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Research: Cell-type- and chromosome-specific chromatin landscapes and DNA replication programs of Drosophila testis tumor stem cell–like cells
- Jennifer A. Urban,
- Daniel Ringwalt,
- John M. Urban,
- Wingel Xue,
- Ryan Gleason,
- Keji Zhao,
- and Xin Chen
Genome Res. January 2026 36: 83-101; Published in Advance December 10, 2025, doi:10.1101/gr.280809.125
...Cell-type- and chromosome-specific chromatin landscapes and DNA replication programs of Drosophila testis tumor stem cell–like cells Jennifer A. Urban1, Daniel Ringwalt1, John M. Urban2,3, Wingel Xue1,5, Ryan Gleason1, Keji Zhao4 and Xin Chen1,2 1Department of Biology, The Johns Hopkins University...
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Research: Orc4 spatiotemporally stabilizes centromeric chromatin
- Lakshmi Sreekumar,
- Kiran Kumari,
- Krishnendu Guin,
- Asif Bakshi,
- Neha Varshney,
- Bhagya C. Thimmappa,
- Leelavati Narlikar,
- Ranjith Padinhateeri,
- Rahul Siddharthan,
- and Kaustuv Sanyal
Genome Res. April 2021 31: 607-621; Published in Advance January 29, 2021, doi:10.1101/gr.265900.120
..., the establishment of centromeric chromatin and its subsequent propagation through many generations depends on a variety of factors that are often species specific. These include centromere-specific DNA sequence elements, replication timing, and transcriptional status of centromere DNA, as well as the influence...
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Research: PR-DUB maintains the expression of critical genes through FOXK1/2- and ASXL1/2/3-dependent recruitment to chromatin and H2AK119ub1 deubiquitination
- Petros Kolovos,
- Koutarou Nishimura,
- Aditya Sankar,
- Simone Sidoli,
- Paul A. Cloos,
- Kristian Helin,
- and Jesper Christensen
Genome Res. August 2020 30: 1119-1130; Published in Advance August 3, 2020, doi:10.1101/gr.261016.120
...in instructing cell type–specific gene expression patterns (Niwa 2018; Stadhouders et al. 2019). In addition, chromatin undergoes covalent histone modifications and DNA methylation, which further recruit chromatin modifying factors to impart precise catalysis of transcription and enhance or repress gene...
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Research: Clustering of Drosophila housekeeping promoters facilitates their expression
- Marc Corrales,
- Aránzazu Rosado,
- Ruggero Cortini,
- Joris van Arensbergen,
- Bas van Steensel,
- and Guillaume J. Filion
Genome Res. July 2017 27: 1153-1161; Published in Advance April 18, 2017, doi:10.1101/gr.211433.116
..., indicating that the chromatin fiber is more open and less compact than in the domains of low expression. This is in line with similar observations based on the expression of endogenous genes in Drosophila embryos (Sexton et al. 2012). Since both chromatin composition and chromosomal conformation could...
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Research: Dynamic changes in replication timing and gene expression during lineage specification of human pluripotent stem cells
- Juan Carlos Rivera-Mulia,
- Quinton Buckley,
- Takayo Sasaki,
- Jared Zimmerman,
- Ruth A. Didier,
- Kristopher Nazor,
- Jeanne F. Loring,
- Zheng Lian,
- Sherman Weissman,
- Allan J. Robins,
- Thomas C. Schulz,
- Laura Menendez,
- Michael J. Kulik,
- Stephen Dalton,
- Haitham Gabr,
- Tamer Kahveci,
- and David M. Gilbert
Genome Res. August 2015 25: 1091-1103; Published in Advance June 8, 2015, doi:10.1101/gr.187989.114
...with spatial organization of chromatin in the nucleus; early and late RDs reside in distinct nuclear compartments (Nakamura et al. 1986; Nakayasu 1989; O'Keefe et al. 1992), and cytogenetic visualization of pulse-labeled DNA synthesis reveals distinct punctate replication foci whose structure remains stable...
