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Research: KDM1A maintains genome-wide homeostasis of transcriptional enhancers
- Saurabh Agarwal,
- Katherine M. Bonefas,
- Patricia M. Garay,
- Emily Brookes,
- Yumie Murata-Nakamura,
- Robert S. Porter,
- Todd S. Macfarlan,
- Bing Ren,
- and Shigeki Iwase
Genome Res. February 2021 31: 186-197; Published in Advance January 7, 2021, doi:10.1101/gr.234559.118
...and Shilatifard 2014; Vallianatos et al. 2018). Genome-wide identification of potential enhancer elements has been facilitated by profiling (1) binding of pioneer transcription factors (TFs), (2) chromatin accessibility, and (3) patterns of histone modifications (for review, see Ren and Yue 2015). Monomethylation...
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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: Genome wide analysis of 3′ UTR sequence elements and proteins regulating mRNA stability during maternal-to-zygotic transition in zebrafish
- Charles E. Vejnar,
- Mario Abdel Messih,
- Carter M. Takacs,
- Valeria Yartseva,
- Panos Oikonomou,
- Romain Christiano,
- Marlon Stoeckius,
- Stephanie Lau,
- Miler T. Lee,
- Jean-Denis Beaudoin,
- Damir Musaev,
- Hiba Darwich-Codore,
- Tobias C. Walther,
- Saeed Tavazoie,
- Daniel Cifuentes,
- and Antonio J. Giraldez
Genome Res. July 2019 29: 1100-1114; Published in Advance June 21, 2019, doi:10.1101/gr.245159.118
...by specific RBPs during zebrafish embryogenesis.Modeling the effect of sequence on mRNA stability in vivoOur analysis identifies several motifs that are enriched within regulated sequences in the mRNA. To determine whether sequence information can be used to model reporter mRNA regulation, we used machine...
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Method: Antibody-free profiling of transcription factor occupancy during early embryogenesis by FitCUT&RUN
- Xiangxiu Wang,
- Wen Wang,
- Yiman Wang,
- Jia Chen,
- Guifen Liu,
- and Yong Zhang
Genome Res. February 2022 32: 378-388; Published in Advance December 29, 2021, doi:10.1101/gr.275837.121
...embryogenesis to profile the time-series occupancy of Nanog during ZGA.ResultsPerformance of FitCUT&RUNTo generate an antibody-free profile of TF occupancy, we developed FitCUT&RUN, a modified CUT&RUN method. In contrast to CUT&RUN, FitCUT&RUN requires the target TF to be tagged by rabbit Fc (r...
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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
...Allele-specific control of replication timing and organization during development Juan Carlos Rivera-Mulia1, Andrew Dimond2, Daniel Vera3, Claudia Trevilla-Garcia1, Takayo Sasaki1, Jared Zimmerman1, Catherine Dupont4, Joost Gribnau4, Peter Fraser1,2,3 and David M. Gilbert1,3 1Department...
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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
...as described above. Genome-wide changes in replication timing throughout developmentwere assessed by comparing replication timing values at each developmental stage in a Pearson’s correlation matrix (Fig. 5B). The correlation coefficients between replicates were very high for each developmental stage, ranging...
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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
...of genes that were only expressed when early replicating. Taken together, these results support a hierarchical model that links global chromatin organization and RT control with gene regulatory networks during human development.ResultsGenome-wide RT programs of human cell typesWe obtained -wide RT profiles...
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Research: Genome-wide DNA methylation patterns in LSH mutant reveals de-repression of repeat elements and redundant epigenetic silencing pathways
- Weishi Yu,
- Carl McIntosh,
- Ryan Lister,
- Iris Zhu,
- Yixing Han,
- Jianke Ren,
- David Landsman,
- Eunice Lee,
- Victorino Briones,
- Minoru Terashima,
- Robert Leighty,
- Joseph R. Ecker,
- and Kathrin Muegge
Genome Res. October 2014 24: 1613-1623; Published in Advance August 28, 2014, doi:10.1101/gr.172015.114
...Genome-wide DNA methylation patterns in LSH mutant reveals de-repression of repeat elements and redundant epigenetic silencing pathways Weishi Yu 1 , Carl McIntosh 2 , Ryan Lister 3 , 7 , Iris Zhu 4 , Yixing Han 1 , Jianke...
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Research: Abnormal developmental control of replication-timing domains in pediatric acute lymphoblastic leukemia
- Tyrone Ryba,
- Dana Battaglia,
- Bill H. Chang,
- James W. Shirley,
- Quinton Buckley,
- Benjamin D. Pope,
- Meenakshi Devidas,
- Brian J. Druker,
- and David M. Gilbert
Genome Res. October 2012 22: 1833-1844; Published in Advance May 24, 2012, doi:10.1101/gr.138511.112
...with similar genetic makeup, including T-cell leukemias (10-799/10-828), those with TCF3/PBX1 translocations (11-064/RCH-ACV), and those with mostly normal karyotype (10-838/11-118). (B) Genome-wide correlations between replication-timing data sets used in this study. Correlations between divergent B cells...
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Research: Genome-wide parent-of-origin DNA methylation analysis reveals the intricacies of human imprinting and suggests a germline methylation-independent mechanism of establishment
- Franck Court,
- Chiharu Tayama,
- Valeria Romanelli,
- Alex Martin-Trujillo,
- Isabel Iglesias-Platas,
- Kohji Okamura,
- Naoko Sugahara,
- Carlos Simón,
- Harry Moore,
- Julie V. Harness,
- Hans Keirstead,
- Jose Vicente Sanchez-Mut,
- Eisuke Kaneki,
- Pablo Lapunzina,
- Hidenobu Soejima,
- Norio Wake,
- Manel Esteller,
- Tsutomu Ogata,
- Kenichiro Hata,
- Kazuhiko Nakabayashi,
- and David Monk
Genome Res. April 2014 24: 554-569; Published in Advance January 8, 2014, doi:10.1101/gr.164913.113
...Genome-wide parent-of-origin DNA methylation analysis reveals the intricacies of human imprinting and suggests a germline methylation-independent mechanism of establishment Franck Court 1 , 15 , Chiharu Tayama 2 , 15 , Valeria Romanelli 1 , 15 , Alex...

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