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Research: Distinct transcription factor complexes act on a permissive chromatin landscape to establish regionalized gene expression in CNS stem cells
- Daniel W. Hagey,
- Cécile Zaouter,
- Gaëlle Combeau,
- Monika Andersson Lendahl,
- Olov Andersson,
- Mikael Huss,
- and Jonas Muhr
Genome Res. July 2016 26: 908-917; Published in Advance May 2, 2016, doi:10.1101/gr.203513.115
...relaxed and dynamic chromatin state, which is permissive to the transcriptional machinery and thus gene activation (Meshorer et al. 2006). Examination of chromatin accessibility by mapping DNase I hypersensitive sites (DHSs) wide, in a large array of stem cells and their more committed progeny, has...
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Resource: Interspecies regulatory landscapes and elements revealed by novel joint systematic integration of human and mouse blood cell epigenomes
- Guanjue Xiang,
- Xi He,
- Belinda M. Giardine,
- Kathryn J. Isaac,
- Dylan J. Taylor,
- Rajiv C. McCoy,
- Camden Jansen,
- Cheryl A. Keller,
- Alexander Q. Wixom,
- April Cockburn,
- Amber Miller,
- Qian Qi,
- Yanghua He,
- Yichao Li,
- Jens Lichtenberg,
- Elisabeth F. Heuston,
- Stacie M. Anderson,
- Jing Luan,
- Marit W. Vermunt,
- Feng Yue,
- Michael E.G. Sauria,
- Michael C. Schatz,
- James Taylor,
- Berthold Göttgens,
- Jim R. Hughes,
- Douglas R. Higgs,
- Mitchell J. Weiss,
- Yong Cheng,
- Gerd A. Blobel,
- David M. Bodine,
- Yu Zhang,
- Qunhua Li,
- Shaun Mahony,
- and Ross C. Hardison
Genome Res. July 2024 34: 1089-1105; Published in Advance July 1, 2024, doi:10.1101/gr.277950.123
...) immortalized mouse cell line capable of differentiation in vitro into more mature myeloid cells, (G1E) immortalized mouse cell line blocked in erythroid maturation by a knockout of the Gata1 gene and its subline ER4 that will further differentiate after restoration of Gata1 function in an estrogen...
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Research: Dynamic shifts in occupancy by TAL1 are guided by GATA factors and drive large-scale reprogramming of gene expression during hematopoiesis
- Weisheng Wu,
- Christapher S. Morrissey,
- Cheryl A. Keller,
- Tejaswini Mishra,
- Maxim Pimkin,
- Gerd A. Blobel,
- Mitchell J. Weiss,
- and Ross C. Hardison
Genome Res. December 2014 24: 1945-1962; Published in Advance October 15, 2014, doi:10.1101/gr.164830.113
...(in the case of the G1E system) they allow us to study synchronized, dynamic changes dependent on a specific TF (GATA1) during erythroid maturation. A comprehensive set of 18,595 TAL1-occupiedDNA segments (TAL1 OSs) across myeloid hematopoiesis was constructed by taking the union of all the peak calls...
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Research: Genome accessibility is widely preserved and locally modulated during mitosis
- Chris C.-S. Hsiung,
- Christapher S. Morrissey,
- Maheshi Udugama,
- Christopher L. Frank,
- Cheryl A. Keller,
- Songjoon Baek,
- Belinda Giardine,
- Gregory E. Crawford,
- Myong-Hee Sung,
- Ross C. Hardison,
- and Gerd A. Blobel
Genome Res. February 2015 25: 213-225; Published in Advance November 4, 2014, doi:10.1101/gr.180646.114
...interphase using a rapidly dividing murine erythroblast cell line, G1E. G1E cells are for the erythroid master regulator GATA1 and arrested in their maturation at the pro-erythroblast stage (Weiss et al. 1997). Restoration of GATA1 activity via stable expression of a GATA1-estrogen receptor fusion...
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Resource: An integrative view of the regulatory and transcriptional landscapes in mouse hematopoiesis
- Guanjue Xiang,
- Cheryl A. Keller,
- Elisabeth Heuston,
- Belinda M. Giardine,
- Lin An,
- Alexander Q. Wixom,
- Amber Miller,
- April Cockburn,
- Michael E.G. Sauria,
- Kathryn Weaver,
- Jens Lichtenberg,
- Berthold Göttgens,
- Qunhua Li,
- David Bodine,
- Shaun Mahony,
- James Taylor,
- Gerd A. Blobel,
- Mitchell J. Weiss,
- Yong Cheng,
- Feng Yue,
- Jim Hughes,
- Douglas R. Higgs,
- Yu Zhang,
- and Ross C. Hardison
Genome Res. March 2020 30: 472-484; Published in Advance March 4, 2020, doi:10.1101/gr.255760.119
...bias in differentiation (Psaila et al. 2016), and this difference in the grouping of MEPs suggests that the regulatory landscape of MEP has shifted toward the erythroid lineage before reflecting that bias in the transcriptome data. G1E and G1E-ER4 cell lines, which are models for GATA1-dependent...
