Research On Sequence Recognition And Transcriptional Regulation Of Conserved And Specific Human Enhancer

The metabolism of individuals is indispensable from the complex transcriptional regulation of genes and genetic mechanisms.With the rapid development of highthroughput sequencing technology,the success for genome sequencing allows us to further explore the regulatory mechanisms behind the sequences.It has been found that the regulation of gene expression in eukaryotic cells is affected by a variety of factors,such as the coordination and cooperation between Transcription Factor,enhancers and DNA transcriptional-related enzymes,which constitute precise and efficient spatialtemporal expression of genes.In recent years,the rapid development of threedimensional genomics has promoted the researches on the identification of genomewide epigenetic modification and regulatory elements and transcriptional regulation of their involvement in gene expression.In this thesis,we take enhancers,an important regulatory element with epigenetic modification,as the main research object.And based on the evolution of enhancer sequences and starting from the three-dimensional interaction and transcriptional regulation of chromatin,the transcriptional regulation process of enhancers on the genome is explored from the relationship between enhancers and transcription factors,enhancers and target genes.The main results are as follows:1.In this study,the sequence of enhancers from human mammary epithelial cells was transformed in the whole genome of 15 mammals,and the sequences were divided into conserved and specific enhancers.It was found that the homologous sequence of the conserved human enhancer sequence can appear in more than 10 species;the conserved enhancers and the specific enhancers have obvious phastCons conservative score differences.And the more homologous sequences an enhancer has on other species,the higher the conservation of the enhancer sequence in this region,and vice versa.2.In order to explore the role of enhancers in transcriptional regulation,we identified the enhancers-RNA PII target genes by finding the regulation interaction regions between enhancers and the regions around gene TSS using RNA PII-mediated ChIA-PET data.Then,using 485 transcription factor binding sites data to find the transcription factor enrichment in the enhancer region,we found that some enhancerRNA PII target genes are transcription factor encoding genes,for which the binding sites are present in the enhancer region.Thus,an enhancer-associated transcription factor self-regulatory circuitry was found.3.Functional annotation for these self-regulating transcription factors revealed that they are mostly enriched in the molecular functions and biological processes of the RNA PII core promoter,in which MYC,JUN,NCOA3 and SP1 were related to the estrogen signaling pathway of breast cancer,and the coding genes of these transcription factors were regulated by multiple enhancers.Further analysis of gene expression levels with clinical breast cancer patients in TCGA database found that the up-regulated enhancer target gene is associated with RNA polymerase I promoter opening and transcription,cell meiosis and recombination.In addition,we also found that the expression of 14 breast cancer-associated tumor suppressor genes was significantly down-regulated.This study discussed the transcriptional regulation mechanisms between enhancers and transcription factors,and found an enhancer-associated regulatory circuitry in breast cancer,and obtained transcriptional regulation of these enhancers under different evolutionary mechanisms,providing a new exploration for the transcriptional regulation of enhancers and transcription factors in breast cancer.