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Method: NicE-C efficiently reveals open chromatin–associated chromosome interactions at high resolution
- Zhengyu Luo,
- Ran Zhang,
- Tengfei Hu,
- Yuting Zhu,
- Yueming Wu,
- Wenfei Li,
- Zhi Zhang,
- Xuebiao Yao,
- Haiyi Liang,
- and Xiaoyuan Song
Genome Res. March 2022 32: 534-544; Published in Advance February 1, 2022, doi:10.1101/gr.275986.121
...P, Spracklin G, Esteve PO, Xu SY, Long HW, Pradhan S. 2020. Universal NicE-seq for high-resolution accessible chromatin profiling for formaldehyde-fixed and FFPE tissues. Clin Epigenetics 12: 143. doi:10.1186/s13148-020-00921-6 ↵Cho SW, Xu J, Sun R, Mumbach MR, Carter AC, Chen YG, Yost KE, Kim J, He...
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Method: Accessible Region Conformation Capture (ARC-C) gives high-resolution insights into genome architecture and regulation
- Ni Huang,
- Wei Qiang Seow,
- Alex Appert,
- Yan Dong,
- Przemyslaw Stempor,
- and Julie Ahringer
Genome Res. February 2022 32: 357-366; Published in Advance December 21, 2021, doi:10.1101/gr.275669.121
...Accessible Region Conformation Capture (ARC-C) gives high-resolution insights into architecture and regulation Ni Huang1,2, Wei Qiang Seow1,2, Alex Appert1, Yan Dong1, Przemyslaw Stempor1 and Julie Ahringer1 1The Gurdon Institute and Department of Genetics, University of Cambridge, Cambridge CB2 1...
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Research: High-resolution structural genomics reveals new therapeutic vulnerabilities in glioblastoma
- Michael J. Johnston,
- Ana Nikolic,
- Nicoletta Ninkovic,
- Paul Guilhamon,
- Florence M.G. Cavalli,
- Steven Seaman,
- Franz J. Zemp,
- John Lee,
- Aly Abdelkareem,
- Katrina Ellestad,
- Alex Murison,
- Michelle M. Kushida,
- Fiona J. Coutinho,
- Yussanne Ma,
- Andrew J. Mungall,
- Richard Moore,
- Marco A. Marra,
- Michael D. Taylor,
- Peter B. Dirks,
- Trevor J. Pugh,
- Sorana Morrissy,
- Bradley St Croix,
- Douglas J. Mahoney,
- Mathieu Lupien,
- and Marco Gallo
Genome Res. August 2019 29: 1211-1222; Published in Advance June 27, 2019, doi:10.1101/gr.246520.118
...et al. 2015) and cancer (Flavahan et al. 2016) through dysregulation of gene expression programs. The global impact of architecture on transcriptional programs in gliomas and other brain tumors has been difficult to assess because of the lack of high-resolution 3D maps for these cancers. We...
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Research: Atypical epigenetic and small RNA control of degenerated transposons and their fragments in clonally reproducing Spirodela polyrhiza
- Rodolphe Dombey,
- Daniel Buendía-Ávila,
- Verónica Barragán-Borrero,
- Laura Diezma-Navas,
- Arturo Ponce-Mañe,
- José Mario Vargas-Guerrero,
- Rana Elias,
- and Arturo Marí-Ordóñez
Genome Res. March 2025 35: 522-544; Published in Advance March 4, 2025, doi:10.1101/gr.279532.124
.... 2017; Xu et al. 2019), including a high-resolution reference assembly of its 20 chromosomes from the S. polyrhiza 9509 (Sp9509) and 7498 (Sp7498) clones (Michael et al. 2017; Hoang et al. 2018; Harkess et al. 2021). For our study, we retrieved Sp9509 from the Landolt duckweed collection, now managed...
