OrthReg: a tool to predict cis-regulatory elements based on cross-species orthologous sequence conservation

Cis-regulatory elements play an important role in the development of traits and disease in organisms (Ma et al., 2020; Woolfe et al., 2005) and their annotation could facilitate genetic studies. The Encyclopedia of DNA Elements (ENCODE) (Davis et al., 2018) and Functional Annotation of Animal Genome...

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Bibliographic Details
Published in:Dōngwùxué yánjiū 2020-07, Vol.41 (4), p.471-475
Main Authors: Ma, Yun-Fei, Huang, Cui-Ping, Lu, Fang-Ru, Li, Jin-Xiu, Han, Xu-Man, Adeola, Adeniyi C, Gao, Yun, Deng, Jia-Kun, Xiev, Hai-Bing, Zhang, Ya-Ping
Format: Article
Language:English
Subjects:
Annotations
Bibliographic information
Binding sites
Chromosomes
Conserved sequence
Consortia
Datasets
Deoxyribonucleic acid
DNA
Domestication
Encyclopaedias
Encyclopedias
Genomes
Hogs
Nucleotide sequence
Organisms
Regulatory sequences
Species
Transcription factors
Wildlife conservation
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Summary:Cis-regulatory elements play an important role in the development of traits and disease in organisms (Ma et al., 2020; Woolfe et al., 2005) and their annotation could facilitate genetic studies. The Encyclopedia of DNA Elements (ENCODE) (Davis et al., 2018) and Functional Annotation of Animal Genomes (FAANG) (FAANG Consortium et al., 2015) offer pioneering data on regulatory elements in several species. Currently, however, regulatory element annotation data remain limited for most organisms. In this study, we developed a tool (OrthReg) for annotating conserved orthologous cis-regulatory elements in targeted genomes using an annotated reference genome. Cross-species validation of this annotation tool using human and mouse ENCODE data confirmed the robustness of this strategy. To identify regulatory elements in genomes, the ENCODE and FAANG projects were launched to annotate genomes in several organisms. However, regulatory element annotation is still very limited for other organisms (except for humans and mice), which has hindered genetic studies from exploring the role of regulatory variants in the development of diverse traits
ISSN:0254-5853
DOI:10.24272/j.issn.2095-8137.2020.099