Fig 1.
Distribution of CTCF and cohesinSA-1 occupancy and co-occupancy in human primary hematopoietic stem and progenitor cell (HSPC) and primary erythroid cell chromatin.
ChIP-seq was performed with antibodies against CTCF and cohesinSA-1 in human primary hematopoietic stem and progenitor cell (HSPC) and primary erythroid cell chromatin. Sites of protein occupancy were determined by MACS. The human genome was portioned into seven bins relative to known genomic features associated with RefSeq genes. The percentage of the human genome represented by each bin was color coded, and the distribution of peaks of CTCF and cohesinSA-1 in each bin graphed on the color coded bar. Abbreviations: TSS: transcriptional start site; TES: transcriptional end site. Intergenic: >50Kb from a gene. 5’ distal 1-50Kb upstream of TSS. Promoter: within 1Kb of TSS. Downstream: within 1 Kb of TES. 3’ Distal 1-50Kb downstream of TES.
Table 1.
Comparison of CTCF binding sites in hematopoietic stem and progenitor cell (HSPC) and erythroid cell chromatin with CTCF binding in multiple cell types.
Fig 2.
Invariant and cell type-specific CTFC sites.
Patterns of CTCF occupancy in HSPC and erythroid cell chromatin were compared to CTCF occupancy in several human ENCODE ChIP-seq data sets, including fibroblast, keratinocyte, endothelial, myocyte, monocyte, lymphocyte, embryonic stem (ES) cell, erythroid and HSPC cells. A. At the TAL1 locus, a 3’ site of invariant CTCF binding marked by the rectangle is present in all cell types. Two sites of erythroid-specific CTCF binding, denoted by the arrows, are present 5’ of the gene. Corresponding RNA-seq tracks in HSPC and erythroid cells are shown at the top. Genomic coordinates: Chr1:47,600–47,700. B. At the UBTF and SLC4A1 loci, there are 2 sets of invariant CTCF binding, marked by rectangles, 3’ of the UBTF locus, present in all cell types. One site of erythroid-specific CTCF binding, denoted by the arrows, are present 5’ of the SLC4A1 locus. Corresponding RNA-seq tracks in HSPC and erythroid cells are shown at the top. Genomic coordinates: Chr17:42,280–42,340.
Fig 3.
Gene expression and CTCF occupancy.
Gene expression levels in primary human HSPC and erythroid cell mRNA were correlated with sites of CTCF occupancy by class within 1kb of the transcription start site.
Table 2.
Repressive chromatin domains and CTCF and cohesinSA-1occupancy at domain boundaries.
Fig 4.
Repressive chromatin domains and CTCF occupancy.
Representative integrated genome viewer (IGV) views of CTCF occupancy, repressive chromatin domains marked by H3K27me3 enrichment, and gene expression determined by RNA-seq in erythroid cells. A. Repressive chromatin domains marked by CTCF occupancy at their boundaries flank the SEC31B, NDUFB8, and HIF1AN genes. These 3 genes are expressed in erythroid cells, while the WNT8B gene, located in a repressive chromatin domain, is not. Genomic coordinates: Chr10:102,220–102,380. B. Repressive chromatin domains marked by CTCF occupancy at their boundaries flank the TROAP and C1QL4 genes. These 2 genes are expressed in erythroid cells, while the flanking PRPH and DNACJ22 genes, located in flanking repressive chromatin domains, are not. Genomic coordinates: Chr12:49,680–49,760.
Fig 5.
Repressive chromatin domains and CTCF-cohesinSA-1 co-occupancy.
Representative integrated genome viewer (IGV) views of CTCF and cohesinSA-1 occupancy, repressive chromatin domains marked by H3K27me3 enrichment, and gene expression determined by RNA-seq in HSPC and erythroid cells. Multiple tissue-specific “exon 1s” are found at the 5’ end of the ANK1 gene which all join in frame to exon 2, creating cDNA transcripts with unique 5’ ends. In erythroid cells (top), the sequence surrounding and including a neural-specific ANK1 exon 1, located 5’ of the erythroid exon 1, is in a region of repressive chromatin, heavily modified by H3K27me3. At the boundary of this repressive chromatin domain are a pair of CTCF/cohesinSA-1 sites, present in erythroid but not HSPC chromatin, followed by the transcribed exons of the ANK1 gene. ANK1 is not expressed in HSPCs and this entire region is modified by H3K27 trimethylation (bottom). Genomic coordinates: Chr8:41,760–41,580.