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Research: DNA replication timing during development anticipates transcriptional programs and parallels enhancer activation
- Joseph C. Siefert,
- Constantin Georgescu,
- Jonathan D. Wren,
- Amnon Koren,
- and Christopher L. Sansam
Genome Res. August 2017 27: 1406-1416; Published in Advance May 16, 2017, doi:10.1101/gr.218602.116
...the majority of the , and epigenetic changes involved in enhancer activation frequently paralleled developmental changes in replication timing. The long arm of Chromosome 4 underwent a dramatic developmentally regulated switch to late replication during gastrulation, reminiscent of mammalian X Chromosome...
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Research: Mutagenesis of human genomes by endogenous mobile elements on a population scale
- Nelson T. Chuang,
- Eugene J. Gardner,
- Diane M. Terry,
- Jonathan Crabtree,
- Anup A. Mahurkar,
- Guillermo L. Rivell,
- Charles C. Hong,
- James A. Perry,
- and Scott E. Devine
Genome Res. December 2021 31: 2225-2235; Published in Advance November 12, 2021, doi:10.1101/gr.275323.121
...of methylated cytosines (Walser et al. 2008).We identified additional internal sequence changes in our 647 FL-L1Hs elements that could potentially impact L1 function (Fig. 4C,D; Supplemental Fig. S3; Supplemental Table S4A,B). In addition to CpG changes, mutations that impact transcription factor binding sites...
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Research: Evolutionary expansion of DNA hypomethylation in the mammalian germline genome
- Jianghan Qu,
- Emily Hodges,
- Antoine Molaro,
- Pascal Gagneux,
- Matthew D. Dean,
- Gregory J. Hannon,
- and Andrew D. Smith
Genome Res. February 2018 28: 145-158; Published in Advance December 19, 2017, doi:10.1101/gr.225896.117
...methylation has substantially impacted the large-scale evolution of mammalian s. Spontaneous deamination elevates the mutation rate at methylated cytosines (Bird 1980). Consequently, germline DNA methylation profiles have shaped the CpG landscape of mammalian s (Cohen et al. 2011), resulting in the CpG island...
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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
..., Audit B, d’Aubenton-Carafa Y, Arneodo A, Hyrien O, et al. 2010. Impact of replication timing on non-CpG and CpG substitution rates in mammalian s. Genome Res 20: 447–457. Cosgrove AJ, Nieduszynski CA, Donaldson AD. 2002. Ku complex controls the replication time of DNA in telomere regions. Genes Dev 16...
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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
...Genome-wide mapping of human DNA-replication origins: Levels of transcription at ORC1 sites regulate origin selection and replication timing Gaetano Ivan Dellino 1 , 2 , 11 , Davide Cittaro 3 , 6 , Rossana Piccioni 1 , Lucilla Luzi 4...
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Methods: Multiplex padlock targeted sequencing reveals human hypermutable CpG variations
- Jin Billy Li,
- Yuan Gao,
- John Aach,
- Kun Zhang,
- Gregory V. Kryukov,
- Bin Xie,
- Annika Ahlford,
- Jung-Ki Yoon,
- Abraham M. Rosenbaum,
- Alexander Wait Zaranek,
- Emily LeProust,
- Shamil R. Sunyaev,
- and George M. Church
Genome Res. September 2009 19: 1606-1615; Published in Advance June 12, 2009, doi:10.1101/gr.092213.109
...variation To estimate the impact of CpG context on mutation rate, we determined the ancestral state of each SNP using the chimpanzee . Comparison of densities of CpG and non-CpG SNPs in our padlock probes suggests that the rate of transitions originated at CpG sites is 13.7 times higher than the rate of non-CpG...
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Research: The (r)evolution of SINE versus LINE distributions in primate genomes: Sex chromosomes are important
- Erika M. Kvikstad and
- Kateryna D. Makova
Genome Res. May 2010 20: 600-613; Published in Advance March 10, 2010, doi:10.1101/gr.099044.109
...of TE densities (for details, see Supplemental Table S2 and Methods). bGC content, L1 target site density, Telomere-containing hexamer frequency, Replication timing, CpG island density, CpG content, Nucleosomefree region density, and Germline-expressed region density are variables used to model local TE...
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Research: A naturally occurring variant of MBD4 causes maternal germline hypermutation in primates
- Alexandra M. Stendahl,
- Rashesh Sanghvi,
- Samuel Peterson,
- Karina Ray,
- Ana C. Lima,
- Raheleh Rahbari,
- and Donald F. Conrad
Genome Res. December 2023 33: 2053-2059; Published in Advance November 20, 2023, doi:10.1101/gr.277977.123
...at the time of the PGC specification. Finally, in addition to the expected excess of CpG mutations in the offspring of 26537, we observed a secondary enrichment in CpA contexts, accounting for 28% of all calls in these children (Fig. 5C). Non-CpG methylation, especially involving CpA, occurs -wide in oocytes...
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Method: Quantification of GC-biased gene conversion in the human genome
- Sylvain Glémin,
- Peter F. Arndt,
- Philipp W. Messer,
- Dmitri Petrov,
- Nicolas Galtier,
- and Laurent Duret
Genome Res. August 2015 25: 1215-1228; Published in Advance May 20, 2015, doi:10.1101/gr.185488.114
..., according to the local recombination rate. For a comparison, both CpG and non-CpG SNPs (same as Fig. 1D) are presented.To assess the impact of polarization errors on DAF spectra and on estimators of gBGC strength, we performed extensive simulation analyses (see details in Methods). Simulation parameters...
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Research: DNA (de)methylation in embryonic stem cells controls CTCF-dependent chromatin boundaries
- Laura Wiehle,
- Graeme J. Thorn,
- Günter Raddatz,
- Christopher T. Clarkson,
- Karsten Rippe,
- Frank Lyko,
- Achim Breiling,
- and Vladimir B. Teif
Genome Res. May 2019 29: 750-761; Published in Advance April 4, 2019, doi:10.1101/gr.239707.118
....Next, we quantified changes of nucleosome occupancy at different genomic features. Although the majority of regions increased their nucleosome occupancy in DKO ESCs, a significant number of functional genomic elements (promoters, enhancers, CpG islands, regions marked by 5hmC in WT cells, 5hmC-to-5m...
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