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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
...eukaryotic systems.Replication of the large and complex s of multicellular organisms occurs during S-phase, once per cell cycle. Full replication depends on the coordinated function of thousands of DNA replication origins (ORIs) scattered across the (Méchali 2010; Sanchez et al. 2012; Méchali et al. 2013...
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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
..., et al. 2011. Genome-scale analysis of metazoan replication origins reveals their organization in specific but flexible sites defined by conserved features. Genome Res 21: 1438–1449. Czajkowsky DM, Liu J, Hamlin JL, Shao Z. 2008. DNA combing reveals intrinsic temporal disorder in the replication...
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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
...localization. They explain the frequently observed links between DNA replication and transcription. They also emphasize the plasticity of metazoan replication origins and suggest that in multicellular eukaryotes, the combination of distinct genetic features and chromatin configurations act in synergy to define...
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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
...distance fromNSCR-SNS peaks. For example, TG dinucleotide repeats show orientation-specific association with ∼7%–8% of NSCR-SNS peaks with a maximum at ∼165 bp 5′ to the peaks. TG dinucleotide repeats have been associated with replication origins defined by lambda exonuclease SNS analyses of Drosophila...
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Research: Population genomics reveals mechanisms and dynamics of de novo expressed open reading frame emergence in Drosophila melanogaster
- Anna Grandchamp,
- Lucas Kühl,
- Marie Lebherz,
- Kathrin Brüggemann,
- John Parsch,
- and Erich Bornberg-Bauer
Genome Res. June 2023 33: 872-890; Published in Advance July 13, 2023, doi:10.1101/gr.277482.122
...). It has been conjectured that over very short evolutionary time scales, most novel genes originate de novo but are then rapidly lost (Schmitz et al. 2018; Rödelsperger et al. 2019; Lange et al. 2021). Most probably, newly emerged de novo genes fail to establish a sufficient advantage to the host organism...
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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
...insight into what defines metazoan origins suffers most from a small sample size of well-characterized origins. The search for sequence motifs, epigenetic marks, and other unifying features that specify metazoan replication origins has been ongoing for many years. Recently, several -wide approaches have...
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Research: Bubble-seq analysis of the human genome reveals distinct chromatin-mediated mechanisms for regulating early- and late-firing origins
- Larry D. Mesner,
- Veena Valsakumar,
- Marcin Cieślik,
- Rebecca Pickin,
- Joyce L. Hamlin,
- and Stefan Bekiranov
Genome Res. November 2013 23: 1774-1788; Published in Advance July 16, 2013, doi:10.1101/gr.155218.113
...than the epigenetic features that characterize their environments. Because of the artificial boundaries that define the 44 ENCODE regions, as well as the largely arbitrary nature of the majority of the selected genomic loci, the origin maps we and others have prepared are necessarily biased and...
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Research: Genome-wide mapping of human DNA-replication origins: Levels of transcription at ORC1 sites regulate origin selection and replication timing
- Gaetano Ivan Dellino,
- Davide Cittaro,
- Rossana Piccioni,
- Lucilla Luzi,
- Stefania Banfi,
- Simona Segalla,
- Matteo Cesaroni,
- Ramiro Mendoza-Maldonado,
- Mauro Giacca,
- and Pier Giuseppe Pelicci
Genome Res. January 2013 23: 1-11; Published in Advance November 27, 2012, doi:10.1101/gr.142331.112
...anti-ORC or -MCM antibodies showed that this consensus is essential but not sufficient for origin activity and identified other features that influence selection and replication timing, including transcription and/or chromatin structure (Eaton et al. 2010). In metazoa, instead, pre-RC does not exhibit...
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Research: The identification and functional annotation of RNA structures conserved in vertebrates
- Stefan E. Seemann,
- Aashiq H. Mirza,
- Claus Hansen,
- Claus H. Bang-Berthelsen,
- Christian Garde,
- Mikkel Christensen-Dalsgaard,
- Elfar Torarinsson,
- Zizhen Yao,
- Christopher T. Workman,
- Flemming Pociot,
- Henrik Nielsen,
- Niels Tommerup,
- Walter L. Ruzzo,
- and Jan Gorodkin
Genome Res. August 2017 27: 1371-1383; Published in Advance May 9, 2017, doi:10.1101/gr.208652.116
...of reducing the false-discovery rate (FDR) of the predicted CRSs. Regulatory features of RNA structures have been extensively studied in bacteria (Waters and Storz 2009), but the vast landscape of RNA regulatory elements in vertebrates remains largely uncharacterized. Conservation, structural or otherwise...
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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
...origins reveals their organization in specific but flexible sites defined by conserved features. Genome Res 21: 1438–1449. Claycomb JM, MacAlpine DM, Evans JG, Bell SP, Orr-Weaver TL. 2002. Visualization of replication initiation and elongation in...
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