Unknown,Transcriptomics,Genomics,Proteomics

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Genome-wide mapping of in vivo SCL/DNA interactions in erythroid cells


ABSTRACT: We have previously proposed two distinct molecular mechanisms by which SCL binds its targets in hematopoiesis; either by direct contact with specific DNA sequences or by indirect recruitment through interaction with other proteins. We have established that direct DNA binding is the major non-redundant mechanism SCL exerts in red cells. A DNA-binding mutant form of SCL (SCLRER) had detrimental effect on erythropoiesis in vivo. To extend these data to a molecular and mechanistic level, we have set out to identify the genomic sequences bound by SCL in vivo in erythroid precursors; we performed anti-SCL ChIP assays on immature, Ter119- erythroid cell populations isolated from day E12.5 wild-type (SCLWT/WT) fetal livers followed by ultra-throughput sequencing (ChIP-SEQ). To compare SCL’s direct versus indirect DNA-binding activities and, thus, gain insight into its mechanisms of action, we also analysed material isolated from SCLRER/RER fetal livers. anti-SCL ChIP-enriched DNA from mouse fetal liver erythroblast chromatin was analysed by Solexa sequencing. Four samples were processed: chromatin from SCL wildtype erythroblasts (WT-SCL) and SCL mutant erythroblasts (RER-SCL) were ChIPed by anti-SCL antibody and sequenced with their respective 'no antibody' controls.

ORGANISM(S): Mus musculus

SUBMITTER: Stephen Taylor 

PROVIDER: E-GEOD-18720 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

Genome-wide identification of TAL1's functional targets: insights into its mechanisms of action in primary erythroid cells.

Kassouf Mira T MT   Hughes Jim R JR   Taylor Stephen S   McGowan Simon J SJ   Soneji Shamit S   Green Angela L AL   Vyas Paresh P   Porcher Catherine C  

Genome research 20100621 8


Coordination of cellular processes through the establishment of tissue-specific gene expression programs is essential for lineage maturation. The basic helix-loop-helix hemopoietic transcriptional regulator TAL1 (formerly SCL) is required for terminal differentiation of red blood cells. To gain insight into TAL1 function and mechanisms of action in erythropoiesis, we performed ChIP-sequencing and gene expression analyses from primary fetal liver erythroid cells. We show that TAL1 coordinates exp  ...[more]

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