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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
...are accompanied by replication checkpoint activation, a delayed cell cycle, and increased lethality in checkpoint-compromised embryos. Our comprehensive analysis of DNA replication in C. elegans reveals the genomic location of replication origins and the dynamics of their firing, and uncovers a role of H3...
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Method: Characterizing and controlling intrinsic biases of lambda exonuclease in nascent strand sequencing reveals phasing between nucleosomes and G-quadruplex motifs around a subset of human replication origins
- Michael S. Foulk,
- John M. Urban,
- Cinzia Casella,
- and Susan A. Gerbi
Genome Res. May 2015 25: 725-735; Published in Advance February 18, 2015, doi:10.1101/gr.183848.114
...to this work. ↵ Present addresses: 2 Mercyhurst University, Department of Biology, Erie, PA 16546, USA; 3 Institute for Molecular Medicine, University of Southern Denmark, 5000 Odense C, Denmark. Abstract Nascent strand sequencing (NS-seq) is used to discover DNA replication origins...
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Research: MRC1-dependent scaling of the budding yeast DNA replication timing program
- Amnon Koren,
- Ilya Soifer,
- and Naama Barkai
Genome Res. June 2010 20: 781-790; Published in Advance March 10, 2010, doi:10.1101/gr.102764.109
...; Schwaiger et al. 2009). The process of DNA replication has been studied extensively. Replication origins are licensed during mitosis and early G1, with the binding of ORC (origin recognition complex) and the subsequent recruitment of the minichromosome maintenance (MCM) complex (part of the replicative DNA...
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Research: Telomerase-independent survival leads to a mosaic of complex subtelomere rearrangements in Chlamydomonas reinhardtii
- Frédéric Chaux,
- Nicolas Agier,
- Clotilde Garrido,
- Gilles Fischer,
- Stephan Eberhard,
- and Zhou Xu
Genome Res. September 2023 33: 1582-1598; Published in Advance August 14, 2023, doi:10.1101/gr.278043.123
...-capped extremities composed of sequences originating from more internal genomic regions were associated with high DNA methylation, suggesting that de novo heterochromatin formation contributes to the restoration of chromosome end stability in C. reinhardtii. The diversity of alternative strategies present...
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Review: The structure, function, and evolution of plant centromeres
- Matthew Naish and
- Ian R. Henderson
Genome Res. February 2024 34: 161-178; Published in Advance March 14, 2024, doi:10.1101/gr.278409.123
...as a primer for DNA synthesis (Liu and Malkova 2022). Following initiation of replication, unidirectional migration of a replication bubble may occur over hundreds of kilobases, followed by DNA repair (Liu and Malkova 2022). In centromere repeat arrays, there may be multiple locations to which the invading...
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Method: Genome-wide detection of chromosomal rearrangements, indels, and mutations in circular chromosomes by short read sequencing
- Ole Skovgaard,
- Mads Bak,
- Anders Løbner-Olesen,
- and Niels Tommerup
Genome Res. August 2011 21: 1388-1393; Published in Advance May 9, 2011, doi:10.1101/gr.117416.110
..., for the identification of mutations that suppress the growth deficiency imposed by excessive initiations from the Escherichia coli origin of replication, oriC . The E. coli chromosome, like the majority of bacterial chromosomes, is circular, and DNA replication is initiated by assembling two replication complexes...
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Research: Diversification and collapse of a telomere elongation mechanism
- Bastien Saint-Leandre,
- Son C. Nguyen,
- and Mia T. Levine
Genome Res. June 2019 29: 920-931; Published in Advance May 28, 2019, doi:10.1101/gr.245001.118
..., telomerase-added DNA repeats (Greider and Blackburn 1989; Zakian 1989, 1996; Blackburn 1991) counteract the “end-replication problem” that otherwise erodes unique DNA sequence at chromosome termini (Watson 1972). However, telomeres of select fungi (Starnes et al. 2012), algae (Higashiyama et al. 1997), moths...
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Research: Sumoylation at chromatin governs coordinated repression of a transcriptional program essential for cell growth and proliferation
- Hélène Neyret-Kahn,
- Moussa Benhamed,
- Tao Ye,
- Stéphanie Le Gras,
- Jack-Christophe Cossec,
- Pierre Lapaquette,
- Oliver Bischof,
- Maia Ouspenskaia,
- Mary Dasso,
- Jacob Seeler,
- Irwin Davidson,
- and Anne Dejean
Genome Res. October 2013 23: 1563-1579; Published in Advance July 26, 2013, doi:10.1101/gr.154872.113
.... Results SUMO1 and SUMO2 are widely distributed over the in proliferating human fibroblasts To profile sumoylated proteins on the of proliferating primary cells, we performed chromatin immunoprecipitation coupled toDNA sequencing (ChIP-seq) inWI38 human fibroblasts using antibodies specific for SUMO1...
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Research: Efficient neocentromere formation is suppressed by gene conversion to maintain centromere function at native physical chromosomal loci in Candida albicans
- Jitendra Thakur and
- Kaustuv Sanyal
Genome Res. April 2013 23: 638-652; Published in Advance February 25, 2013, doi:10.1101/gr.141614.112
...formation in C. albicans, we propose a model shown in Figure 8D. The presence of neocentromere hotspots within the centromere proximal regions indicates that the nature of DNA sequences such as structural motifs or replication origins may play an important role in the assembly of CENPA on centromeres...
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Method: Inhibition of transcription leads to rewiring of locus-specific chromatin proteomes
- Deepani W. Poramba-Liyanage,
- Tessy Korthout,
- Christine E. Cucinotta,
- Ila van Kruijsbergen,
- Tibor van Welsem,
- Dris El Atmioui,
- Huib Ovaa,
- Toshio Tsukiyama,
- and Fred van Leeuwen
Genome Res. April 2020 30: 635-646; Published in Advance March 18, 2020, doi:10.1101/gr.256255.119
....200604072 ↵Aparicio OM, Weinstein DM, Bell SP. 1997. Components and dynamics of DNA replication complexes in S. cerevisiae: redistribution of MCM proteins and Cdc45p during S phase. Cell 91: 59–69. doi:10.1016/S0092-8674(01)80009-X ↵Aragon AD, Rodriguez AL, Meirelles O, Roy S, Davidson GS, Tapia PH, Allen C...
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