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

doi:10.1007/s40484-020-0195-4

Quantitative Biology

2020, Vol. 8

Issue (1): 43-50 https://doi.org/10.1007/s40484-020-0195-4

本期目录

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

Jingxue Xin^1,^6,⁷, Junjun Hao², Lang Chen¹, Tao Zhang³, Lei Li^1,^5,⁷, Luonan Chen^3,⁵, Wenmin Zhao⁴, Xuemei Lu^2,⁵, Peng Shi^2,⁵(

), Yong Wang^1,^5,⁷(

)

¹. CEMS, NCMIS, MDIS, Academy of Mathematics and Systems Science, Chinese Academy of Sciences, Beijing 100190, China
². State Key Laboratory of Genetic Resources and Evolution, Laboratory of Evolutionary and Functional Genomics, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
³. Key Laboratory of Systems Biology, Innovation Center for Cell Signaling Network, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
⁴. Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
⁵. Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming 650223, China
⁶. Department of Statistics, Department of Biomedical Data Science, Bio-X Program, Stanford University, Stanford, CA 94305, USA
⁷. University of Chinese Academy of Sciences, Beijing 100049, China

全文: PDF(888 KB) HTML

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/).

Key words： tissue specific regulatory network non-coding element plateau zokor non-model species

收稿日期: 2019-09-04 出版日期: 2020-03-23

Corresponding Author(s): Peng Shi,Yong Wang

引用本文:

. [J]. Quantitative Biology, 2020, 8(1): 43-50.
Jingxue Xin, Junjun Hao, Lang Chen, Tao Zhang, Lei Li, Luonan Chen, Wenmin Zhao, Xuemei Lu, Peng Shi, Yong Wang. ZokorDB: tissue specific regulatory network annotation for non-coding elements of plateau zokor. Quant. Biol., 2020, 8(1): 43-50.

链接本文:

https://academic.hep.com.cn/qb/CN/10.1007/s40484-020-0195-4
https://academic.hep.com.cn/qb/CN/Y2020/V8/I1/43

