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Article: Erythroid GATA1 function revealed by genome-wide analysis of transcription factor occupancy, histone modifications, and mRNA expression
- Yong Cheng,
- Weisheng Wu,
- Swathi Ashok Kumar,
- Duonan Yu,
- Wulan Deng,
- Tamara Tripic,
- David C. King,
- Kuan-Bei Chen,
- Ying Zhang,
- Daniela Drautz,
- Belinda Giardine,
- Stephan C. Schuster,
- Webb Miller,
- Francesca Chiaromonte,
- Yu Zhang,
- Gerd A. Blobel,
- Mitchell J. Weiss,
- and Ross C. Hardison
Genome Res. December 2009 19: 2172-2184; Published in Advance November 3, 2009, doi:10.1101/gr.098921.109
...Erythroid GATA1 function revealed by genome-wide analysis of transcription factor occupancy, histone modifications, and mRNA expression Yong Cheng 1 , 2 , Weisheng Wu 1 , 2 , Swathi Ashok Kumar 1 , 2 , Duonan Yu 3 , Wulan Deng 3...
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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 contrast, target genes in erythroblasts are specifically enriched for red cell functions. Furthermore, shifts in TAL1 occupancy during erythroid differentiation are associated with gene repression (dissociation) and induction (co-occupancy with GATA1). Based on both enrichment for transcription factor...
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Research: Dynamics of the epigenetic landscape during erythroid differentiation after GATA1 restoration
- Weisheng Wu,
- Yong Cheng,
- Cheryl A. Keller,
- Jason Ernst,
- Swathi Ashok Kumar,
- Tejaswini Mishra,
- Christapher Morrissey,
- Christine M. Dorman,
- Kuan-Bei Chen,
- Daniela Drautz,
- Belinda Giardine,
- Yoichiro Shibata,
- Lingyun Song,
- Max Pimkin,
- Gregory E. Crawford,
- Terrence S. Furey,
- Manolis Kellis,
- Webb Miller,
- James Taylor,
- Stephan C. Schuster,
- Yu Zhang,
- Francesca Chiaromonte,
- Gerd A. Blobel,
- Mitchell J. Weiss,
- and Ross C. Hardison
Genome Res. October 2011 21: 1659-1671; Published in Advance July 27, 2011, doi:10.1101/gr.125088.111
...in directing gene regulation during differentiation, we mapped chromatin accessibility, histone modifications, and nuclear factor occupancy genome-wide during mouse erythroid differentiation dependent on the master regulatory transcription factor GATA1. Notably, despite extensive changes in gene expression...
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LETTER: Experimental validation of predicted mammalian erythroid cis-regulatory modules
- Hao Wang,
- Ying Zhang,
- Yong Cheng,
- Yuepin Zhou,
- David C. King,
- James Taylor,
- Francesca Chiaromonte,
- Jyotsna Kasturi,
- Hanna Petrykowska,
- Brian Gibb,
- Christine Dorman,
- Webb Miller,
- Louis C. Dore,
- John Welch,
- Mitchell J. Weiss,
- and Ross C. Hardison
Genome Res. December 2006 16: 1480-1492; Published in Advance October 12, 2006, doi:10.1101/gr.5353806
...predicted to be inactive were not occupied. We verify four previously known erythroid CRMs and identify 28 novel ones. Thus, high RP in combination with another feature of a CRM, such as a conserved transcription factor binding site, is a good predictor of functional CRMs. Genome-wide predictions based...
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Research: Novel roles for KLF1 in erythropoiesis revealed by mRNA-seq
- Michael R. Tallack,
- Graham W. Magor,
- Benjamin Dartigues,
- Lei Sun,
- Stephen Huang,
- Jessica M. Fittock,
- Sally V. Fry,
- Evgeny A. Glazov,
- Timothy L. Bailey,
- and Andrew C. Perkins
Genome Res. December 2012 22: 2385-2398; Published in Advance July 26, 2012, doi:10.1101/gr.135707.111
...−/− erythroid tissue. This has revealed novel target genes not previously obtainable by traditional microarray technology, and provided novel insights into the function of KLF1 as a transcriptional activator. We define a cis -regulatory module bound by KLF1, GATA1, TAL1, and EP300 that coordinates a core set...
