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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
...chromatin is protected by localization of Orc4 at S phase, G2/metaphase, and anaphase. Scm3 localizes to the kinetochore toward the end of mitosis, loading new CENPA molecules by late anaphase/telophase, and remains associated with the kinetochore at G1, after which it is undetectable. Although...
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Research: Cohesin occupancy and composition at enhancers and promoters are linked to DNA replication origin proximity in Drosophila
- Michelle Pherson,
- Ziva Misulovin,
- Maria Gause,
- and Dale Dorsett
Genome Res. April 2019 29: 602-612; Published in Advance February 22, 2019, doi:10.1101/gr.243832.118
..., Rodríguez HK, Bell SP. 2004. Coordination of replication and transcription along a Drosophila chromosome. Genes Dev 18: 3094–3105. doi:10.1101/gad.1246404 ↵MacAlpine HK, Gordân R, Powell SK, Hartemink AJ, MacAlpine DM. 2010. Drosophila ORC localizes to open chromatin and marks sites of cohesin complex...
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Research: Chromatin conformation and transcriptional activity are permissive regulators of DNA replication initiation in Drosophila
- Robin L. Armstrong,
- Taylor J.R. Penke,
- Brian D. Strahl,
- A. Gregory Matera,
- Daniel J. McKay,
- David M. MacAlpine,
- and Robert J. Duronio
Genome Res. November 2018 28: 1688-1700; Published in Advance October 2, 2018, doi:10.1101/gr.239913.118
...-poor, inaccessible heterochromatin, a causal relationship between chromatin structure and replication initiation remains elusive. Here, we combined histone gene engineering and whole- sequencing in Drosophila to determine how perturbing chromatin structure affects replication initiation. We found that most...
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Research: The role of insulators and transcription in 3D chromatin organization of flies
- Keerthi T. Chathoth,
- Liudmila A. Mikheeva,
- Gilles Crevel,
- Jareth C. Wolfe,
- Ioni Hunter,
- Saskia Beckett-Doyle,
- Sue Cotterill,
- Hongsheng Dai,
- Andrew Harrison,
- and Nicolae Radu Zabet
Genome Res. April 2022 32: 682-698; Published in Advance March 30, 2022, doi:10.1101/gr.275809.121
...not affect A/B compartmentsThe checkerboard pattern seen on Hi-C maps led to the identification of A and B compartments which mark active and inactive regions of chromatin (Lieberman-Aiden et al. 2009). A/B compartments were also identified in Drosophila (Rowley et al. 2017) using 10-kb bins, and we showed...
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Research: Chromatin signatures of the Drosophila replication program
- Matthew L. Eaton,
- Joseph A. Prinz,
- Heather K. MacAlpine,
- George Tretyakov,
- Peter V. Kharchenko,
- and David M. MacAlpine
Genome Res. February 2011 21: 164-174; Published in Advance December 22, 2010, doi:10.1101/gr.116038.110
...(Berbenetz et al. 2010; Eaton et al. 2010). In both yeast and Drosophila, the nucleosomes surrounding potential origins of replication marked by ORC are dynamic and undergo rapid nucleosome exchange (Kaplan et al. 2008; Deal et al. 2010). This chromatin turnover may involve specific chromatin remodeling...
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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
...the Arabidopsis into nine chromatin states characterized by unique signatures, as reported for Drosophila and human cells (Ernst et al. 2011; Kharchenko et al. 2011). The Arabidopsis chromatin states show a preferred linear sequence defining proximal promoters (state 2), TSS (state 1), 5′ end of genes (state 3...
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Research: The chromatin environment shapes DNA replication origin organization and defines origin classes
- Christelle Cayrou,
- Benoit Ballester,
- Isabelle Peiffer,
- Romain Fenouil,
- Philippe Coulombe,
- Jean-Christophe Andrau,
- Jacques van Helden,
- and Marcel Méchali
Genome Res. December 2015 25: 1873-1885; Published in Advance November 11, 2015, doi:10.1101/gr.192799.115
...rDNA (Zellner et al. 2007), and a recent biochemical analysis showed that purifiedORC could bind toG4 RNA or DNA (Hoshina et al. 2013). In the Drosophila , ORC binding sites contain a central GC-rich region surrounded by AT-rich sequences (Vorobyeva et al. 2013). G-rich motifs/G4 may help...
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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 the marked by elevated ORC levels. As S phase progresses and more of the early replication domains are replicated, the likelihood of activating late origins will be increased. This may account for the near dichotic distribution of early and late replicating domains in the Drosophila . As precursor cells...
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Research: Heterochromatin protein 1 (HP1) modulates replication timing of the Drosophila genome
- Michaela Schwaiger,
- Hubertus Kohler,
- Edward J. Oakeley,
- Michael B. Stadler,
- and Dirk Schübeler
Genome Res. June 2010 20: 771-780; Published in Advance April 30, 2010, doi:10.1101/gr.101790.109
.... Bari-1, a new transposon-like family inDrosophila melanogaster with a unique heterochromatic organization. Genetics 133: 335–345. Calvi BR, Byrnes BA, Kolpakas AJ. 2007. Conservation of epigenetic regulation, ORC binding and developmental timing of DNA...
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Research: The TAGteam motif facilitates binding of 21 sequence-specific transcription factors in the Drosophila embryo
- Rahul Satija and
- Robert K. Bradley
Genome Res. April 2012 22: 656-665; Published in Advance January 13, 2012, doi:10.1101/gr.130682.111
...motifs The Drosophila origin recognition complex (ORC) preferentially binds regions with open chromatin (MacAlpine et al. 2010), can interact withmultiple transcription factors (Bosco et al. 2001; Beall et al. 2002; Dominguez-Sola et al. 2007), and reportedly localizes to regions with high levels...
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