Tab.1

Fig.1

Tab.2

Fig.2

1	N. Fan, and Y. Shi, (1982) A revision of the zokors of subgenus Eospalax. Acta Theriol. Sin., 2, 183–199, in Chinese
2	N. Fan, and S. Gu, (1981) The structure of the tunnel system of the Chinese zokor. Acta Theriol. Sin., 1, 67–71, In Chinese
3	J. Zeng, , Z. Wang, and Z. Shi, (1984) Metabolic characteristics and some physiological parameters of the mole rat (Myospalax baileyi) in an alpine area. Acta Biol. Plat. Sin., 3, 163–171
4	B. K. Mcnab, (1984) The metabolism of fossorial rodents: a study of convergence. Ecology, 47, 712–733
5	O. Reichman,, S.C. Smith, (1990) Burrows and burrowing behavior by mammals.Curr. Mammal., 2,197–244
6	Y. M. Zhang, and J. Liu, (2003) Effects of plateau zokors (Myospalax fontanierii) on plant community and soil in an alpine meadow. J. Mammal., 84, 644–651 https://doi.org/10.1644/1545-1542(2003)084<0644:EOPZMF>2.0.CO;2
7	Y. Shao, , J. X. Li, , R. L. Ge, , L. Zhong, , D. M. Irwin, , R. W. Murphy, and Y. P. Zhang, (2015) Genetic adaptations of the plateau zokor in high-elevation burrows. Sci. Rep., 5, 17262 https://doi.org/10.1038/srep17262 pmid: 26602147
8	R. C. Hardison, (2000) Conserved noncoding sequences are reliable guides to regulatory elements. Trends Genet., 16, 369–372 https://doi.org/10.1016/S0168-9525(00)02081-3 pmid: 10973062
9	The ENCODE Project Consortium. (2012) An integrated encyclopedia of DNA elements in the human genome. Nature, 489, 57–74 https://doi.org/10.1038/nature11247 pmid: 22955616
10	F. Yue, , Y. Cheng, , A. Breschi, , J. Vierstra, , W. Wu, , T. Ryba, , R. Sandstrom, , Z. Ma, , C. Davis, , B. D. Pope, , et al. (2014) A comparative encyclopedia of DNA elements in the mouse genome. Nature, 515, 355–364 https://doi.org/10.1038/nature13992 pmid: 25409824
11	C. Trapnell, , B. A. Williams, , G. Pertea, , A. Mortazavi, , G. Kwan, , M. J. van Baren, , S. L. Salzberg, , B. J. Wold, and L. Pachter, (2010) Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat. Biotechnol., 28, 511–515 https://doi.org/10.1038/nbt.1621 pmid: 20436464
12	Z. Duren, , X. Chen, , R. Jiang, , Y. Wang, and W. H. Wong, (2017) Modeling gene regulation from paired expression and chromatin accessibility data. Proc. Natl. Acad. Sci. USA, 114, E4914–E4923 https://doi.org/10.1073/pnas.1704553114 pmid: 28576882
13	J. Butler, , I. MacCallum, , M. Kleber, , I. A. Shlyakhter, , M. K. Belmonte, , E. S. Lander, , C. Nusbaum, and D. B. Jaffe, (2008) ALLPATHS: de novo assembly of whole-genome shotgun microreads. Genome Res., 18, 810–820 https://doi.org/10.1101/gr.7337908 pmid: 18340039
14	Y. X. He, , X. B. Qi, , Ouzhuluobu, , S. Liu, , J. Li, , H. Zhang, , Baimakangzhuo, C. Bai, , , W. Zheng, Y. Guo, , et al. (2018) Blunted nitric oxide regulation in Tibetans under high-altitude hypoxia. Natl. Sci. Rev., 5, 516–529 https://doi.org/10.1093/nsr/nwy037
15	C. Burge, and S. Karlin, (1997) Prediction of complete gene structures in human genomic DNA. J. Mol. Biol., 268, 78–94 https://doi.org/10.1006/jmbi.1997.0951 pmid: 9149143
16	M. Stanke, , R. Steinkamp, , S. Waack, and B. Morgenstern, (2004) AUGUSTUS: a web server for gene finding in eukaryotes. Nucleic Acids Res., 32, W309–W312 https://doi.org/10.1093/nar/gkh379 pmid: 15215400
17	T. D. Wu, and C. K. Watanabe, (2005) GMAP: a genomic mapping and alignment program for mRNA and EST sequences. Bioinformatics, 21, 1859–1875 https://doi.org/10.1093/bioinformatics/bti310 pmid: 15728110
18	S. Heinz, , C. Benner, , N. Spann, , E. Bertolino, , Y. C. Lin, , P. Laslo, , J. X. Cheng, , C. Murre, , H. Singh, and C. K. Glass, (2010) Simple combinations of lineage-determining transcription factors prime cis-regulatory elements required for macrophage and B cell identities. Mol. Cell, 38, 576–589 https://doi.org/10.1016/j.molcel.2010.05.004 pmid: 20513432
19	Z. P. Liu, , C. Wu, , H. Miao, , H Wu, . (2015) RegNetwork: an integrated database of transcriptional and post-transcriptional regulatory networks in human and mouse. Database (Oxford) 2015, bav095
20	C. T. Lopes, , M. Franz, , F. Kazi, , S. L. Donaldson, , Q. Morris, and G. D. Bader, (2010) Cytoscape Web: an interactive web-based network browser. Bioinformatics, 26, 2347–2348 https://doi.org/10.1093/bioinformatics/btq430 pmid: 20656902
21	The modENCODE Consortium. (2010) Identification of functional elements and regulatory circuits by Drosophila modENCODE. Science, 33, 1787–1797

Viewed

Full text

Abstract

Cited

Shared

Discussed