Regulation of intestinal genes by CDX2 and other tissue-restricted transcription factors

CDX2 和其他组织限制性转录因子对肠道基因的调节

• 批准号: 10222655
• 负责人: Ramesh A Shivdasani
• 金额: $ 38.22万
• 依托单位: DANA-FARBER CANCER INST
• 依托单位国家: 美国
• 财政年份: 2010
• 资助国家: 美国
• 起止时间: 2010-09-01 至 2023-02-28
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/10222655
• 关键词: Active Sites; Address; Adult; Affect; Barrett Esophagus; Biochemical; CDX2 gene; Cells; Chromatin; Colorectal Cancer; Data Set; Dependence; Deposition; Development; Digestive System Disorders; Disease; Distant; Ectopic Expression; Elements; Embryo; Endoderm; Enhancers; Enterocytes; Epithelial; Functional disorder; Funding; Gastrointestinal tract structure; Gene Expression; Gene Expression Regulation; Genes; Genetic; Genomics; Goals; Growth; HNF4A gene; Health; Histones; Hormonal; Immunoprecipitation; Inflammatory Bowel Diseases; Intestinal Cancer; Intestines; Knowledge; Life; Maps; Metabolic; Molecular; Mus; Nucleic Acid Regulatory Sequences; Organ; Process; Proliferating; Property; Proteins; Regulation; Regulator Genes; Repression; Role; Site; Specificity; Stomach; Structure; Technology; Testing; Time; Tissues; Transactivation; Transcript; Villus; Wild Type Mouse; crypt cell; epigenome; experimental study; fetal; gastrointestinal epithelium; gene complementation; gene repression; hepatic nuclear factor 1; improved; in vivo; innovation; intestinal crypt; intestinal epithelium; intestinal villi; mRNA Expression; novel; novel therapeutics; progenitor; recruit; spatiotemporal; transcription factor; transcription factor CDX2

Project Description Common disorders of the digestive tract, such as Inflammatory Bowel Disease, colorectal cancer and Barrett's esophagus reflect profound epithelial dysfunction and gene dysregulation. Improved treatments require better understanding of the basis for intestine-specific gene control. Certain transcription factors (TFs) – CDX2, HNF4 and HNF1 – act at the distant enhancers of genes that define gut epithelial identity and function, but mechanisms of enhancer assembly, specificity, and activity are not well understood. Nor is it known how chromatin and TF dynamics in gut endoderm allow the emergence of distinctive digestive epithelia. This proposal addresses some of these fundamental questions in mouse intestinal cells in vivo. Among thousands of cis-elements that control intestinal genes, we identify a new class of tissue-specific enhancers that require CDX2 to exclude the repressive histone mark H3K27me3 from large genomic domains; H3K27me3 was not previously implicated at distant enhancers in adult tissues. These findings ascribe a novel, unexpected function for CDX2 at `anti-repressive' Type 1A enhancers that control the most quantitatively vulnerable genes in Cdx2-/- villus cells. Specific Aim 1 addresses the requirements and mechanisms of these novel enhancers. We propose genetic and biochemical experiments to test two central hypotheses: (a) that ~500 key intestinal loci are particularly susceptible to repression by virtue of extensive local deposition of H3K27me3, and (b) that CDX2 recruits the specific H3K27 demethylases KDM6A/B to oppose that locus-wide effect. We will use Eed-/- intestines, which lack methylated H3K27, to determine whether this feature is causally repressive and to attempt rescue of the genes most perturbed in Cdx2-/- intestines. Because Type 1A enhancers show a large difference in H3K27me3 levels between enterocyte progenitors in intestinal crypts and terminally mature enterocytes along the villi, we propose studies to test the hypothesis that this repressive mark limits high expression of enterocyte genes in replicating crypt cells. Specific Aim 2 considers the developmental origins and determinants of intestinal enhancers and asks why certain genomic domains acquire tissue-specific H3K27me3. This Aim builds on our discovery that nascent enhancers for all digestive epithelia are initially accessible throughout the early endoderm and that tissue-specific sites later strengthen in each organ while inappropriate enhancers are shut down. We will test the hypothesis that regions dependent on Type 1A enhancers in the adult intestine are the vestiges of enhancers that were used in development. We will also test the hypotheses that: (a) unless regional TFs reinforce open endodermal chromatin, enhancers shut down in a rostral-caudal wave, and (b) the state of chromatin at any time determines how the developing intestine responds to absence of CDX2. This proposal thus applies innovative state-of-the-art approaches to pursue exciting discoveries and address fundamental questions about intestinal gene regulation in vivo.

项目描述 消化道的常见疾病，例如炎症性肠病，结直肠癌和 巴雷特的食道反映了深刻的上皮功能障碍和基因失调。改进的治疗方法 需要更好地理解特定肠道基因控制的基础。某些转录因子 （TFS） - CDX2，HNF4和HNF1 - 在定义肠上皮身份的基因的遥远增强子上起作用 和功能，但是增强子组装，特异性和活性的机制尚不清楚。也不 是否知道肠内胚层中的染色质和TF动力学如何允许出现独特的消化 上皮。该建议解决了体内小鼠肠细胞中的一些基本问题。 在控制肠基因的数千种顺式元素中，我们确定了一类新的组织特异性 需要CDX2从大基因组中排除反射性组蛋白标记H3K27me3的增强剂 域； H3K27me3以前在成人组织的遥远增强子上没有实施。这些发现 在“反抑制” 1A型增强子处的CDX2的新颖，出乎意料的功能，控制最多 CDX2 - / - 绒毛细胞中的定量脆弱基因。具体目标1解决了要求 这些新型增强剂的机制。我们提出了遗传和生化实验，以测试两个 中央假设：（a）〜500个关键肠道局部尤其容易受到表达的影响 H3K27me3的广泛局部沉积，（b）CDX2募集了特定的H3K27脱甲基酶 kdm6a/b反对该基因座的效应。我们将使用缺乏甲基化H3K27的EED - / - 肠 确定此功能有时是否受到压制，并尝试营救最受扰动的基因 CDX2 - / - 肠。因为类型1a增强剂在H3K27me3水平上显示很大的差异 我们提出 研究该假设的研究是，这种反射标记限制了肠肠细胞基因的高表达 复制隐窝细胞。特定目的2考虑了发育起源，并确定肠道 增强剂并询问为什么某些基因组域获得组织特异性H3K27ME3。这个目标是基于 我们发现，最初可以在整个早期访问所有消化性上皮的新生增强剂 内胚层和组织特异性部位后来在每个器官中加强，而不适当的增强剂是 关闭。我们将检验以下假设：成人肠中取决于1A型增强子的区域 是开发中使用的增强剂的痕迹。我们还将检验：（a）的假设 除非区域TF加强开放性内皮染色质，否 （b）染色质的状态随时确定如何发展的肠道反应如何 CDX2。因此，该提案采用创新的最先进方法来购买令人兴奋的发现和 解决有关体内肠道基因调节的基本问题。