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Research: Replication timing networks reveal a link between transcription regulatory circuits and replication timing control
- Juan Carlos Rivera-Mulia,
- Sebo Kim,
- Haitham Gabr,
- Abhijit Chakraborty,
- Ferhat Ay,
- Tamer Kahveci,
- and David M. Gilbert
Genome Res. September 2019 29: 1415-1428; Published in Advance August 21, 2019, doi:10.1101/gr.247049.118
...as the replication timing (RT) program and is regulated during development, coordinated with 3D organization and transcriptional activity. However, transcription and RT are not sufficiently coordinated to predict each other, suggesting an indirect relationship. Here, we exploit -wide RT profiles from 15 human cell...
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Research: Topologically associating domains and their long-range contacts are established during early G1 coincident with the establishment of the replication-timing program
- Vishnu Dileep,
- Ferhat Ay,
- Jiao Sima,
- Daniel L. Vera,
- William S. Noble,
- and David M. Gilbert
Genome Res. August 2015 25: 1104-1113; Published in Advance May 20, 2015, doi:10.1101/gr.183699.114
...T, Hiratani I, Lu J, Itoh M, Kulik M, Zhang J, Dalton S, Gilbert DM. 2010. Evolutionarily conserved replication timing profiles predict long-range chromatin interactions and distinguish closely related cell types. Genome Res 20: 761–770. ↵Sima J, Gilbert DM. 2014. Complex correlations: replication...
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Resource: Haplotype-resolved 3D chromatin architecture of the hybrid pig
- Yu Lin,
- Jing Li,
- Yiren Gu,
- Long Jin,
- Jingyi Bai,
- Jiaman Zhang,
- Yujie Wang,
- Pengliang Liu,
- Keren Long,
- Mengnan He,
- Diyan Li,
- Can Liu,
- Ziyin Han,
- Yu Zhang,
- Xiaokai Li,
- Bo Zeng,
- Lu Lu,
- Fanli Kong,
- Ying Sun,
- Yongliang Fan,
- Xun Wang,
- Tao Wang,
- An'an Jiang,
- Jideng Ma,
- Linyuan Shen,
- Li Zhu,
- Yanzhi Jiang,
- Guoqing Tang,
- Xiaolan Fan,
- Qingyou Liu,
- Hua Li,
- Jinyong Wang,
- Li Chen,
- Liangpeng Ge,
- Xuewei Li,
- Qianzi Tang,
- and Mingzhou Li
Genome Res. February 2024 34: 310-325; Published in Advance March 13, 2024, doi:10.1101/gr.278101.123
...revealed the tissue dependence of 3D chromatin conformation, suggesting that parent-of-origin-specific conformation may drive gene imprinting. We quantify the effects of genetic variations and histone modifications on allelic differences of long-range promoter–enhancer contacts, which likely contribute...
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Resource: A chromosome-scale epigenetic map of the Hydra genome reveals conserved regulators of cell state
- Jack F. Cazet,
- Stefan Siebert,
- Hannah Morris Little,
- Philip Bertemes,
- Abby S. Primack,
- Peter Ladurner,
- Matthias Achrainer,
- Mark T. Fredriksen,
- R. Travis Moreland,
- Sumeeta Singh,
- Suiyuan Zhang,
- Tyra G. Wolfsberg,
- Christine E. Schnitzler,
- Andreas D. Baxevanis,
- Oleg Simakov,
- Bert Hobmayer,
- and Celina E. Juliano
Genome Res. February 2023 33: 283-298; Published in Advance January 13, 2023, doi:10.1101/gr.277040.122
...–J) Predicted domain boundaries fall within regions of heterochromatin. Domain boundaries are associated with reduced chromatin accessibility (F), H3K4me1 (G), and sequence conservation (H) and with elevated repeat element density (I) and H3K27me3 (J).We next explored intra-chromosomal interactions in our Hi...
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Research: Patterns of regulatory activity across diverse human cell types predict tissue identity, transcription factor binding, and long-range interactions
- Nathan C. Sheffield,
- Robert E. Thurman,
- Lingyun Song,
- Alexias Safi,
- John A. Stamatoyannopoulos,
- Boris Lenhard,
- Gregory E. Crawford,
- and Terrence S. Furey
Genome Res. May 2013 23: 777-788; Published in Advance March 12, 2013, doi:10.1101/gr.152140.112
...Patterns of regulatory activity across diverse human cell types predict tissue identity, transcription factor binding, and long-range interactions Nathan C. Sheffield 1 , 2 , Robert E. Thurman 3 , Lingyun Song 2 , Alexias Safi 2 , John A...
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Research: Allele-specific control of replication timing and genome organization during development
- Juan Carlos Rivera-Mulia,
- Andrew Dimond,
- Daniel Vera,
- Claudia Trevilla-Garcia,
- Takayo Sasaki,
- Jared Zimmerman,
- Catherine Dupont,
- Joost Gribnau,
- Peter Fraser,
- and David M. Gilbert
Genome Res. June 2018 28: 800-811; Published in Advance May 7, 2018, doi:10.1101/gr.232561.117
...presented higher densities of long-range chromatin interactions with shorter distances in comparison with the synchronously late replicating allelic regions (Fig. 3B). Similarly, we found that synchronously early replicating regions were more accessible and the genes located within them expressed at higher...
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Research: Delayed DNA replication in haploid human embryonic stem cells
- Matthew M. Edwards,
- Michael V. Zuccaro,
- Ido Sagi,
- Qiliang Ding,
- Dan Vershkov,
- Nissim Benvenisty,
- Dieter Egli,
- and Amnon Koren
Genome Res. December 2021 31: 2155-2169; Published in Advance November 22, 2021, doi:10.1101/gr.275953.121
...of the samples. Long-range autocorrelation was observed in haploid, isogenic diploidized (hereafter referred to as “diploid” for simplicity) and control cells across all chromosomes (Supplemental Fig. S2A). We then compared the replication timing profiles of the haploid, diploid, and control cell lines, as well...
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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
...to open and closed chromatin, respectively (Ryba et al. 2010; Pope et al. 2014). Therefore, replication timing can also be used to assess changes in chromatin organization during development. The timing program is modulated when embryonic stem cells (ESCs) and induced pluripotent stem cells (i...
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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
...that H4K16 modification is dispensable for replication and gene expression.Animal cells duplicate large, complex s by initiating replication at distinct locations within the at different times during S phase. An evolutionarily conserved feature of this regulatory paradigm is a temporal order of DNA...
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Research: Dynamic changes in replication timing and gene expression during lineage specification of human pluripotent stem cells
- Juan Carlos Rivera-Mulia,
- Quinton Buckley,
- Takayo Sasaki,
- Jared Zimmerman,
- Ruth A. Didier,
- Kristopher Nazor,
- Jeanne F. Loring,
- Zheng Lian,
- Sherman Weissman,
- Allan J. Robins,
- Thomas C. Schulz,
- Laura Menendez,
- Michael J. Kulik,
- Stephen Dalton,
- Haitham Gabr,
- Tamer Kahveci,
- and David M. Gilbert
Genome Res. August 2015 25: 1091-1103; Published in Advance June 8, 2015, doi:10.1101/gr.187989.114
...for many cell cycles (Jackson and Pombo 1998; Ma et al. 1998; Dimitrova and Gilbert 1999; Berezney et al. 2000; Sadoni et al. 2004). More recently, chromatin conformation methods that map long-range chromatin interactions (Lieberman-Aiden et al. 2009) have revealed that chromosomes consist of topologically...

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