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Research: The interaction of PRC2 with RNA or chromatin is mutually antagonistic
- Manuel Beltran,
- Christopher M. Yates,
- Lenka Skalska,
- Marcus Dawson,
- Filipa P. Reis,
- Keijo Viiri,
- Cynthia L. Fisher,
- Christopher R. Sibley,
- Benjamin M. Foster,
- Till Bartke,
- Jernej Ule,
- and Richard G. Jenner
Genome Res. July 2016 26: 896-907; Published in Advance May 9, 2016, doi:10.1101/gr.197632.115
...activity. Although PcG recruitment mechanisms differ between mammals and Drosophila, it has previously been suggested that the process of transcription through Polycomb response elements (PREs) removes PcG complexes from chromatin (Schmitt et al. 2005). At the vestigial PRE, it was reported...
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Research: Active chromatin and transcription play a key role in chromosome partitioning into topologically associating domains
- Sergey V. Ulianov,
- Ekaterina E. Khrameeva,
- Alexey A. Gavrilov,
- Ilya M. Flyamer,
- Pavel Kos,
- Elena A. Mikhaleva,
- Aleksey A. Penin,
- Maria D. Logacheva,
- Maxim V. Imakaev,
- Alexander Chertovich,
- Mikhail S. Gelfand,
- Yuri Y. Shevelyov,
- and Sergey V. Razin
Genome Res. January 2016 26: 70-84; Published in Advance October 30, 2015, doi:10.1101/gr.196006.115
...reported that 42% of TADs are shared between Kc167 cells and 16-h embryos. Active chromatin and transcription but not architectural proteins dCTCF and Su(Hw) are typical for TAD boundaries and inter-TAD regions Previous studies revealed that TAD boundaries in 16-h Drosophila embryos (Sexton et al. 2012...
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Research: Regulation of nucleosome positioning by a CHD Type III chromatin remodeler and its relationship to developmental gene expression in Dictyostelium
- James L. Platt,
- Nicholas A. Kent,
- Alan R. Kimmel,
- and Adrian J. Harwood
Genome Res. April 2017 27: 591-600; Published in Advance March 22, 2017, doi:10.1101/gr.216309.116
...control of -wide nucleosome positioning and developmental gene expression and its requirement for a ChromodomainHelicase-DNA binding (CHD) Type III chromatin remodeling protein. Nucleosome positions can be described by several physical parameters: occupancy, the relative enrichment or depletion...
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Research: Epigenetic activation of meiotic recombination near Arabidopsis thaliana centromeres via loss of H3K9me2 and non-CG DNA methylation
- Charles J. Underwood,
- Kyuha Choi,
- Christophe Lambing,
- Xiaohui Zhao,
- Heïdi Serra,
- Filipe Borges,
- Joe Simorowski,
- Evan Ernst,
- Yannick Jacob,
- Ian R. Henderson,
- and Robert A. Martienssen
Genome Res. April 2018 28: 519-531; Published in Advance March 12, 2018, doi:10.1101/gr.227116.117
...(Recombination In K) heterochromatin, which lose H3K9me2 and undergo mitotic and meiotic recombination (Ellermeier et al. 2010; Zaratiegui et al. 2011). Mouse dnmt3l mutants also have altered DNA methylation and chromatin signatures and increased DSB initiation within retrotransposons, which is associated...
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Research: Lamin A/C-promoter interactions specify chromatin state–dependent transcription outcomes
- Eivind Lund,
- Anja R. Oldenburg,
- Erwan Delbarre,
- Christel T. Freberg,
- Isabelle Duband-Goulet,
- Ragnhild Eskeland,
- Brigitte Buendia,
- and Philippe Collas
Genome Res. October 2013 23: 1580-1589; Published in Advance July 16, 2013, doi:10.1101/gr.159400.113
...that are mostly inactiveor expressed at a low level (Guelenet al. 2008). Lamins can also interact with shorter chromatin domains in HeLa cells (Euskirchen et al. 2011), and inmice and yeast, short DNA sequences canmediate localization of loci to the nuclear periphery (Ahmed et al. 2010; Brickner et al. 2012...

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