Abstract

The liver plays a key role in metabolism and affects pig production. However, the functional annotation of noncoding regions of the pig liver remains poorly understood. We revealed the landscape of cis-regulatory elements and their functional characterization in pig liver. We identified 102,373 cis-regulatory elements in the pig liver, including enhancers, promoters, super-enhancers, and broad H3K4me3 domains, and highlighted 26 core transcription regulatory factors in the pig liver as well. We found similarity of cis-regulatory elements among those of pigs, humans, and cattle. Despite the low proportion of functionally conserved enhancers (~30%) between pig and human liver tissue, ~78% of the pig liver enhancer orthologues sequence could play an enhancer role in other human tissues. Additionally, we observed that the ratio of consistent super-enhancer-associated genes was significantly higher than the ratio of functionally conserved super-enhancers. Approximately 54% of the core regulation factors driven by super-enhancers were consistent across the liver from these three species. Our pig liver annotation and functional characterization studies provide a system and resource for noncoding annotation for future gene regulatory studies in pigs. Furthermore, our study also showed the high level functional conservation of cis-regulatory elements in mammals; it also improved our understanding of regulation function of mammal cis-regulatory elements.

Highlights

  • Several years after the complete genome sequencing, scientists have annotated the functional genomes of different species, including human [1,2,3], mice [4,5], Drosophila melanogaster and Caenorhabditis elegans [6,7,8]

  • Resources, such as Encyclopedia of DNA Elements (ENCODE) and Roadmap Epigenome Project, have shown that variants of cis-regulatory elements are related to physiological traits and diseases at considerable genome-wide association values [1,2,3]

  • We systematically identified the cis-regulatory elements, including enhancers, promoters, super-enhancers, broad H3K4me3 domain, and core transcription regulatory factors, in the pig liver tissue by using ChIP-seq data [14]

Read more

Summary

Introduction

Several years after the complete genome sequencing, scientists have annotated the functional genomes of different species, including human [1,2,3], mice [4,5], Drosophila melanogaster and Caenorhabditis elegans [6,7,8]. Economical traits in pigs [27,28,29]; the cis-regulatory elements, especially enhancers, active promoters, super-enhancers, and broad H3K4me domain, in pig liver tissue remain unknown. We systematically identified the cis-regulatory elements, including enhancers, promoters, super-enhancers, broad H3K4me domain, and core transcription regulatory factors, in the pig liver tissue by using ChIP-seq data [14]. These cis-regulatory elements were related to the physiological and metabolic processes of the liver. We compared the characteristics of cis-regulatory elements among pigs, humans, and cattle, and found that a certain number of elements are conserved between these three species

ChIP-Seq Data Processing
RNA-Seq Data Analysis
Identification of Cis-Regulatory Elements
Identification of Functionally Conserved Cis-Regulatory Elements
Differential Expression Analysis
Identification of Cis-Regulatory Elements in Pig Liver Tissue
Conservation of Cis-Regulatory Elements
Characteristics of Super and Typical Enhancer Crossing Three Mammals
Discussion
Full Text
Paper version not known

Talk to us

Join us for a 30 min session where you can share your feedback and ask us any queries you have

Schedule a call