Mutations in genes involved in DNA methylation (DNAme; e.g.,
TET2, DNMT3A)
, are frequently observed in hematological malignancies
1
–
3
and clonal hematopoiesis
4
,
5
. Applying single-cell sequencing to murine hematopoietic stem and progenitor cells, we observed that these mutations disrupt hematopoietic differentiation, causing opposite shifts in the frequencies of erythroid vs. myelo-monocytic progenitors upon
Tet2
or
Dnmt3a
loss. Notably, these shifts trace back to transcriptional priming skews in uncommitted hematopoietic stem cells (HSCs). To reconcile genome-wide DNAme changes with specific erythroid vs. myelo-monocytic skews, we provide evidence in support of differential sensitivity of transcription factors due to biases in CpG enrichment in their binding motif. Single-cell transcriptomes with targeted genotyping showed similar skews in transcriptional priming of
DNMT3A
-mutated human clonal hematopoiesis bone marrow progenitors. These data show that DNAme shapes the hematopoietic differentiation topography, and support a model in which genome-wide methylation changes are transduced to differentiation skews through biases in transcription factor binding-motif CpG enrichment.
SUMMARY
Eukaryotic chromosomes are partitioned into topologically associating domains (TADs) that are demarcated by distinct insulator-binding proteins (IBPs) in Drosophila. Whether IBPs regulate specific long-range contacts and how this may impact gene expression remains unclear. Here we identify ‘indirect peaks’ of multiple IBPs, that represent their distant sites of interactions through long-range contacts. Indirect peaks depend on protein-protein interactions among multiple IBPs and their common co-factors, including CP190, as confirmed by high-resolution analyses of long-range contacts. Mutant IBPs unable to interact with CP190 impair long-range contacts as well as the expression of hundreds of distant genes that are specifically flanked by indirect peaks. Regulation of distant genes strongly correlates with RNAPII pausing, highlighting how this key transcriptional stage may trap insulator-based long-range interactions. Our data illustrate how indirect peaks may decipher gene regulatory networks through specific long-range interactions.
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