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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