Abstract
BackgroundGermline 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.ResultsHere, 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.ConclusionsTo 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.
Highlights
Germline cells are important carriers of genetic and epigenetic information transmitted across generations in mammals
Studies that characterized the dynamics of transcriptional and epigenetic features reported the local relationships of these dynamics at different phases of the mammalian germline cycle by using high-throughput sequencing technologies
By querying ATRX in the human germline cycle using GLEANER, we found that the expression level of ATRX was 1.07fold higher in the early female primordial germ cell (PGC) than in the early male PGCs, which indicated that the reactivation of ATRX is incomplete (Fig. 4)
Summary
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. The germline cycle runs through the whole process of ontogenesis and contains three phases: preimplantation embryogenesis, primordial germ cell (PGC) development in postimplantation embryos and gametogenesis in individuals after birth [2]. During these three phases of the germline cycle, the cell potency of germline cells changes cyclically, accompanied by dynamic transcriptional changes and epigenetic reprogramming. A systematic study of these cyclical changes in the mammalian germline cycle will help us to understand the mechanism of genetic and epigenetic information transmission across generations. In the PGC development phase of the mouse germline cycle, Lesch et al reported that the transcription activated epigenetic marker
Sign-in/Register to view highlights & summary Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a callDisclaimer: All third-party content on this website/platform is and will remain the property of their respective owners and is provided on "as is" basis without any warranties, express or implied. Use of third-party content does not indicate any affiliation, sponsorship with or endorsement by them. Any references to third-party content is to identify the corresponding services and shall be considered fair use under The CopyrightLaw.
