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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
...). Regardless of the complexity in cell-fate pathways, it is clear that changes in patterns of gene expression drive the differentiation program (Cantor and Orkin 2002; Graf and Enver 2009). Misregulation of gene expression patterns can cause diseases such as leukemias and anemias (Higgs 2013; Lee and Young...
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Research: Cytosine modifications modulate the chromatin architecture of transcriptional enhancers
- Elise A. Mahé,
- Thierry Madigou,
- Aurélien A. Sérandour,
- Maud Bizot,
- Stéphane Avner,
- Frédéric Chalmel,
- Gaëlle Palierne,
- Raphaël Métivier,
- and Gilles Salbert
Genome Res. June 2017 27: 947-958; Published in Advance April 10, 2017, doi:10.1101/gr.211466.116
...for MEIS1 sites with no CpGswithin the ChIP-seq peaks (n = 3628) and the 958MEIS1 sites with centered SCL-exo signal (m =mean ChIP-seq signal). 5hmC roles at enhancers Genome Research 951 www..org to MF5), and five bound by FOXA1 but not by MEIS1 (enhancers F1 to F5). As a control, we selected an enhancer...
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Research: A KMT2A-AFF1 gene regulatory network highlights the role of core transcription factors and reveals the regulatory logic of key downstream target genes
- Joe R. Harman,
- Ross Thorne,
- Max Jamilly,
- Marta Tapia,
- Nicholas T. Crump,
- Siobhan Rice,
- Ryan Beveridge,
- Edward Morrissey,
- Marella F.T.R. de Bruijn,
- Irene Roberts,
- Anindita Roy,
- Tudor A. Fulga,
- and Thomas A. Milne
Genome Res. July 2021 31: 1159-1173; Published in Advance June 4, 2021, doi:10.1101/gr.268490.120
...; Baxter et al. 2014). Disruption of these genes can lead to abnormal development and human diseases such as leukemia (Thoms et al. 2019). Gene regulatory patterns are controlled by transcription factors (TFs), that often function together in complex cooperative patterns that are hard to functionally...
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RESOURCE: Analysis of Multiple Genomic Sequence Alignments: A Web Resource, Online Tools, and Lessons Learned From Analysis of Mammalian SCL Loci
- Michael A. Chapman,
- Ian J. Donaldson,
- James Gilbert,
- Darren Grafham,
- Jane Rogers,
- Anthony R. Green,
- and Berthold Göttgens
Genome Res. February 2004 14: 313-318; Published in Advance January 12, 2004, doi:10.1101/gr.1759004
...with peaks of conserved noncoding sequences. Genome Res. 11 : 87 -97. ↵ Göttgens, B., Barton, L.M., Chapman, M.A., Sinclair, A.M., Knudsen, B., Grafham, D., Gilbert, J.G., Rogers, J., Bentley, D.R., and Green, A.R. 2002a . Transcriptional regulation of the stem cell leukemia gene (SCL)—Comparative analysis...
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LETTER: Long-Range Comparison of Human and Mouse SCL Loci: Localized Regions of Sensitivity to Restriction Endonucleases Correspond Precisely with Peaks of Conserved Noncoding Sequences
- Berthold Göttgens,
- James G.R. Gilbert,
- Linda M. Barton,
- Darren Grafham,
- Jane Rogers,
- David R. Bentley,
- and Anthony R. Green
Genome Res. January 1, 2001 11: 87-97; doi:10.1101/gr.153001
..., Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK Abstract Long-range comparative sequence analysis provides a powerful strategy for identifying conserved regulatory elements. The stem cell leukemia ( SCL ) gene encodes a bHLH transcription factor with a pivotal role in hemopoiesis...
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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
...are from Pilon et al. (2011). Direction of transcription for each gene is left to right. The graphs on the right show levels of expression in hematopoietic stem progenitor cells (HSPCs), which are a proxy for expression in HPC-7 cells, erythroblasts, and megakaryocytes (Pimkin et al. 2014). (A) The Pf4...
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ARTICLE: Comparative Analysis of Vertebrate Dystrophin Loci Indicate Intron Gigantism as a Common Feature
- Uberto Pozzoli,
- Greg Elgar,
- Rachele Cagliani,
- Laura Riva,
- Giacomo P. Comi,
- Nereo Bresolin,
- Alessandra Bardoni,
- and Manuela Sironi
Genome Res. May 1, 2003 13: 764-772; doi:10.1101/gr.776503
...and characterization of alternatively spliced isoforms of Dp71. Hum. Mol. Genet. 4 : 1475 – 1483 . ↵ Barton L.M. , Göttgens B. , Gering M. , Gilbert J.G.R , Grafham D. , Rogers J. , Bentley D. , Patient R. , Green A.R. ( 2001 ) Regulation of the stem cell leukemia (SCL) gene: A tale of two fishes. Proc. Natl. Acad...
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LETTER: Long noncoding RNAs in mouse embryonic stem cell pluripotency and differentiation
- Marcel E. Dinger,
- Paulo P. Amaral,
- Tim R. Mercer,
- Ken C. Pang,
- Stephen J. Bruce,
- Brooke B. Gardiner,
- Marjan E. Askarian-Amiri,
- Kelin Ru,
- Giulia Soldà,
- Cas Simons,
- Susan M. Sunkin,
- Mark L. Crowe,
- Sean M. Grimmond,
- Andrew C. Perkins,
- and John S. Mattick
Genome Res. September 2008 18: 1433-1445; Published in Advance June 18, 2008, doi:10.1101/gr.078378.108
...-coding genes where sequence motifs are usually indicative of function, at least in the biochemical sense, ncRNA sequence information is currently uninformative for predicting function. However, many long ncRNAs have been found to originate from complex transcriptional loci, in which the ncRNAs are coordinately...
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LETTER: A novel mode of enhancer evolution: The Tal1 stem cell enhancer recruited a MIR element to specifically boost its activity
- Aileen M. Smith,
- Maria-Jose Sanchez,
- George A. Follows,
- Sarah Kinston,
- Ian J. Donaldson,
- Anthony R. Green,
- and Berthold Göttgens
Genome Res. September 2008 18: 1422-1432; Published in Advance August 7, 2008, doi:10.1101/gr.077008.108
...9PT, United Kingdom Abstract Altered cis -regulation is thought to underpin much of metazoan evolution, yet the underlying mechanisms remain largely obscure. The stem cell leukemia TAL1 (also known as SCL) transcription factor is essential for the normal development of blood stem cells...
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LETTER: Long-range comparison of human and mouse Sprr loci to identify conserved noncoding sequences involved in coordinate regulation
- Natalia Martin,
- Satyakam Patel,
- and Julia A. Segre
Genome Res. December 2004 14: 2430-2438; doi:10.1101/gr.2709404
...with peaks of conserved noncoding sequences. Genome Res. 11 : 87 -97. ↵ Göttgens, B., Barton, L.M., Chapman, M.A., Sinclair, A.M., Knudsen, B., Grafham, D., Gilbert, J.G., Rogers, J., Bentley, D.R., and Green, A.R. 2002 . Transcriptional regulation of the stem cell leukemia gene (SCL)—Comparative analysis...

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