ZokorDB: tissue specific regulatory network annotation for non-coding elements of plateau zokor

• Published in: Quantitative biology Vol. 8; no. 1; pp. 43 - 50
• Main Authors: Xin, Jingxue, Hao, Junjun, Chen, Lang, Zhang, Tao, Li, Lei, Chen, Luonan, Zhao, Wenmin, Lu, Xuemei, Shi, Peng, Wang, Yong
• Format: Journal Article
• Language: English
• Published: Beijing Higher Education Press 01.03.2020; Higher Education Press and Springer‐Verlag GmbH Germany, part of Springer Nature; John Wiley & Sons, Inc
• Subjects: Annotations; Binding sites; Bioinformatics; Biomedical and Life Sciences; Burrows; Carbon dioxide; Computational Biology/Bioinformatics; Computer Appl. in Life Sciences; Deoxyribonuclease; Genomes; Hypoxia; Kidneys; Life Sciences; Low temperature; Mathematical and Computational Biology; non-coding element; Non-coding RNA; non-model species; plateau zokor; Regulatory sequences; Research Article; Ribonucleic acid; RNA; tissue specific regulatory network; non-coding element; non-model species; tissue specific regulatory network; plateau zokor
• ISSN: 2095-4689; 2095-4697
• DOI: 10.1007/s40484-020-0195-4

Background: Plateau zokor inhabits in sealed burrows from 2,000 to 4,200 meters at Qinghai-Tibet Plateau. This extreme living environment makes it a great model to study animal adaptation to hypoxia, low temperature, and high carbon dioxide concentration. Methods: We provide an integrated resource, ZokorDB, for tissue specific regulatory network annotation for zokor. ZokorDB is based on a high-quality draft genome of a plateau zokor at 3,300 m and its transcriptional profiles in brain, heart, liver, kidney, and lung. The conserved non-coding elements of zokor are annotated by their nearest genes and upstream transcriptional factor motif binding sites. Results: ZokorDB provides a general draft gene regulatory network (GRN), i.e., potential transcription factor (TF) binds to non-coding regulatory elements and regulates the expression of target genes (TG). Furthermore, we refined the GRN by incorporating matched RNA-seq and DNase-seq data from mouse ENCODE project and reconstructed five tissue-specific regulatory networks. Conclusions: A web-based, open-access database is developed for easily searching, visualizing, and downloading the annotation and data. The pipeline of non-coding region annotation for zokor will be useful for other non-model species. ZokorDB is free available at the website (bigd.big.ac.cn/zokordb/).