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Animal-eRNAdb: a comprehensive animal enhancer RNA database
Weiwei Jin1, Guanghui Jiang1, Yanbo Yang1
1Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan 430070, P.R. China.
Nucleic Acids Research
|September 22, 2021
Summary
Enhancer RNAs (eRNAs), non-coding RNAs from active enhancers, are crucial for gene regulation. This study comprehensively characterizes animal eRNAs, revealing their expression, regulation, and functions, and introduces a new database for further research.
Area of Science:
- Genomics
- Non-coding RNA Biology
- Comparative Genomics
Background:
- Enhancer RNAs (eRNAs) are transcribed from active enhancers and serve as key non-coding RNAs in gene regulation.
- While eRNAs are increasingly studied in humans, their landscape, regulatory networks, and functions in animals remain largely unexplored.
- Understanding animal eRNAs is crucial for deciphering complex traits and biological processes.
Purpose of the Study:
- To systematically characterize enhancer RNAs (eRNAs) across multiple animal species.
- To investigate the evolutionary conservation, regulatory associations, and trait-related functions of animal eRNAs.
- To develop a comprehensive database (Animal-eRNAdb) for facilitating eRNA research.
Main Methods:
- Systematic characterization of 185,177 eRNAs from 5085 samples across 10 species using RNA sequencing data mapped to enhancer regions.
- Analysis of sequence similarity for evolutionary conservation assessment.
- Identification of associations between eRNAs, transcription factors (TFs), and nearby genes.
- Characterization of trait-related eRNAs for functional insights.
Main Results:
- A large-scale dataset of 185,177 eRNAs from 5085 animal samples was compiled and analyzed.
- Evolutionary conservation patterns and sequence similarities of eRNAs across species were investigated.
- Potential regulators (TFs) and target genes for identified eRNAs were predicted.
- Trait-related eRNAs were characterized, shedding light on their roles in biological processes.
- The Animal-eRNAdb database was established, providing a resource for accessing and analyzing eRNA data.
Conclusions:
- This study provides a comprehensive characterization of eRNAs in various animal tissues and species.
- The findings elucidate the regulatory networks and potential functions of animal eRNAs.
- The Animal-eRNAdb database serves as a valuable resource to accelerate the exploration of eRNA functions and mechanisms in animals.
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