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Research: Intrinsic DNA binding properties demonstrated for lineage-specifying basic helix-loop-helix transcription factors
- Bradford H. Casey,
- Rahul K. Kollipara,
- Karine Pozo,
- and Jane E. Johnson
Genome Res. April 2018 28: 484-496; Published in Advance March 2, 2018, doi:10.1101/gr.224360.117
...compared their DNA binding properties when ectopically expressed in embryonic stem cells (Fig. 1C). Although the genomic binding pattern of this subset of bHLH factors has previously been compared in their respective lineages, their DNA binding behavior in a single, common cell type mitigates the influence...
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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
...with spatial organization of chromatin in the nucleus; early and late RDs reside in distinct nuclear compartments (Nakamura et al. 1986; Nakayasu 1989; O'Keefe et al. 1992), and cytogenetic visualization of pulse-labeled DNA synthesis reveals distinct punctate replication foci whose structure remains stable...
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Research: Functional genomics analysis of developing zebrafish and human endoderm reveals highly conserved cis-regulatory modules acting during vertebrate organogenesis
- Daniela M Riley,
- Randa Elsayed,
- Mark D Walsh,
- Simaran Johal,
- Ying Lin,
- Harry Walton,
- Till Bretschneider,
- Sascha Ott,
- and Andrew C Nelson
Genome Res. March 4, 2026 gr.280838.125; Published in Advance March 4, 2026, doi:10.1101/gr.280838.125
...analyses reveal a highly significant association between 285 endoderm HCNEs and genes encoding DNA-binding and gene regulatory proteins, including 286 HMG domain-containing and chromatin binding factors. Notably, however, the endoderm 287 HCNEs appear to show a greater enrichment of such genes compared...
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Research: Imprints and DPPA3 are bypassed during pluripotency- and differentiation-coupled methylation reprogramming in testicular germ cell tumors
- J. Keith Killian,
- Lambert C.J. Dorssers,
- Britton Trabert,
- Ad J.M. Gillis,
- Michael B. Cook,
- Yonghong Wang,
- Joshua J. Waterfall,
- Holly Stevenson,
- William I. Smith, Jr.,
- Natalia Noyes,
- Parvathy Retnakumar,
- J. Hans Stoop,
- J. Wolter Oosterhuis,
- Paul S. Meltzer,
- Katherine A. McGlynn,
- and Leendert H.J. Looijenga
Genome Res. November 2016 26: 1490-1504; Published in Advance October 20, 2016, doi:10.1101/gr.201293.115
...of DNA Elements Project) annotations for this domain as viewed in the UCSC Genome Browser reveal CTCF transcription factor binding, Figure 2. Lymphoid cell fraction in TGCT samples. (A) Genome-wide methylation β-density distribution in TGCT subtypes, without and after correction for lymphoid infiltrates...
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Method: Functional DNA methylation differences between tissues, cell types, and across individuals discovered using the M&M algorithm
- Bo Zhang,
- Yan Zhou,
- Nan Lin,
- Rebecca F. Lowdon,
- Chibo Hong,
- Raman P. Nagarajan,
- Jeffrey B. Cheng,
- Daofeng Li,
- Michael Stevens,
- Hyung Joo Lee,
- Xiaoyun Xing,
- Jia Zhou,
- Vasavi Sundaram,
- GiNell Elliott,
- Junchen Gu,
- Taoping Shi,
- Philippe Gascard,
- Mahvash Sigaroudinia,
- Thea D. Tlsty,
- Theresa Kadlecek,
- Arthur Weiss,
- Henriette O’Geen,
- Peggy J. Farnham,
- Cécile L. Maire,
- Keith L. Ligon,
- Pamela A.F. Madden,
- Angela Tam,
- Richard Moore,
- Martin Hirst,
- Marco A. Marra,
- Baoxue Zhang,
- Joseph F. Costello,
- and Ting Wang
Genome Res. September 2013 23: 1522-1540; Published in Advance June 26, 2013, doi:10.1101/gr.156539.113
...-specific DMRs across four tissue types We applied M&M to understand how DNA methylation underlies identity at three levels: tissue types, different cell types within tissues, and matched cell types from different individuals. We generated 19 methylomes from embryonic stem cells, adult blood cells, adult breast...
