Assessment of Histone Tail Modifications and Transcriptional Profiling During Colon Cancer and Role of fish oil/pectin Diet Against Colon Carcinogen. Rattus norvegicus

In an effort to gain insight into the extensive dimension of post-translational modifications in histones (including H3K4me3 and H3K9ac) and elucidate the chemoprotective impact of dietary bioactive compounds on transcriptional control in a colon cancer preclinical model, we generated high-resolution genome-wide RNA (RNA-Seq) and “chromatin-state” (H3K4me3-seq and H3K9ac-seq) maps for intestinal (epithelial colonocytes) crypts in rats treated with a colon carcinogen and fed bioactive (i) fish oil (ii) butyrate (in the form of a fermentable fiber a rich source of SCFA), (iii) a combination of fish oil plus butyrate or (iv) control diets. Poor correlation was observed between differentially transcribed (DE) and enriched genes (DERs) at multiple epigenetic levels in fat x fiber dietary combinations and in the presence/absence of carcinogen. We also demonstrated that the combinatorial diet (fish oil + pectin) was synergistically chemoprotective, and uniquely affected epigenetic profiles in the intestinal epithelium, e.g., upregulating lipid catabolism and beta-oxidation associated genes. Overall design: Examination of 2 different histone modifications in rat colonocytes in a 2x2x2 factorial study cancer x oil x fiber

为深入解析组蛋白（histones）广泛的翻译后修饰（涵盖H3K4me3与H3K9ac），并阐明膳食生物活性化合物对结肠癌临床前模型（colon cancer preclinical model）中转录调控的化学预防作用，本研究对经结肠致癌物处理、并喂食四种膳食的大鼠肠隐窝上皮结肠细胞（epithelial colonocytes），生成了高分辨率全基因组RNA测序（RNA-Seq）及"染色质状态（chromatin-state）"图谱（含H3K4me3-seq与H3K9ac-seq）。四种膳食分别为：(i) 鱼油膳食；(ii) 丁酸盐膳食（丁酸盐由富含短链脂肪酸（short-chain fatty acids, SCFA）的可发酵膳食纤维提供）；(iii) 鱼油+丁酸盐联合膳食；(iv) 空白对照膳食。
在脂肪×膳食纤维膳食组合及致癌物存在/缺失的实验条件下，多个表观遗传水平上的差异转录基因（DE）与富集基因（DERs）之间相关性较弱。
本研究同时证实，鱼油+果胶联合膳食具有协同化学预防作用，并可特异性重塑肠上皮（intestinal epithelium）的表观遗传谱（epigenetic profiles），例如上调脂质分解代谢与β氧化相关基因。
实验设计概述：采用2×2×2析因设计，针对大鼠结肠细胞中的2种不同组蛋白修饰展开检测，实验因素组合为致癌物×鱼油×膳食纤维。