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Research: Cohesin organizes 3D DNA contacts surrounding active enhancers in C. elegans
- Jun Kim,
- Haoyu Wang,
- and Sevinç Ercan
Genome Res. May 2025 35: 1108-1123; Published in Advance April 10, 2025, doi:10.1101/gr.279365.124
...loading of cohesin is the basis of fountains, distribution of the NIPBL ortholog PQN-85 binding sites should correlate with the diversity of fountain patterns. Indeed, fountains with a broad base of interactions have a wide distribution of shorter PQN-85 ChIP-seq peaks near the fountain origin...
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Research: Loss of histone H3.3 results in DNA replication defects and altered origin dynamics in C. elegans
- Maude Strobino,
- Joanna M. Wenda,
- Laura Padayachy,
- and Florian A. Steiner
Genome Res. December 2020 30: 1740-1751; Published in Advance November 10, 2020, doi:10.1101/gr.260794.120
.... Although the enrichment of CDT-1 and TRES-1 overlaps within a narrow window at the replication origins, the distribution of EdU-seq signal is more broad, which likely reflects short stretches of fork progression away from the replication origins after the release from the initial HU block (Supplemental Fig...
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Research: Characterization of the distribution and dynamics of chromatin states in the C. elegans germline reveals substantial H3K4me3 remodeling during oogenesis
- Mariateresa Mazzetto,
- Lauren E. Gonzalez,
- Nancy Sanchez,
- and Valerie Reinke
Genome Res. January 2024 34: 57-69; Published in Advance December 26, 2023, doi:10.1101/gr.278247.123
...in each stage (Supplemental Fig. S7C), indicating that dynamic remodeling is not a general characteristic of activating modifications.In C. elegans somatic tissues, broad H3K4me3 domains have been shown to emerge upon aging (Pu et al. 2018), suggesting that the broad pattern in adult IGN might...
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Research: Characterization of human transcription factor function and patterns of gene regulation in HepG2 cells
- Belle A. Moyers,
- E. Christopher Partridge,
- Mark Mackiewicz,
- Michael J. Betti,
- Roshan Darji,
- Sarah K. Meadows,
- Kimberly M. Newberry,
- Laurel A. Brandsmeier,
- Barbara J. Wold,
- Eric M. Mendenhall,
- and Richard M. Myers
Genome Res. November 2023 33: 1879-1892; Published in Advance October 18, 2023, doi:10.1101/gr.278205.123
...-associated proteins, histone modifiers, and a broad suite of transcription factors (TFs) and associated cofactors. Together, these DNA-associated proteins (DAPs) are encoded by ∼10% of all protein-coding genes in the human (Vaquerizas et al. 2009; Lambert et al. 2018). DAPs are known to associate with DNA either...
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Research: De novo genome assemblies of two cryptodiran turtles with ZZ/ZW and XX/XY sex chromosomes provide insights into patterns of genome reshuffling and uncover novel 3D genome folding in amniotes
- Basanta Bista,
- Laura González-Rodelas,
- Lucía Álvarez-González,
- Zhi-qiang Wu,
- Eugenia E. Montiel,
- Ling Sze Lee,
- Daleen B. Badenhorst,
- Srihari Radhakrishnan,
- Robert Literman,
- Beatriz Navarro-Dominguez,
- John B. Iverson,
- Simon Orozco-Arias,
- Josefa González,
- Aurora Ruiz-Herrera,
- and Nicole Valenzuela
Genome Res. October 2024 34: 1553-1569; Published in Advance October 16, 2024, doi:10.1101/gr.279443.124
...De novo assemblies of two cryptodiran turtles with ZZ/ZW and XX/XY sex chromosomes provide insights into patterns of reshuffling and uncover novel 3D folding in amniotes Basanta Bista1,7, Laura González-Rodelas2,3,7, Lucía Álvarez-González2, Zhi-qiang Wu1,4, Eugenia E. Montiel1,8, Ling Sze Lee1...
