Integrative Alignments Of Eight Epi-genomic Modifications Regulating Transcription In Three Types Of Swine Cells

Swine production is of great importance for guaranteeing china economy development and food supply.Meanwhile,due to its high genome similarity with human being,pigs are widely used as animal model to study human disease.Consequently,figuring out the functional elements of its genome is of great significance to reveal the growth pattern of pigs and the medical application.Since the launch of the human and mouse ENCODE program,researchers have sequenced human being and mouse genome in depth and annotated functional elements in its genome comprehensively.But similar work is scarce in pigs,there is an urgent demand to fill the gap of pig epigenomics.This experiment employed the pig alveolar macrophage cell line 3D4/21,the porcine primary alveolar cell PAM and the porcine kidney epithelial cell line PK-15 as model to conduct epigenetic study in order to provide fundamental data for pig epigenetic database and establish basis for further work.The main results were as following:(1)We decipher whole-genome expression profile based on RNA-seq data of3D4/21,PAM and PK-15 cells.We identified co-expression genes and cell-specific expression genes and related biological processes.Results showed that co-expression mainly enriched in basic biological processes such as the formation of cellular ribosome structures while majority of cell specific expression genes are related to specific cell functions.(2)We identified epigenetic modification differences of 3D4/21,PAM,and PK-15 cells using Ch IP-seq data which was based on eight classic modification markers including H3K4me1,H3K4me3,H3K27me3,H3K27 ac,H3K9me3,H3K36me3,POL2 and CTCF.Therefore,in combination with RNA-seq data,we described profile of gene expression and four histone modification patterns from genome-level and analyzed relationship between gene expression and epigenetic modification.Results showed that H3K4 me and H3K27 ac modifications were largely enriched in transcription start position and gene body region of active gene.Specifically,H3K27me3 histone modification was associated with silenced genes.H3K4me1 modification that characterizes the enhancer region exhibited enormous deletion in the gene body region.(3)Further analysis showed that high gene expression was closely associated with POL2,H3K4me3,H3K27 ac modifications while H3K27me3 and H3K9me3 modifications mainly marked chromatin inhibitory regions.What's more,gene activity was also regulated by gene three dimensions structure(e.g:CTCF TAD)and regulatory elements such as enhancers.(4)Chromatin status of 3D4/21,PAM and PK-15 cells was classified based on six histone modifications.Pig genome was divided into fifteen biologically functional segments which provided reference for identifying histone-based pig whole-genome functional elements in the future.(5)We successfully identified enhancers differences in 3D4/21 cells under distinct status across pig whole genome using STARR-seq technology.We also verified the accuracy of results.In summary,this study explored the regulatory mechanism of epigenetic factors on gene expression through RNA-seq and Ch IP-seq data.The application of STARR-seq technology also extended our weapon to identify enhancers.