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Method: DNA-m6A calling and integrated long-read epigenetic and genetic analysis with fibertools
- Anupama Jha,
- Stephanie C. Bohaczuk,
- Yizi Mao,
- Jane Ranchalis,
- Benjamin J. Mallory,
- Alan T. Min,
- Morgan O. Hamm,
- Elliott Swanson,
- Danilo Dubocanin,
- Connor Finkbeiner,
- Tony Li,
- Dale Whittington,
- William Stafford Noble,
- Andrew B. Stergachis,
- and Mitchell R. Vollger
Genome Res. November 2024 34: 1976-1986; Published in Advance June 7, 2024, doi:10.1101/gr.279095.124
..., Seattle, Washington 98195, USA ↵8 These authors contributed equally to this work. Corresponding authors: absterga@uw.edu, mvollger@uw.eduAbstractLong-read DNA sequencing has recently emerged as a powerful tool for studying both genetic and epigenetic architectures at single-molecule and single...
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Method: SLIC-CAGE: high-resolution transcription start site mapping using nanogram-levels of total RNA
- Nevena Cvetesic,
- Harry G. Leitch,
- Malgorzata Borkowska,
- Ferenc Müller,
- Piero Carninci,
- Petra Hajkova,
- and Boris Lenhard
Genome Res. December 2018 28: 1943-1956; Published in Advance November 7, 2018, doi:10.1101/gr.235937.118
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Method: Single-nucleus CUT&RUN elucidates the function of intrinsic and genomics-driven epigenetic heterogeneity in head and neck cancer progression
- Howard J. Womersley,
- Daniel Muliaditan,
- Ramanuj DasGupta,
- and Lih Feng Cheow
Genome Res. January 2025 35: 162-177; Published in Advance December 2, 2024, doi:10.1101/gr.279105.124
...single-nucleus CUT&RUN (snCUT&RUN) in order to gain more insights in the role of the epi and epigenetic heterogeneity during HNSCC progression. Altogether, we demonstrate that high-resolution profiling of histone modifications in single cells with snCUT&RUN can yield valuable insights into epigenetic...
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Research: Dynamic reversal of random X-Chromosome inactivation during iPSC reprogramming
- Adrian Janiszewski,
- Irene Talon,
- Joel Chappell,
- Samuel Collombet,
- Juan Song,
- Natalie De Geest,
- San Kit To,
- Greet Bervoets,
- Oskar Marin-Bejar,
- Caterina Provenzano,
- Lotte Vanheer,
- Jean-Christophe Marine,
- Florian Rambow,
- and Vincent Pasque
Genome Res. October 2019 29: 1659-1672; Published in Advance September 12, 2019, doi:10.1101/gr.249706.119
...unclear how epigenetic memory of stable gene silencing is reversed by transcription factors (TFs) and accompanying chromatin mechanisms. Chromosome-wide transitions between active and inactive chromatin states are excellently modeled by X-Chromosome inactivation (XCI) and reactivation (XCR) in female...
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Method: High resolution mapping of modified DNA nucleobases using excision repair enzymes
- D. Suzi Bryan,
- Monica Ransom,
- Biniam Adane,
- Kerri York,
- and Jay R. Hesselberth
Genome Res. September 2014 24: 1534-1542; Published in Advance July 11, 2014, doi:10.1101/gr.174052.114
...High resolution mapping of modified DNA nucleobases using excision repair enzymes D. Suzi Bryan 1 , Monica Ransom 1 , Biniam Adane , Kerri York and Jay R. Hesselberth Department of Biochemistry and Molecular Genetics, Program...
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Research: High-resolution mapping of transcriptional dynamics across tissue development reveals a stable mRNA–tRNA interface
- Bianca M. Schmitt,
- Konrad L.M. Rudolph,
- Panagiota Karagianni,
- Nuno A. Fonseca,
- Robert J. White,
- Iannis Talianidis,
- Duncan T. Odom,
- John C. Marioni,
- and Claudia Kutter
Genome Res. November 2014 24: 1797-1807; Published in Advance August 13, 2014, doi:10.1101/gr.176784.114
...High-resolution mapping of transcriptional dynamics across tissue development reveals a stable mRNA–tRNA interface Bianca M. Schmitt 1 , 5 , Konrad L.M. Rudolph 2 , 5 , Panagiota Karagianni 3 , Nuno A. Fonseca 2 , Robert J. White...
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