Hospital, Houston, Texas 77030, USA Corresponding author: jlupski...
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Research: In vivo binding of PRDM9 reveals interactions with noncanonical genomic sites
- Corinne Grey,
- Julie A.J. Clément,
- Jérôme Buard,
- Benjamin Leblanc,
- Ivo Gut,
- Marta Gut,
- Laurent Duret,
- and Bernard de Massy
Genome Res. April 2017 27: 580-590; Published in Advance March 23, 2017, doi:10.1101/gr.217240.116
...), University of Copenhagen, 2200 Copenhagen, Denmark; 3CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), 08028 Barcelona, Spain; 4Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain; 5Université de Lyon, Université Claude Bernard, CNRS, Laboratoire de...
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Letter: Evolutionary constraint facilitates interpretation of genetic variation in resequenced human genomes
- David L. Goode,
- Gregory M. Cooper,
- Jeremy Schmutz,
- Mark Dickson,
- Eidelyn Gonzales,
- Ming Tsai,
- Kalpana Karra,
- Eugene Davydov,
- Serafim Batzoglou,
- Richard M. Myers,
- and Arend Sidow
Genome Res. March 2010 20: 301-310; Published in Advance January 12, 2010, doi:10.1101/gr.102210.109
...functional variants. We resequenced 575 amplicons within 432 individuals at genomic sites enriched for evolutionary constraint and also analyzed variation within three published human genomes. We find that single-site measures of evolutionary constraint derived from mammalian multiple sequence alignments...

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