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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
...-translational modifications, play a crucial role in regulating programs integral to a cell's identity, like gene expression and DNA replication. However, the transcriptional, chromatin, and replication timing profiles of adult stem cells in vivo remain poorly understood. Containing germline stem cells (GSCs) and somatic cyst...
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Research: Developmental timing of programmed DNA elimination in Paramecium tetraurelia recapitulates germline transposon evolutionary dynamics
- Coralie Zangarelli,
- Olivier Arnaiz,
- Mickaël Bourge,
- Kevin Gorrichon,
- Yan Jaszczyszyn,
- Nathalie Mathy,
- Loïc Escoriza,
- Mireille Bétermier,
- and Vinciane Régnier
Genome Res. November/December 2022 32: 2028-2042; Published in Advance November 23, 2022, doi:10.1101/gr.277027.122
...established four classes of IESs according to their excision timing (Fig. 4A). We also showed that the progression of IES elimination, once it has started, is independent of replication, suggesting that the excision machinery is recruited to its chromatin targets independently of replication fork passage...
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Research: Delayed DNA replication in haploid human embryonic stem cells
- Matthew M. Edwards,
- Michael V. Zuccaro,
- Ido Sagi,
- Qiliang Ding,
- Dan Vershkov,
- Nissim Benvenisty,
- Dieter Egli,
- and Amnon Koren
Genome Res. December 2021 31: 2155-2169; Published in Advance November 22, 2021, doi:10.1101/gr.275953.121
...). Polyploidization is often accompanied by genomic regions of reduced relative DNA copy number. In Drosophila polyploid cells, underreplication is due to active inhibition of replication fork progression in a subset of late-replicating genomic regions. At least two negative regulators of DNA replication, Suppressor...
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Research: Differences in firing efficiency, chromatin, and transcription underlie the developmental plasticity of the Arabidopsis DNA replication origins
- Joana Sequeira-Mendes,
- Zaida Vergara,
- Ramon Peiró,
- Jordi Morata,
- Irene Aragüez,
- Celina Costas,
- Raul Mendez-Giraldez,
- Josep M. Casacuberta,
- Ugo Bastolla,
- and Crisanto Gutierrez
Genome Res. May 2019 29: 784-797; Published in Advance March 7, 2019, doi:10.1101/gr.240986.118
...from increased frequency of ORI usage in the cell population or from failures of replication fork progression. This can be discarded because replication fork arrest due to termination signals would occur in most cases in large bubbles and, consequently, nascent strands would appear in the sucrose...
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Research: Chromatin dynamics during DNA replication
- Raz Bar-Ziv,
- Yoav Voichek,
- and Naama Barkai
Genome Res. September 2016 26: 1245-1256; Published in Advance May 25, 2016, doi:10.1101/gr.201244.115
...intensified H3K9ac in front of the replication fork and in sites where RNA polymerase II was trapped, suggesting supercoiling stresses trigger H3K9 acetylation. Our results assign complementary roles for DNA replication and gene expression in defining the pattern of histone modification.In eukaryotic cells...
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Research: Synchronized replication of genes encoding the same protein complex in fast-proliferating cells
- Ying Chen,
- Ke Li,
- Xiao Chu,
- Lucas B. Carey,
- and Wenfeng Qian
Genome Res. December 2019 29: 1929-1938; Published in Advance October 29, 2019, doi:10.1101/gr.254342.119
...Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China Corresponding authors: wfqian@genetics.ac.cn, ychen@genetics.ac.cnAbstractDNA replication perturbs the dosage balance among genes; at mid-S phase, early-replicating genes have doubled their copies while late-replicating...
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Research: Large tandem duplications affect gene expression, 3D organization, and plant–pathogen response
- Ariadna Picart-Picolo,
- Stefan Grob,
- Nathalie Picault,
- Michal Franek,
- Christel Llauro,
- Thierry Halter,
- Tom R. Maier,
- Edouard Jobet,
- Julie Descombin,
- Panpan Zhang,
- Vijayapalani Paramasivan,
- Thomas J. Baum,
- Lionel Navarro,
- Martina Dvořáčková,
- Marie Mirouze,
- and Frédéric Pontvianne
Genome Res. November 2020 30: 1583-1592; Published in Advance October 8, 2020, doi:10.1101/gr.261586.120
...RNA gene copies are located at the top of both Chromosomes 2 (NOR2) and 4 (NOR4) (Copenhaver and Pikaard 1996). Only a portion of these copies is actively transcribed in the nucleolus to produce ribosomes. Most rRNA genes indeed remain transcriptionally inactive and accumulate repressive chromatin...
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Research: Replication timing is regulated by the number of MCMs loaded at origins
- Shankar P. Das,
- Tyler Borrman,
- Victor W.T. Liu,
- Scott C.-H. Yang,
- John Bechhoefer,
- and Nicholas Rhind
Genome Res. December 2015 25: 1886-1892; Published in Advance September 10, 2015, doi:10.1101/gr.195305.115
...previously initiated forks terminate, coupling origin firing timing to fork progression (Rhind 2008). Another advantage of the multiple-MCMmodel is that it explains how events that impact origin licensing during G1 can affect the timing of origin firing during S phase. The timing and affinity of ORC binding...
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Research: DNA replication and transcription programs respond to the same chromatin cues
- Yoav Lubelsky,
- Joseph A. Prinz,
- Leyna DeNapoli,
- Yulong Li,
- Jason A. Belsky,
- and David M. MacAlpine
Genome Res. July 2014 24: 1102-1114; Published in Advance July 1, 2014, doi:10.1101/gr.160010.113
...of potential origins (ORC-binding sites). Alternatively, H4K16ac may facilitate replication fork progression downstream from replication initiation. In support of increased initiation of DNA replication, the Schubeler group noted increased origin activity on the male X chromosome (Schwaiger et al. 2009). Our...
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Research: Multidimensional regulation of gene expression in the C. elegans embryo
- John Isaac Murray,
- Thomas J. Boyle,
- Elicia Preston,
- Dionne Vafeados,
- Barbara Mericle,
- Peter Weisdepp,
- Zhongying Zhao,
- Zhirong Bao,
- Max Boeck,
- and Robert H. Waterston
Genome Res. July 2012 22: 1282-1294; Published in Advance April 16, 2012, doi:10.1101/gr.131920.111
...or more genes, in two or more replicates 96.84% 6.90% C. elegans embryonic gene expression Genome Research 1285 www..org Figs. 5,6). POP-1 protein is preferentially depleted in posterior nuclei by a Wnt-dependent mechanism after most A–P oriented divisions in the C. elegans embryo, is known to repress...
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