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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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Research: Genome-wide identification of TAL1's functional targets: Insights into its mechanisms of action in primary erythroid cells
- Mira T. Kassouf,
- Jim R. Hughes,
- Stephen Taylor,
- Simon J. McGowan,
- Shamit Soneji,
- Angela L. Green,
- Paresh Vyas,
- and Catherine Porcher
Genome Res. August 2010 20: 1064-1083; Published in Advance June 21, 2010, doi:10.1101/gr.104935.110
...Genome-wide identification of TAL1's functional targets: Insights into its mechanisms of action in primary erythroid cells Mira T. Kassouf 1 , Jim R. Hughes 1 , Stephen Taylor 2 , Simon J. McGowan 2 , Shamit Soneji 1 , Angela L. Green 1...
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Research: Effects of sequence variation on differential allelic transcription factor occupancy and gene expression
- Timothy E. Reddy,
- Jason Gertz,
- Florencia Pauli,
- Katerina S. Kucera,
- Katherine E. Varley,
- Kimberly M. Newberry,
- Georgi K. Marinov,
- Ali Mortazavi,
- Brian A. Williams,
- Lingyun Song,
- Gregory E. Crawford,
- Barbara Wold,
- Huntington F. Willard,
- and Richard M. Myers
Genome Res. May 2012 22: 860-869; Published in Advance February 2, 2012, doi:10.1101/gr.131201.111
...of differential allelic occupancy on expression, we used ultrahigh-throughput mRNA sequencing (RNA-seq) (Mortazavi et al. 2008) to measure differential allelic gene expression across the human (Pant et al. 2006; Gimelbrant et al. 2007; Zhang et al. 2009). To avoid biases from mapping to the reference (Degner et...
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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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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
...nonconsensus GATA-1 binding sites (cncGATA1BSs). Genome-wide preCRMs generated by a similar method are provided at http://www.bx.psu.edu/~ross/dataset/DatasetHome.html . The file can be uploaded to browsers ( Kent et al. 2002 ) to identify erythroid preCRMs anywhere in the mouse , or to databases ( Giardine et...
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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
...during MEG differentiation. Discussion We used global transcriptome profiling and ChIP-seq to define and compare DNA occupancy by hematopoietic transcription factors, histone modifications, and mRNA expression during erythro-megakaryocytic differentiation. Integrating our findings with prior studies...
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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
...to be artifacts as they frequently contain an extended CACC motif at a high frequency (46%) (Fig. 2B). KLF1 mRNA-seq reveals a set of novel erythroid gene promoters We and others have previously identified that KLF1, GATA1, and TAL1 frequently bind target genes at sites other than the promoter, particularly...
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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
...T, King DC, Chen KB, Zhang Y, Drautz D, et al. 2009. Erythroid GATA1 function revealed by -wide analysis of transcription factor occupancy, histone modifications, and mRNA expression. Genome Res 19: 2172–2184. Chepelev I, Wei G, Tang Q, Zhao K. 2009. Detection of single nucleotide variations...
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Research: NF-Y coassociates with FOS at promoters, enhancers, repetitive elements, and inactive chromatin regions, and is stereo-positioned with growth-controlling transcription factors
- Joseph D. Fleming,
- Giulio Pavesi,
- Paolo Benatti,
- Carol Imbriano,
- Roberto Mantovani,
- and Kevin Struhl
Genome Res. August 2013 23: 1195-1209; Published in Advance April 17, 2013, doi:10.1101/gr.148080.112
..., that were highly significant. Upon further analysis, it was apparent that NF-Y significantly targeted genes involved in transcription, mRNA splicing, mRNA editing, mRNA 39-end processing, and mRNA transport. Included is a large and diverse set of TFs, including the NF-Y genes themselves, members...
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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
...homozygous for both gata1a:dsRed and kdrl:mCherry transgenes (Fig. 1B). We 145 then used fluorescence activated cell sorting (FACS) to separate sox17+ vascular and 146 erythroid mesodermal lineages (termed sox17M) from endoderm-enriched sox17+ lineages 147 (sox17E) and all other sox17- lineages (sox17N...
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