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Resource: Comprehensive characterization of tissue-specific chromatin accessibility in L2 Caenorhabditis elegans nematodes
- Timothy J. Durham,
- Riza M. Daza,
- Louis Gevirtzman,
- Darren A. Cusanovich,
- Olubusayo Bolonduro,
- William Stafford Noble,
- Jay Shendure,
- and Robert H. Waterston
Genome Res. October 2021 31: 1952-1969; Published in Advance April 22, 2021, doi:10.1101/gr.271791.120
..., Seattle, Washington 98195, USA; 6Allen Discovery Center for Cell Lineage Tracing, University of Washington, Seattle, Washington 98195, USA ↵Present addresses: 7Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; 8Committee on Genetics, Genomics, and System Biology, The University of Chicago...
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Research: Plasticity in patterns of histone modifications and chromosomal proteins in Drosophila heterochromatin
- Nicole C. Riddle,
- Aki Minoda,
- Peter V. Kharchenko,
- Artyom A. Alekseyenko,
- Yuri B. Schwartz,
- Michael Y. Tolstorukov,
- Andrey A. Gorchakov,
- Jacob D. Jaffe,
- Cameron Kennedy,
- Daniela Linder-Basso,
- Sally E. Peach,
- Gregory Shanower,
- Haiyan Zheng,
- Mitzi I. Kuroda,
- Vincenzo Pirrotta,
- Peter J. Park,
- Sarah C.R. Elgin,
- and Gary H. Karpen
Genome Res. February 2011 21: 147-163; Published in Advance December 22, 2010, doi:10.1101/gr.110098.110
...Umea, Sweden; 7 Proteomics Group, The Broad Institute, Cambridge, Massachusetts 02139, USA; 8 Biological Mass Spectrometry Resource, Center for Advanced Biotechnology and Medicine, University of Dentistry and Medicine of New Jersey, Piscataway, New Jersey 08854, USA...
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Resource: Chromatin accessibility dynamics reveal novel functional enhancers in C. elegans
- Aaron C. Daugherty,
- Robin W. Yeo,
- Jason D. Buenrostro,
- William J. Greenleaf,
- Anshul Kundaje,
- and Anne Brunet
Genome Res. December 2017 27: 2096-2107; Published in Advance November 15, 2017, doi:10.1101/gr.226233.117
...Department of Computer Science, Stanford University, Stanford, California 94305, USA 4Glenn Laboratories for the Biology of Aging, Stanford University, Stanford, California 94305, USA ↵5 These authors contributed equally to this work. ↵6 Present address: Broad Institute of MIT and Harvard, Harvard University...
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Resource: The time-resolved transcriptome of C. elegans
- Max E. Boeck,
- Chau Huynh,
- Lou Gevirtzman,
- Owen A. Thompson,
- Guilin Wang,
- Dionna M. Kasper,
- Valerie Reinke,
- LaDeana W. Hillier,
- and Robert H. Waterston
Genome Res. October 2016 26: 1441-1450; Published in Advance August 16, 2016, doi:10.1101/gr.202663.115
...C. elegans core replicative histones are aggregated into seven clusters (Supplemental Table S11),with eachcluster containing one ormore sets of each of thefourcorehistones(H2B:H2A—H3:H4, where “:” denotes head to head orientation). The two clusters on Chromosome IV show substantial levels at the earliest...
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Research: Natural variation of histone modification and its impact on gene expression in the rat genome
- Carola Rintisch,
- Matthias Heinig,
- Anja Bauerfeind,
- Sebastian Schafer,
- Christin Mieth,
- Giannino Patone,
- Oliver Hummel,
- Wei Chen,
- Stuart Cook,
- Edwin Cuppen,
- Maria Colomé-Tatché,
- Frank Johannes,
- Ritsert C. Jansen,
- Helen Neil,
- Michel Werner,
- Michal Pravenec,
- Martin Vingron,
- and Norbert Hubner
Genome Res. June 2014 24: 942-953; Published in Advance May 2, 2014, doi:10.1101/gr.169029.113
...factors between individuals of different strains. For the broad histone marks H3K27me3 and H4K20me1we observed overall less strain differences. We cannot attribute this to reagents or technical factors except that the experiments were done subsequently at different time points, which may or may not have...

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