GLEANER: a Web Server for GermLine Cycle Expression ANalysis and Epigenetic Roadmap Visualization

Overview

Journal BMC Bioinformatics

Publisher Biomed Central

Specialty Biology

Date 2021 Jun 1

PMID 34058973

Citations 1

Authors

Shiyang Zeng

Yuwei Hua

Yong Zhang

Guifen Liu

Chengchen Zhao

Affiliations

Soon will be listed here.

Abstract

Background: Germline cells are important carriers of genetic and epigenetic information transmitted across generations in mammals. During the mammalian germline cell development cycle (i.e., the germline cycle), cell potency changes cyclically, accompanied by dynamic transcriptional changes and epigenetic reprogramming. Recently, to understand these dynamic and regulatory mechanisms, multiomic analyses, including transcriptomic and epigenomic analyses of DNA methylation, chromatin accessibility and histone modifications of germline cells, have been performed for different stages in human and mouse germline cycles. However, the long time span of the germline cycle and material scarcity of germline cells have largely limited the understanding of these dynamic characteristic changes. A tool that integrates the existing multiomics data and visualizes the overall continuous dynamic trends in the germline cycle can partially overcome such limitations.

Results: Here, we present GLEANER, a web server for GermLine cycle Expression ANalysis and Epigenetics Roadmap visualization. GLEANER provides a comprehensive collection of the transcriptome, DNA methylome, chromatin accessibility, and H3K4me3, H3K27me3, and H3K9me3 histone modification characteristics in human and mouse germline cycles. For each input gene, GLEANER shows the integrative analysis results of its transcriptional and epigenetic features, the genes with correlated transcriptional changes, and the overall continuous dynamic trends in the germline cycle. We further used two case studies to demonstrate the detailed functionality of GLEANER and highlighted that it can provide valuable clues to the epigenetic regulation mechanisms in the genetic and epigenetic information transmitted during the germline cycle.

Conclusions: To the best of our knowledge, GLEANER is the first web server dedicated to the analysis and visualization of multiomics data related to the mammalian germline cycle. GLEANER is freely available at http://compbio-zhanglab.org/GLEANER .

Citing Articles

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References

Grabole N, Tischler J, Hackett J, Kim S, Tang F, Leitch H . Prdm14 promotes germline fate and naive pluripotency by repressing FGF signalling and DNA methylation. EMBO Rep. 2013; 14(7):629-37. PMC: 3701237. DOI: 10.1038/embor.2013.67. View

Magnusdottir E, Dietmann S, Murakami K, Gunesdogan U, Tang F, Bao S . A tripartite transcription factor network regulates primordial germ cell specification in mice. Nat Cell Biol. 2013; 15(8):905-15. PMC: 3796875. DOI: 10.1038/ncb2798. View

Xi Y, Li W . BSMAP: whole genome bisulfite sequence MAPping program. BMC Bioinformatics. 2009; 10:232. PMC: 2724425. DOI: 10.1186/1471-2105-10-232. View

Wen L, Tang F . Human Germline Cell Development: from the Perspective of Single-Cell Sequencing. Mol Cell. 2019; 76(2):320-328. DOI: 10.1016/j.molcel.2019.08.025. View

Seki Y, Yamaji M, Yabuta Y, Sano M, Shigeta M, Matsui Y . Cellular dynamics associated with the genome-wide epigenetic reprogramming in migrating primordial germ cells in mice. Development. 2007; 134(14):2627-38. DOI: 10.1242/dev.005611. View

Hajkova P, Erhardt S, Lane N, Haaf T, El-Maarri O, Reik W . Epigenetic reprogramming in mouse primordial germ cells. Mech Dev. 2002; 117(1-2):15-23. DOI: 10.1016/s0925-4773(02)00181-8. View

Sugimoto M, Abe K . X chromosome reactivation initiates in nascent primordial germ cells in mice. PLoS Genet. 2007; 3(7):e116. PMC: 1950944. DOI: 10.1371/journal.pgen.0030116. View

Barrett T, Wilhite S, Ledoux P, Evangelista C, Kim I, Tomashevsky M . NCBI GEO: archive for functional genomics data sets--update. Nucleic Acids Res. 2012; 41(Database issue):D991-5. PMC: 3531084. DOI: 10.1093/nar/gks1193. View

Sun D, Xi Y, Rodriguez B, Park H, Tong P, Meong M . MOABS: model based analysis of bisulfite sequencing data. Genome Biol. 2014; 15(2):R38. PMC: 4054608. DOI: 10.1186/gb-2014-15-2-r38. View

10.

Tam P, Zhou S, Tan S . X-chromosome activity of the mouse primordial germ cells revealed by the expression of an X-linked lacZ transgene. Development. 1994; 120(10):2925-32. DOI: 10.1242/dev.120.10.2925. View

11.

Heard E, Clerc P, Avner P . X-chromosome inactivation in mammals. Annu Rev Genet. 1997; 31:571-610. DOI: 10.1146/annurev.genet.31.1.571. View

12.

Chuva de Sousa Lopes S, Hayashi K, Shovlin T, Mifsud W, Surani M, Mclaren A . X chromosome activity in mouse XX primordial germ cells. PLoS Genet. 2008; 4(2):e30. PMC: 2233679. DOI: 10.1371/journal.pgen.0040030. View

13.

Lesch B, Dokshin G, Young R, McCarrey J, Page D . A set of genes critical to development is epigenetically poised in mouse germ cells from fetal stages through completion of meiosis. Proc Natl Acad Sci U S A. 2013; 110(40):16061-6. PMC: 3791702. DOI: 10.1073/pnas.1315204110. View

14.

Yamaji M, Seki Y, Kurimoto K, Yabuta Y, Yuasa M, Shigeta M . Critical function of Prdm14 for the establishment of the germ cell lineage in mice. Nat Genet. 2008; 40(8):1016-22. DOI: 10.1038/ng.186. View

15.

Guo F, Yan L, Guo H, Li L, Hu B, Zhao Y . The Transcriptome and DNA Methylome Landscapes of Human Primordial Germ Cells. Cell. 2015; 161(6):1437-52. DOI: 10.1016/j.cell.2015.05.015. View

16.

Edgar R, Domrachev M, Lash A . Gene Expression Omnibus: NCBI gene expression and hybridization array data repository. Nucleic Acids Res. 2001; 30(1):207-10. PMC: 99122. DOI: 10.1093/nar/30.1.207. View

17.

Lee J, Inoue K, Ono R, Ogonuki N, Kohda T, Kaneko-Ishino T . Erasing genomic imprinting memory in mouse clone embryos produced from day 11.5 primordial germ cells. Development. 2002; 129(8):1807-17. DOI: 10.1242/dev.129.8.1807. View

18.

Liu X, Wang C, Liu W, Li J, Li C, Kou X . Distinct features of H3K4me3 and H3K27me3 chromatin domains in pre-implantation embryos. Nature. 2016; 537(7621):558-562. DOI: 10.1038/nature19362. View

19.

Tang W, Kobayashi T, Irie N, Dietmann S, Surani M . Specification and epigenetic programming of the human germ line. Nat Rev Genet. 2016; 17(10):585-600. DOI: 10.1038/nrg.2016.88. View

20.

Weber S, Eckert D, Nettersheim D, Gillis A, Schafer S, Kuckenberg P . Critical function of AP-2 gamma/TCFAP2C in mouse embryonic germ cell maintenance. Biol Reprod. 2009; 82(1):214-23. DOI: 10.1095/biolreprod.109.078717. View