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Research: Loss of multilevel 3D genome organization during breast cancer progression
- Roberto Rossini,
- Saleh Oshaghi,
- Maxim Nekrasov,
- Aurélie Bellanger,
- Renae Domaschenz,
- Yasmin Dijkwel,
- Mohamed Abdelhalim,
- Rahul Agrawal,
- Marit Ledsaak,
- Philippe Collas,
- Ragnhild Eskeland,
- David Tremethick,
- and Jonas Paulsen
Genome Res. January 2026 36: 20-37; Published in Advance October 9, 2025, doi:10.1101/gr.280791.125
...′-sgRNA pair or control EGFP/mCherry sgRNAs Lenti-multi-CRISPR plasmid-transfected cells was purified using a RNeasy kit with an on-column DNase I treatment according to the manufacturer's protocol (Qiagen). RNA was eluted in 25 µL ddH2O, quantified using NanoDrop, and quality-controlled by agarose gel...
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Method: A novel approach for in vivo DNA footprinting using short double-stranded cell-free DNA from plasma
- Jan Müller,
- Christina Hartwig,
- Mirko Sonntag,
- Lisa Bitzer,
- Christopher Adelmann,
- Yevhen Vainshtein,
- Karolina Glanz,
- Sebastian O. Decker,
- Thorsten Brenner,
- Georg F. Weber,
- Arndt von Haeseler,
- and Kai Sohn
Genome Res. August 2024 34: 1185-1195; Published in Advance September 13, 2024, doi:10.1101/gr.279326.124
...occupancy adjacent to these binding sites (Fig. 2B). In good agreement, DNase-seq data show a combination of a footprint peak with adjacent oscillation patterns, whereas ATAC-seq detects a peak representative for open chromatin at the CTCF binding sites (Fig. 2B). Our data suggest that short cfDNA most...
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Resource: Common and specific gene regulatory programs in zebrafish caudal fin regeneration at single-cell resolution
- Yujie Chen,
- Yiran Hou,
- Qinglin Zeng,
- Irene Wang,
- Meiru Shang,
- Kwangdeok Shin,
- Christopher Hemauer,
- Xiaoyun Xing,
- Junsu Kang,
- Guoyan Zhao,
- and Ting Wang
Genome Res. January 2025 35: 202-218; Published in Advance January 14, 2025, doi:10.1101/gr.279372.124
...and chromatin accessibility map across regenerative stages provides new insights into regeneration regulatory mechanisms and serves as a valuable resource for the community.The zebrafish (Danio rerio) serves as an excellent model organism for studying complex tissue regeneration processes owing to its...
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Method: Examining the dynamics of three-dimensional genome organization with multitask matrix factorization
- Da-Inn Lee and
- Sushmita Roy
Genome Res. May 2025 35: 1179-1193; Published in Advance March 20, 2025, doi:10.1101/gr.279930.124
...Examining the dynamics of three-dimensional organization with multitask matrix factorization Da-Inn Lee1 and Sushmita Roy1,2 1Department of Biostatistics and Medical Informatics, University of Wisconsin–Madison, Madison, Wisconsin 53715, USA; 2Wisconsin Institute for Discovery, Madison, Wisconsin...
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Research: Common cis-regulatory variation modifies the penetrance of pathogenic SHROOM3 variants in craniofacial microsomia
- Hao Zhu,
- Jiao Zhang,
- Soumya Rao,
- Matthew D. Durbin,
- Ying Li,
- Ruirui Lang,
- Jiqiang Liu,
- Baichuan Xiao,
- Hailin Shan,
- Ziqiu Meng,
- Jinmo Wang,
- Xiaokai Tang,
- Zhenni Shi,
- Liza L. Cox,
- Shouqin Zhao,
- Stephanie M. Ware,
- Tiong Y. Tan,
- Michelle de Silva,
- Lyndon Gallacher,
- Ting Liu,
- Jie Mi,
- Changqing Zeng,
- Hou-Feng Zheng,
- Qingguo Zhang,
- Stylianos E. Antonarakis,
- Timothy C. Cox,
- and Yong-Biao Zhang
Genome Res. May 2025 35: 1065-1079; Published in Advance April 15, 2025, doi:10.1101/gr.280047.124
...calculation, which was adjusted according to the respective populations. Additionally, we utilized HaploReg to annotate deleterious-associated variants to identify those potentially affecting SHROOM3 expression. Variants situated in enhancer or promoter regions, as indicated by histone or DNase marks in stem...
