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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: 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
..., Luzi L, Banfi S, Segalla S, Cesaroni M, Mendoza-Maldonado R, Giacca M, Pelicci PG. 2013. Genome-wide mapping of human DNA-replication origins: levels of transcription at ORC1 sites regulate origin selection and replication timing. Genome Res 23: 1–11. doi:10.1101/gr.142331.112 ↵Desprat R, Thierry...
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Method: Effect of minichromosome maintenance protein 2 deficiency on the locations of DNA replication origins
- Dimiter Kunnev,
- Amy Freeland,
- Maochun Qin,
- Robert W. Leach,
- Jianmin Wang,
- Rajani M. Shenoy,
- and Steven C. Pruitt
Genome Res. April 2015 25: 558-569; Published in Advance March 11, 2015, doi:10.1101/gr.176099.114
...in measureable changes in DNA replication origin usage. To identify sites of DNA replication initiation, previous studies have used newly replicated nascent DNA strands that are size selected for those sufficiently short to lie near to origins of replication but not so short that they include Okazaki fragments...
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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
...in the Drosophila genome were static across all cell lines; however, a small subset of domains was dynamic and exhibited differences in replication timing between the cell lines. Both origin selection and activation contribute to defining the DNA replication program. Our results suggest that static early and late...
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Research: Noncoding transcription influences the replication initiation program through chromatin regulation
- Julien Soudet,
- Jatinder Kaur Gill,
- and Françoise Stutz
Genome Res. December 2018 28: 1882-1893; Published in Advance November 6, 2018, doi:10.1101/gr.239582.118
...transcription compared to non-ORC-bound and nonreplicated ARSs (nr-ARSs) (Supplemental Fig. S4E; Eaton et al. 2010).View larger version: In this window In a new window Figure 3. Natural pervasive transcription correlates with timing/efficiency and specific chromatin features of replication origins. (A) Metagene...
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Research: Genome-wide mapping of nuclear mitochondrial DNA sequences links DNA replication origins to chromosomal double-strand break formation in Schizosaccharomyces pombe
- Sandrine Lenglez,
- Damien Hermand,
- and Anabelle Decottignies
Genome Res. September 2010 20: 1250-1261; Published in Advance August 5, 2010, doi:10.1101/gr.104513.109
...Genome-wide mapping of nuclear mitochondrial DNA sequences links DNA replication origins to chromosomal double-strand break formation in Schizosaccharomyces pombe Sandrine Lenglez 1 , Damien Hermand 2 and Anabelle Decottignies 1 , 3 1 Catholic...
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Research: Conservation of replication timing reveals global and local regulation of replication origin activity
- Carolin A. Müller and
- Conrad A. Nieduszynski
Genome Res. October 2012 22: 1953-1962; Published in Advance July 5, 2012, doi:10.1101/gr.139477.112
..., whereas dormant origins are poorly conserved. Second, we generated genome-wide replication profiles for each of these species and discovered that the temporal order of genome replication is highly conserved. Therefore, active origins are not only conserved in location, but also in activation time. Only...
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Research: Integrated genome and transcriptome sequencing identifies a noncoding mutation in the genome replication factor DONSON as the cause of microcephaly-micromelia syndrome
- Gilad D. Evrony,
- Dwight R. Cordero,
- Jun Shen,
- Jennifer N. Partlow,
- Timothy W. Yu,
- Rachel E. Rodin,
- R. Sean Hill,
- Michael E. Coulter,
- Anh-Thu N. Lam,
- Divya Jayaraman,
- Dianne Gerrelli,
- Diana G. Diaz,
- Chloe Santos,
- Victoria Morrison,
- Antonella Galli,
- Ulrich Tschulena,
- Stefan Wiemann,
- M. Jocelyne Martel,
- Betty Spooner,
- Steven C. Ryu,
- Princess C. Elhosary,
- Jillian M. Richardson,
- Danielle Tierney,
- Christopher A. Robinson,
- Rajni Chibbar,
- Dana Diudea,
- Rebecca Folkerth,
- Sheldon Wiebe,
- A. James Barkovich,
- Ganeshwaran H. Mochida,
- James Irvine,
- Edmond G. Lemire,
- Patricia Blakley,
- and Christopher A. Walsh
Genome Res. August 2017 27: 1323-1335; Published in Advance June 19, 2017, doi:10.1101/gr.219899.116
...-expressed with DONSON were again strikingly enriched for genes coding for components of the DNA replication machinery, including (1) the ORC1 origin recognition complex subunit 1, (2) CDC6, which together with CDT1 loads the MCM2-7 replication helicase onto replication origins, (3) GINS1, a component of the active CMG...
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Research: Developmental control of gene copy number by repression of replication initiation and fork progression
- Noa Sher,
- George W. Bell,
- Sharon Li,
- Jared Nordman,
- Thomas Eng,
- Matthew L. Eaton,
- David M. MacAlpine,
- and Terry L. Orr-Weaver
Genome Res. January 2012 22: 64-75; Published in Advance November 16, 2011, doi:10.1101/gr.126003.111
...be repressed, we examined regions selectively under-replicated in Drosophila polytene salivary glands, and found they are transcriptionally silent and enriched for the repressive H3K27me3 mark. In the first -wide analysis of binding of the origin recognition complex (ORC) in a differentiated metazoan tissue...
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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
...be attributed to the differential timing of firing of DNA initiation sites or DNA replication origins within the . Replication origins initiate DNA replication with the help of the prereplication complex (pre-RC), two major components of which are the origin recognition complex (Orc1-6) and the minichromosome...

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