Transcriptional, epigenetic and retroviral signatures identify regulatory regions involved in hematopoietic lineage commitment

Abstract

Genome-wide approaches allow investigating the molecular circuitry wiring the genetic and epigenetic programs of human somatic stem cells. Hematopoietic stem/progenitor cells (HSPC) give rise to the different blood cell types; however, the molecular basis of human hematopoietic lineage commitment is poorly characterized. Here, we define the transcriptional and epigenetic profile of human HSPC and early myeloid and erythroid progenitors by a combination of Cap Analysis of Gene Expression (CAGE), ChIP-seq and Moloney leukemia virus (MLV) integration site mapping. Most promoters and transcripts were shared by HSPC and committed progenitors, while enhancers and super-enhancers consistently changed upon differentiation, indicating that lineage commitment is essentially regulated by enhancer elements. A significant fraction of CAGE promoters differentially expressed upon commitment were novel, harbored a chromatin enhancer signature, and may identify promoters and transcribed enhancers driving cell commitment. MLV-targeted genomic regions co-mapped with cell-specific active enhancers and super-enhancers. Expression analyses, together with an enhancer functional assay, indicate that MLV integration can be used to identify bona fide developmentally regulated enhancers. Overall, this study provides an overview of transcriptional and epigenetic changes associated to HSPC lineage commitment, and a novel signature for regulatory elements involved in cell identity.

Editing a γ-globin repressor binding site restores fetal hemoglobin synthesis and corrects the sickle cell disease phenotype

“…ChIP experiments to detect H3K27Ac were performed as previously described (53). After 5 days of differentiation, −197 and AAVS1 HUDEP-2 bulk populations were collected for ChIP assays.…”

Gene therapy targeting haematopoietic stem cells for inherited diseases: progress and challenges

“…The general patterns of retroviral integration are now well understood 1 . Gammaretroviral vectors integrate primarily within transcriptional regulatory elements (such as promoters and enhancers 100,101 ), whereas lentiviral vectors integrate primarily within active transcription units [102][103][104] . The integration pattern varies from one retroviral genus to another, indicating that the mere exposure of different sequences in open chromatin does not account for differences in targeting [102][103][104][105][106][107][108] .…”

Interactions between Retroviruses and the Host Cell Genome

“…Genome-wide integration and association studies showed that the MLV bias for TSSs is just a consequence of a more general preference of MLV PICs for active regulatory elements, particularly enhancers and super-enhancers. 17 , 18 , 76 , 77 , 78 High-resolution studies carried out in human HSPCs and committed progenitors, 17 , 18 , 78 T cells, 20 , 79 and keratinocytes 77 indicated that MLV ISs are highly clustered and occur almost exclusively in regions carrying epigenetic signatures of transcriptionally active regulatory regions, such as acetylation of H3K27 and H3K9, and mono-, di- and tri-methylation of H3K4 ( Figure 1 ). Symmetrically, typical heterochromatic marks, such as H3K27me3 and H3K9me3, are significantly under-represented at these genomic loci.…”