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Research: Elasmobranch genome sequencing reveals evolutionary trends of vertebrate karyotype organization
- Kazuaki Yamaguchi,
- Yoshinobu Uno,
- Mitsutaka Kadota,
- Osamu Nishimura,
- Ryo Nozu,
- Kiyomi Murakumo,
- Rui Matsumoto,
- Keiichi Sato,
- and Shigehiro Kuraku
Genome Res. September 2023 33: 1527-1540; Published in Advance August 17, 2023, doi:10.1101/gr.276840.122
...Elasmobranch sequencing reveals evolutionary trends of vertebrate karyotype organization Kazuaki Yamaguchi1,6, Yoshinobu Uno1,7, Mitsutaka Kadota1, Osamu Nishimura1, Ryo Nozu2,8, Kiyomi Murakumo3, Rui Matsumoto3, Keiichi Sato2,3 and Shigehiro Kuraku1,4,5 1Laboratory for Phyloinformatics, RIKEN...
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Method: Low-input RNase footprinting for simultaneous quantification of cytosolic and mitochondrial translation
- Qianru Li,
- Haiwang Yang,
- Emily K. Stroup,
- Hongbin Wang,
- and Zhe Ji
Genome Res. March 2022 32: 545-557; Published in Advance February 22, 2022, doi:10.1101/gr.276139.121
..., Illinois 60628, USA ↵3 These authors contributed equally to this work. Corresponding author: zhe.ji@northwestern.eduAbstractWe describe a low-input RNase footprinting approach for the rapid quantification of ribosome-protected fragments with as few as 1000 cultured cells. The assay uses a simplified...
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Research: Suv39h-catalyzed H3K9me3 is critical for euchromatic genome organization and the maintenance of gene transcription
- Christine R. Keenan,
- Hannah D. Coughlan,
- Nadia Iannarella,
- Andres Tapia del Fierro,
- Andrew Keniry,
- Timothy M. Johanson,
- Wing Fuk Chan,
- Alexandra L. Garnham,
- Lachlan W. Whitehead,
- Marnie E. Blewitt,
- Gordon K. Smyth,
- and Rhys S. Allan
Genome Res. April 2024 34: 556-571; Published in Advance May 6, 2024, doi:10.1101/gr.279119.124
...Suv39h-catalyzed H3K9me3 is critical for euchromatic organization and the maintenance of gene transcription Christine R. Keenan1,2,4,6, Hannah D. Coughlan1,2,4, Nadia Iannarella1, Andres Tapia del Fierro1,2, Andrew Keniry1,2, Timothy M. Johanson1,2, Wing Fuk Chan1,2,7, Alexandra L. Garnham1...
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Method: Mapping nucleosome positions using DNase-seq
- Jianling Zhong,
- Kaixuan Luo,
- Peter S. Winter,
- Gregory E. Crawford,
- Edwin S. Iversen,
- and Alexander J. Hartemink
Genome Res. March 2016 26: 351-364; Published in Advance January 15, 2016, doi:10.1101/gr.195602.115
...along the genome. Compared to methods that require genetically modified histones, our DNase-based approach is easily applied in any organism, which we demonstrate by producing maps in yeast and human. Compared to micrococcal nuclease (MNase)-based methods that map nucleosomes based on cuts in linker...
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Method: TRACE: transcription factor footprinting using chromatin accessibility data and DNA sequence
- Ningxin Ouyang and
- Alan P. Boyle
Genome Res. July 2020 30: 1040-1046; Published in Advance July 6, 2020, doi:10.1101/gr.258228.119
...limitations. We have developed a footprinting method to predict TF footprints in active chromatin elements (TRACE) to improve the prediction of TFBS footprints. TRACE incorporates DNase-seq data and PWMs within a multivariate hidden Markov model (HMM) to detect footprint-like regions with matching motifs...

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