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

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. Overall design: 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.