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

Abstract

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/).

Graphical abstract

Keywords

tissue specific regulatory network / non-coding element / plateau zokor / non-model species

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ACKNOWLEDGEMENTS

ZokorDB is supported by the Strategic Priority Research Program of the Chinese Academy of Sciences (No. XDB13000000). The authors are also supported by the National Natural Science Foundation of China (NSFC) (Nos. 11871463, 11871462, 61671444 and 61621003). We thank all the lab members for discussions on data collection, genome alignment, annotation, GRN reconstruction. We thank Dr. Yilei Wu and his group for help on database design and management.

COMPLIANCE WITH ETHICS GUIDELINES

The authors Jingxue Xin, Junjun Hao, Lang Chen, Tao Zhang, Lei Li, Luonan Chen, Wenmin Zhao, Xuemei Lu, Peng Shi and Yong Wang declare that they have no conflicts of interest.ƒThis article does not contain any studies with human or animal subjects performed by any of the authors

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