Genome binding/occupancy profiling by high throughput sequencing
Summary
Cohesin shapes the chromatin architecture, including enhancer-promoter interactions. Its components, especially STAG2 but not its paralogue STAG1, are frequently mutated in myeloid malignancies. To elucidate the underlying mechanisms of leukemogenesis, we comprehensively characterized genetic, epigenetic, transcriptional, and chromatin conformational changes in acute myeloid leukemia (AML) patient samples. Specific loci displayed altered cohesin occupancy, gene expression and local chromatin activation which were not compensated by STAG1. These changes could be linked to disrupted spatial chromatin looping in cohesin-mutated AMLs. We performed complementary depletion of STAG2 or STAG1 in primary human hematopoietic progenitors (HSPCs). We detected effects overlapping STAG2-mutant AML-specific changes following STAG2 knockdown, not invoked by depletion of STAG1. STAG2-deficient HSPCs displayed impaired differentiation capacity and maintained HSPC-like gene expression. This work establishes STAG2 as a key regulator of chromatin contacts, gene expression and differentiation in the hematopoietic system and identifies candidate target genes that may be implicated in human leukemogenesis.
Overall design
To determine the impact of cohesin loss on genome-wide cohesin subunit (RAD21/STAG2/STAG1) occupancy and distribution as well as to define active enhancer/promotor (H3K27ac) and CTCF sites, we performed ChIP-seq on STAG2-mutant, RAD21-mutant and cohesin wildtype AML patients samples. In addition we aslo used primary CD34+ cord-blood derived HSPC cultures of independent donors electroporated with siRNAs for knockdown targeting either STAG2, STAG1, RAD21. As controls a non-targeting (luciferase-specific) control siRNA (siCtrl) transfected samples were used. HSPCs were additonally used to define Mediator binding sites (MED12) and to assay chromatin-binding of the transcription factor PU.1.
*************************************************************** Due to patient privacy concerns, raw sequencing data of adult AML patients is deposited in the European Genome Archive (EGA) under study number EGAS00001007405. Due to special legal and ethical privacy concerns regarding newborns, raw sequencing data of cord blood HSPC samples cannot be deposited in any online repository. ***************************************************************
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