Animal-eRNAdb: a comprehensive animal enhancer RNA database

Abstract

Enhancer RNAs (eRNAs) are a class of non-coding RNAs transcribed from enhancers. As the markers of active enhancers, eRNAs play important roles in gene regulation and are associated with various complex traits and characteristics. With increasing attention to eRNAs, numerous eRNAs have been identified in different human tissues. However, the expression landscape, regulatory network and potential functions of eRNAs in animals have not been fully elucidated. Here, we systematically characterized 185 177 eRNAs from 5085 samples across 10 species by mapping the RNA sequencing data to the regions of known enhancers. To explore their potential functions based on evolutionary conservation, we investigated the sequence similarity of eRNAs among multiple species. In addition, we identified the possible associations between eRNAs and transcription factors (TFs) or nearby genes to decipher their possible regulators and target genes, as well as characterized trait-related eRNAs to explore their potential functions in biological processes. Based on these findings, we further developed Animal-eRNAdb (http://gong_lab.hzau.edu.cn/Animal-eRNAdb/), a user-friendly database for data searching, browsing and downloading. With the comprehensive characterization of eRNAs in various tissues of different species, Animal-eRNAdb may greatly facilitate the exploration of functions and mechanisms of eRNAs.

Genome-wide analysis of transcription-coupled repair reveals novel transcription events inCaenorhabditis elegans

“…Our results reveal that a substantial portion of repair reads aligned to intergenic regions in XR-seq exhibit significant overlap with reads from short-and long-capped RNA sequencing (RNA-seq), far surpassing the capabilities of the polyadenylated RNA-seq 16 . Furthermore, the integration of epigenetic markers, chromatin states, enhancer RNA (eRNA) and long intergenic non-coding RNA (lincRNA) annotations supports the robust detection of intergenic nascent transcription by XR-seq [16][17][18][19] . In this article, we provide comprehensive results, which shed light on the transcription-coupled repair landscape in C. elegans and its relevance to intergenic transcription.…”

IAnimal: a cross-species omics knowledgebase for animals

“…However, it is still a major challenge to unite and utilize these very large data sets to systematically explore the genetic mechanisms that underlie the formation of a trait, especially in the domain of animal studies. Most existing animal databases, such as AnimalTFDB ( 48 ), AnimalQTLdb ( 7 ), Animal-ImputeDB ( 49 ) and Animal-eRNAdb ( 8 ), focus mainly on a single type of omics data. In this area of research, IAnimal is currently the most comprehensive multi-omics database, covering the largest number of animal species.…”

“…This strategy is very effective for solving specific problems, but it sacrifices the flexibility and reusability of data, and it indirectly wastes computing resources and time. For example, in Animal-eRNAdb ( 8 ), enhancer RNA (eRNA) expression level can be queried easily in all available individuals for a given species, but the data need to be re-downloaded, cleaned, and analyzed if the expression level in a particular subset of individuals needs to be fetched. Similarly, GVM ( 5 ) allows users to query genotype information easily on any particular marker site of all available individuals in a given species, but it does not support queries or computational operations at the individual level.…”

Animal-SNPAtlas: a comprehensive SNP database for multiple animals

“…With the rapid progress in animal genomic research in recent years, some animal-related databases have been developed, such as Animal-APAdb ( 31 ), Animal-eRNAdb ( 32 ), AnimalTFDB 3.0 ( 33 ) and Animal QTLdb ( 34 ). In the field of animal genetics, several databases were developed for specific domestic animals and aquaculture species.…”