Genome-wide analysis of the rat colon reveals proximal-distal differences in histone modifications and proto-oncogene expression

Abstract

Since disease susceptibility of the intestine exhibits an anatomical bias, we propose that the chromatin landscape, especially the site-specific epigenetic differences in histone modification patterns throughout the colonic longitudinal axis, contributes to the differential incidence of site-specific pathology. To test this hypothesis, we assessed the chromatin structure associated with gene expression profiles in the rat proximal and distal colon by globally correlating chromatin immunoprecipitation next-generation sequencing analysis (ChIP-Seq) with mRNA transcription (RNA-Seq) data. Crypts were isolated from the proximal and distal colonic regions from rats maintained on a semipurified diet, and mRNA gene expression profiles were generated by RNA-Seq. The remaining isolated crypts were formaldehyde-cross-linked and chromatin immunoprecipitated with antibodies against H3K4me3, H3K9me3, and RNA polymerase II. Globally, RNA-Seq results indicate that 9,866 genes were actively expressed, of which 540 genes were differentially expressed between the proximal and distal colon. Gene ontology analysis indicates that crypt location significantly affected both chromatin and transcriptional regulation of genes involved in enterocyte movement, lipid metabolism, lymphatic development, and immune cell trafficking. Gene function analysis indicates that the PI3-kinase signaling pathway was regulated in a site-specific manner, e.g., proto-oncogenes, JUN, FOS, and ATF, were upregulated in the distal colon. Middle and long noncoding RNAs (lncRNAs) were also detected in the colon, including select lncRNAs formerly only detected in the rat nervous system. In summary, distinct combinatorial patterns of histone modifications exist in the proximal versus distal colon. These site-specific differences may explain the differential effects of chemoprotective agents on cell transformation in the ascending (proximal) and descending (distal) colon.

Dietary fat and fiber interactively modulate apoptosis and mitochondrial bioenergetic profiles in mouse colon in a site-specific manner

“…The significantly higher levels of OCR and ECAR in the distal colon may be explained by an increase in mitochondrial numbers, larger mitochondria, or enhanced function (Faris et al, 2014). The higher basal respiration profile observed in the distal colon is consistent with a recent report indicating that ATPase gene expression is higher in the distal colon vs. proximal colon (Triff et al, 2013). Based on our apoptosis findings, we hypothesized that the metabolic profile in intact crypts isolated from fish oil and pectin fed mice would be altered in a manner consistent with a more proapoptotic phenotype, e.g., increased proton leak (Ott et al, 2007; Green et al, 2014).…”

“…Since higher levels of apoptosis are considered protective against colon cancer (Qiu et al, 2010; Zhang et al, 2010), our dietary fish oil and pectin apoptosis data are consistent with previous reports indicating a reduction in colonic tumors (Chang et al, 1997). Although additional studies are needed to determine why dietary fat and fiber interactively modulate apoptosis and mitochondrial proton leak in a site-specific manner, it is not altogether unexpected based on the fact that the proximal and distal colon exhibit distinct gene-specific methylation profiles, transcriptional profiles, and molecular and clinical characteristics (Deng et al, 2008; Triff et al, 2013; Kaz et al, 2014). These differences may explain why subsite-specific responses to diet are observed (Hjartaker et al, 2013).…”

Comprehensive site-specific whole genome profiling of stromal and epithelial colonic gene signatures in human sigmoid colon and rectal tissue

“…"Functional enrichment" analysis was performed using Ingenuity Pathway Analysis (IPA) version 2.0 software (Ingenuity Systems, Redwood City, CA) (54). For this purpose, all differentially expressed genes (corrected P values Ͻ 0.05) for the two major comparisons with respect to tissue type and location were uploaded into three columns consisting of Illumina probe ID, t value (fold-change), and corrected P value data.…”

Nutrient-Gene Interaction in Colon Cancer, from the Membrane to Cellular Physiology

“…For example, histone H3 lysine 4 trimethylation is associated with active gene transcription, whereas H3 lysine 9 trimethylation is associated with repressed gene expression (18). We have demonstrated using rat colonic epithelial cells that there are differences in histone modification and proto-oncogene expression between proximal and distal colon (208). Studies are in progress to determine the effect of dietary fat and fiber composition on global histone posttranslational epigenetic programming in preclinical models of colon cancer.…”