Quantitative classification of chromatin dynamics reveals regulators of intestinal stem cell differentiation

Abstract

Intestinal stem cell (ISC) plasticity is thought to be regulated by broadly-permissive chromatin shared between ISCs and their progeny. Here, we utilize a Sox9 EGFP reporter to examine chromatin across ISC differentiation. We find that open chromatin regions (OCRs) can be defined as broadly-permissive or dynamic in a locus-specific manner, with dynamic OCRs found primarily in loci consistent with distal enhancers. By integrating gene expression with chromatin accessibility at transcription factor (TF) motifs in context of Sox9 EGFP populations, we classify broadly-permissive and dynamic chromatin relative to TF usage. These analyses identify known and potential regulators of ISC differentiation via their association with dynamic changes in chromatin. We observe ISC expansion in Id3-null mice, consistent with computational predictions. Finally, we examine the relationship between gene expression and 5hydroxymethylcytosine (5hmC) in Sox9 EGFP populations, which reveals 5hmC enrichment in absorptive lineage specific genes. Our data demonstrate that intestinal chromatin dynamics can be quantitatively defined in a locus-specific manner, identify novel potential regulators of ISC differentiation, and provide a chromatin roadmap for further dissecting the role of cis regulation of cell fate in the intestine. Tetteh et al., 2016). The genetic mechanisms that allow IECs to adopt metastable differentiated fates while exhibiting facultative ISC function are not fully understood.Chromatin landscapes consist of histone post-translational modifications, DNA modifications, and higher-order structural organization, and are known to exert regulatory control on cell fate.

A Planar Culture Model of Human Absorptive Enterocytes Reveals Metformin Increases Fatty Acid Oxidation and Export

“…The absorptive lineage is the default pathway taken by progenitor cells unless the master regulator of secretory lineage fate, Atoh1, is expressed. 54 Chromatin states across the genome are associated with hardwiring of some lineagespecification programs, 73,74 and dynamic chromatin states have been described as cells move through ISC to secretory and absorptive lineage states. 73,74 Data presented here show that removal of ISC maintenance factors from ISC monolayers promote a stereotypical absorptive enterocyte lineage program in an epithelial-autonomous manner, suggesting human absorptive enterocytes are hardwired to undergo progressive maturation over time.…”

Transcriptomics informs design of a planar human enterocyte culture system that reveals metformin enhances fatty acid export

“…The absorptive lineage is the default pathway taken by progenitor cells unless the master regulator of secretory lineage fate, Atoh1, is expressed 55 . Chromatin states across the genome are associated with hardwiring of some lineage-specification programs 71,72 , and dynamic chromatin states have been described as cells move through ISC to secretory and absorptive lineage states 71,72 . Data presented here demonstrate that removal of ISC maintenance factors from ISC monolayers promote a stereotypical AE lineage program in an epithelial autonomous manner suggesting human AEs are hardwired to undergo progressive maturation over time.…”

LSD1 represses a neonatal/reparative gene program in adult intestinal epithelium

“…Adult ISCs give rise to all intestinal epithelial subtypes, and ISCs have a strikingly similar chromatin landscape compared to enterocytes (12,14). In contrast, the epigenetic makeup of secretory progenitors is distinguishable from ISCs and enterocytes (12,15), which was reversed upon irradiation when these secretory precursors dedifferentiate into ISCs (12). Three groups separately identified a crucial role for the polycomb repressive complex 2 (PRC2) in maintaining crypt physiology (16)(17)(18).…”