Vemuri Kiranmayi, Kumar Sneha, Chen Lei, Verzi Michael P
Department of Genetics, Human Genetics Institute of New Jersey, Rutgers University, Piscataway, NJ 08854, USA.
School of Life Science and Technology, Key Laboratory of Developmental Genes and Human Disease, Southeast University, Nanjing 210096, China.
bioRxiv. 2023 Nov 10:2023.11.08.566322. doi: 10.1101/2023.11.08.566322.
Terminal differentiation requires a massive restructuring of the transcriptome. During intestinal differentiation, the expression patterns of nearly 4000 genes are altered as cells transition from progenitor cells in crypts to differentiated cells in villi. We identified dynamic recruitment of RNA Polymerase II (Pol II) to gene promoters as the primary driver of transcriptomic shifts during intestinal differentiation Changes in enhancer-promoter looping interactions accompany dynamic Pol II recruitment and are dependent upon HNF4, a pro-differentiation transcription factor. Using genetic loss-of- function, ChIP-seq and IP mass spectrometry, we demonstrate that HNF4 collaborates with chromatin remodelers and loop-stabilizing proteins and facilitates Pol II recruitment at hundreds of genes pivotal to differentiation. We also explore alternate mechanisms which drive differentiation gene expression and find pause-release of Pol II and post- transcriptional mRNA stability regulate smaller subsets of differentially expressed genes. These studies provide insights into the mechanisms of differentiation in a renewing adult tissue.
终末分化需要转录组进行大规模重组。在肠道分化过程中，随着细胞从隐窝中的祖细胞转变为绒毛中的分化细胞，近4000个基因的表达模式发生改变。我们确定RNA聚合酶II（Pol II）向基因启动子的动态募集是肠道分化过程中转录组变化的主要驱动因素。增强子-启动子环化相互作用的变化伴随着Pol II的动态募集，并依赖于促分化转录因子HNF4。通过基因功能缺失、染色质免疫沉淀测序（ChIP-seq）和免疫沉淀质谱分析，我们证明HNF4与染色质重塑因子和环稳定蛋白协同作用，并促进Pol II在数百个对分化至关重要的基因上的募集。我们还探索了驱动分化基因表达的其他机制，发现Pol II的暂停释放和转录后mRNA稳定性调节差异表达基因的较小子集。这些研究为成年再生组织中的分化机制提供了见解。