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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
...of relatively few transcription factors control hematopoietic differentiation. To investigate this process in erythro-megakaryopoiesis, we correlated the genome-wide chromatin occupancy signatures of four master hematopoietic transcription factors (GATA1, GATA2, TAL1, and FLI1) and three diagnostic histone...
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Research: Regulation of nucleosome landscape and transcription factor targeting at tissue-specific enhancers by BRG1
- Gangqing Hu,
- Dustin E. Schones,
- Kairong Cui,
- River Ybarra,
- Daniel Northrup,
- Qingsong Tang,
- Luca Gattinoni,
- Nicholas P. Restifo,
- Suming Huang,
- and Keji Zhao
Genome Res. October 2011 21: 1650-1658; Published in Advance July 27, 2011, doi:10.1101/gr.121145.111
...AJ, Tillo D, Field Y, LeProust EM, Hughes TR, Lieb JD, Widom J, et al. 2009. The DNAencoded nucleosome organization of a eukaryotic . Nature 458: 362–366. Kassouf MT, Hughes JR, Taylor S, McGowan SJ, Soneji S, Green AL, Vyas P, Porcher C. 2010. Genome-wide identification of TAL1’s functional targets...
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Methods: Identifying gene regulatory elements by genomic microarray mapping of DNaseI hypersensitive sites
- George A. Follows,
- Pawan Dhami,
- Berthold Göttgens,
- Alexander W. Bruce,
- Peter J. Campbell,
- Shane C. Dillon,
- Aileen M. Smith,
- Christoph Koch,
- Ian J. Donaldson,
- Mike A. Scott,
- Ian Dunham,
- Mary E. Janes,
- David Vetrie,
- and Anthony R. Green
Genome Res. October 2006 16: 1310-1319; Published in Advance September 8, 2006, doi:10.1101/gr.5373606
...precise, large-scale identification of such sites from as few as 5 million cells. Using ADHM we identified all previously recognized hematopoietic regulatory elements across 200 kb of the mouse T-cell acute lymphocytic leukemia-1 ( Tal1 ) locus, and, in addition, identified two novel elements within...
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Resource: Dynamics of cardiomyocyte transcriptome and chromatin landscape demarcates key events of heart development
- Michal Pawlak,
- Katarzyna Z. Kedzierska,
- Maciej Migdal,
- Karim Abu Nahia,
- Jordan A. Ramilowski,
- Lukasz Bugajski,
- Kosuke Hashimoto,
- Aleksandra Marconi,
- Katarzyna Piwocka,
- Piero Carninci,
- and Cecilia L. Winata
Genome Res. March 2019 29: 506-519; Published in Advance February 13, 2019, doi:10.1101/gr.244491.118
...analysis of the brown module (Supplemental Table 7) revealed the presence of genes implicated in embryonic hematopoiesis. Notably, we have identified a number of hub TFs including myb (v-myb) and prdm1a, mybl2, tbx16l, e2f8, klf17 as well as their effector genes, such as lmo2, tal1, alas2, slc4a1a...
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Method: Scalable cell-specific coexpression networks for granular regulatory pattern discovery with NeighbourNet
- Yidi Deng,
- Jiadong Mao,
- Jarny Choi,
- and Kim-Anh Le Cao
Genome Res. March 5, 2026 gr.281171.125; Published in Advance March 5, 2026, doi:10.1101/gr.281171.125
...deep insights into cellular function 45 and have contributed to the identification of key regulators of disease development, providing 46 potential avenues for therapeutic intervention. 47 Single-cell RNA sequencing (scRNA-seq) has provided an unprecedented view of gene regulation 49 by capturing gene...
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