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Method: Estimating absolute methylation levels at single-CpG resolution from methylation enrichment and restriction enzyme sequencing methods
- Michael Stevens,
- Jeffrey B. Cheng,
- Daofeng Li,
- Mingchao Xie,
- Chibo Hong,
- Cécile L. Maire,
- Keith L. Ligon,
- Martin Hirst,
- Marco A. Marra,
- Joseph F. Costello,
- and Ting Wang
Genome Res. September 2013 23: 1541-1553; Published in Advance June 26, 2013, doi:10.1101/gr.152231.112
...CRF accuracy is robust when applied to a second sample Having demonstrated that methylCRF can accurately predict differential DNA methylation of CpGs independent of the characteristic methylation status of their genomic feature, we tested whether ourmodel, trained on data fromH1 embryonic stem cells, would...
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Research: Examination of transcriptional networks reveals an important role for TCFAP2C, SMARCA4, and EOMES in trophoblast stem cell maintenance
- Benjamin L. Kidder and
- Stephen Palmer
Genome Res. April 2010 20: 458-472; Published in Advance February 22, 2010, doi:10.1101/gr.101469.109
...-renewal and pluripotency, little is know about TF networks that regulate self-renewal in TS cells. To further understand transcriptional networks in TS cells, we used chromatin immunoprecipitation with DNA microarray hybridization (ChIP-chip) analysis to investigate targets of the TFs—TCFAP2C, EOMES, ETS2, and GATA3—and...
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REVIEW: Locating mammalian transcription factor binding sites: A survey of computational and experimental techniques
- Laura Elnitski,
- Victor X. Jin,
- Peggy J. Farnham,
- and Steven J.M. Jones
Genome Res. December 2006 16: 1455-1464; Published in Advance October 19, 2006, doi:10.1101/gr.4140006
...details on the coordinated timing of replication by detecting twofold increases in DNA copy number, or heavy isotope incorporation into newly synthesized DNA (for review, see Schwob 2004 ; MacAlpine and Bell 2005 ; ENCODE Consortium, in prep.). Along with newly emerging techniques, a few historically...
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Mini-Review: The chromatin tapestry as a framework for neurodevelopment
- Ben Nolan,
- Timothy E. Reznicek,
- Christopher T. Cummings,
- and M. Jordan Rowley
Genome Res. October 2024 34: 1477-1486; doi:10.1101/gr.278408.123
...on enhancers and promoters, and that there was a substantial reduction of NIPBL binding in the CdLS patient samples. Genome-wide DNA methylation analysis identified 123 differential methylation positions in the CdLS fibroblasts, suggesting that the NIPBL variant can impact DNA methylation and chromatin looping...
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Research: Single-cell multi-omics of human preimplantation embryos shows susceptibility to glucocorticoids
- Cheng Zhao,
- Savana Biondic,
- Katherine Vandal,
- Åsa K. Björklund,
- Michael Hagemann-Jensen,
- Theresa Maria Sommer,
- Jesica Canizo,
- Stephen Clark,
- Pascal Raymond,
- Daniel R. Zenklusen,
- Nicolas Rivron,
- Wolf Reik,
- and Sophie Petropoulos
Genome Res. September 2022 32: 1627-1641; Published in Advance August 10, 2022, doi:10.1101/gr.276665.122
...DMRs and an associated correlation in gene expression, including polar lineage markers TEAD3, KRT23, and IL1R1 (Supplemental Fig. S7; Supplemental Table S4; Petropoulos et al. 2016). The role of DNA methylation in mural–polar establishment would be of interest to further explore as studies examining...
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