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Accession PRJCA030053
Title Epigenetic Basis for the Establishment of Ruminal Tissue-Specific Functions
Relevance Agricultural
Data types Epigenomics
Transcriptome or Gene expression
Raw sequence reads
Genome sequencing
Organisms Bos taurus
Description While DNA methylation in other tissues can be approximated through model species, the dynamic distribution and regulatory significance of DNA methylation in the rumen, a unique organ in ruminant, remain largely unknown. Here, we employed whole-genome bisulfite sequencing (WGBS), transcriptomics, and histone modification data to compare fetal and adult stages of bovine rumen with other tissues, including pluripotent stem cells (PSCs) approximating pre-implantation embryos. We found extensive methylation differences, including CG methylation (mCG) and non-CG methylation (mCH; H represents A, C and T) between the rumen at fetal and adult stages and other tissues and PSCs. These differentially methylated regions (DMRs) are closely associated with other epigenetic regulatory components, such as transcription factors (TFs) and histone modifications. These DMRs can also combine to form large hypo CG-DMRs to regulate a cluster of functionally related genes. We elucidated the reasons for morphological and functional differences between fetal and adult rumen at the epigenetic level and the interactions between epigenetic modifications and gene expression. This study highlights the differences in methylation patterns between the rumen and other tissues during development and the role of DNA methylation in controlling gene expression and establishing tissue-specific functions.
Sample scope Multiisolate
Release date 2024-09-10
Grants
Agency program Grant ID Grant title
Education Department of Inner Mongolia Autonomous Region General Program NMGIRT2204 Research on the Maintenance Mechanism and Differentiation Ability of Pluripotent Stem Cells in Grassland Livestock
National Natural Science Foundation of China (NSFC) International (Regional) Cooperation and Exchange Program 32160172 Establishing an efficient differentiation system for inducing SSCs formation in bovine EPSCs using PLZF reporting system
Accessions in other database
Accession Database name
GSE264346 NCBI
Submitter jing wang (nnlrl@mail.imu.edu.cn)
Organization Inner Mongolia University
Submission date 2024-09-10

Project Data

Resource name Description
BioSample (48)  show -
GSA (5) -
CRA019132 Epigenetic Basis for the Establishment of Ruminal Tissue-Specific Functions (RNA-seq)
CRA019386 Epigenetic Basis for the Establishment of Ruminal Tissue-Specific Functions
CRA018995 Epigenetic Basis for the Establishment of Ruminal Tissue-Specific Functions (BS-seq)
CRA018940 Epigenetic Basis for the Establishment of Ruminal Tissue-Specific Functions (cut&tag-seq)
CRA018938 Epigenetic Basis for the Establishment of Ruminal Tissue-Specific Functions (ATAC-seq)