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Research: Divergent functions of hematopoietic transcription factors in lineage priming and differentiation during erythro-megakaryopoiesis
- Maxim Pimkin,
- Andrew V. Kossenkov,
- Tejaswini Mishra,
- Christapher S. Morrissey,
- Weisheng Wu,
- Cheryl A. Keller,
- Gerd A. Blobel,
- Dongwon Lee,
- Michael A. Beer,
- Ross C. Hardison,
- and Mitchell J. Weiss
Genome Res. December 2014 24: 1932-1944; Published in Advance October 15, 2014, doi:10.1101/gr.164178.113
...by GATA1 or TAL1, and its epigenetic signature includes decreased H3K4me1 and H3K4me3, whereas the promoter acquires (or retains) the repressive H3K27me3 methylation mark. Many Pimkin et al. 1936 Genome Research www..org Figure 3. Mechanisms of transcriptional regulation correlate with patterns of erythro...
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Research: Whole-transcriptome sequencing identifies a distinct subtype of acute lymphoblastic leukemia with predominant genomic abnormalities of EP300 and CREBBP
- Maoxiang Qian,
- Hui Zhang,
- Shirley Kow-Yin Kham,
- Shuguang Liu,
- Chuang Jiang,
- Xujie Zhao,
- Yi Lu,
- Charnise Goodings,
- Ting-Nien Lin,
- Ranran Zhang,
- Takaya Moriyama,
- Zhaohong Yin,
- Zhenhua Li,
- Thuan Chong Quah,
- Hany Ariffin,
- Ah Moy Tan,
- Shuhong Shen,
- Deepa Bhojwani,
- Shaoyan Hu,
- Suning Chen,
- Huyong Zheng,
- Ching-Hon Pui,
- Allen Eng-Juh Yeoh,
- and Jun J. Yang
Genome Res. February 2017 27: 185-195; Published in Advance November 30, 2016, doi:10.1101/gr.209163.116
...through interactions with other hematopoietic transcription factors (e.g., GATA1, TCF3, and RUNX1) (Blobel 2000). Leukemia-associated translations involving CREBBP have been identified in acute myeloid leukemia (KAT6A-CREBBP and KMT2A-CREBBP) (Yang 2004), whereas EP300 translocation is exceedingly rare...
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Research: Interplay between chromatin state, regulator binding, and regulatory motifs in six human cell types
- Jason Ernst and
- Manolis Kellis
Genome Res. July 2013 23: 1142-1154; Published in Advance April 17, 2013, doi:10.1101/gr.144840.112
.... At themolecular level, the binding landscape of a given regulator can be extremely dynamic, although its sequence specificity remains unchanged (Harbison et al. 2004; Zhong et al. 2010; Mullen et al. 2011; Trompouki et al. 2011). This is attributed at least in part to the dynamic chromatin landscape of each cell...
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Research: Hydroxycarbamide effects on DNA methylation and gene expression in myeloproliferative neoplasms
- Stephania Contreras Castillo,
- Bertille Montibus,
- Azucena Rocha,
- Will Duke,
- Ferdinand von Meyenn,
- Donal McLornan,
- Claire Harrison,
- Ann Mullally,
- Reiner Schulz,
- and Rebecca J. Oakey
Genome Res. August 2021 31: 1381-1394; Published in Advance July 9, 2021, doi:10.1101/gr.270066.120
...genes were commonly regulated in both species. Commonly up-regulated genes were enriched for neutrophil degranulation and innate immune system pathways (Fig. 4B), like individually observed in MPN patients and mice. SPI1 and GATA1 were shown by enrichment analysis to act as regulators for up- and down...
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Method: Spatiotemporal clustering of the epigenome reveals rules of dynamic gene regulation
- Pengfei Yu,
- Shu Xiao,
- Xiaoyun Xin,
- Chun-Xiao Song,
- Wei Huang,
- Darina McDee,
- Tetsuya Tanaka,
- Ting Wang,
- Chuan He,
- and Sheng Zhong
Genome Res. February 2013 23: 352-364; Published in Advance October 2, 2012, doi:10.1101/gr.144949.112
...and protein variations to the DNA and histones, and some of these modifications and variations can be passed down to an organism’s offspring (Bernstein et al. 2007). Epis are dynamic, and epigenetic modifications are associated with changes in gene expression (Creyghton et al. 2010; Hawkins et al. 2011). Thus...

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