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GLEANER: a web server for GermLine cycle Expression ANalysis and Epigenetic Roadmap visualization.

Shiyang Zeng1, Yuwei Hua1, Yong Zhang1

  • 1Institute for Regenerative Medicine, Shanghai East Hospital, Shanghai Key Laboratory of Signaling and Disease Research, Frontier Science Center for Stem Cell Research, School of Life Science and Technology, Tongji University, Shanghai, 200092, China.

BMC Bioinformatics
|June 1, 2021
PubMed
Summary
This summary is machine-generated.

GLEANER is a new web server that visualizes dynamic changes in germline cell development. It integrates multiomics data to reveal epigenetic regulation of genetic information transmission across generations.

Keywords:
BioinformaticsEpigeneticsGermline cycle

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Area of Science:

  • Mammalian reproduction and developmental biology.
  • Epigenetics and genomics.
  • Bioinformatics and computational biology.

Background:

  • Germline cells transmit genetic and epigenetic information across generations.
  • Mammalian germline development involves cyclical changes in cell potency, transcription, and epigenetic reprogramming.
  • Existing multiomics data for germline cycles are limited by the long cell cycle duration and scarce cell material.

Purpose of the Study:

  • To develop a tool for integrating and visualizing multiomics data of the mammalian germline cycle.
  • To overcome limitations in understanding dynamic changes due to long germline cycles and limited cell availability.
  • To provide insights into epigenetic regulation mechanisms during germline development.

Main Methods:

  • Development of GLEANER, a web server for GermLine cycle Expression ANalysis and Epigenetics Roadmap visualization.
  • Integration of transcriptomic and epigenomic data (DNA methylation, chromatin accessibility, H3K4me3, H3K27me3, H3K9me3) for human and mouse germline cycles.
  • Analysis of individual gene features, correlated transcriptional changes, and dynamic trends within the germline cycle.

Main Results:

  • GLEANER offers a comprehensive collection of multiomics data for mammalian germline cycles.
  • The tool visualizes integrative analysis of transcriptional and epigenetic features for user-input genes.
  • Case studies demonstrate GLEANER's utility in identifying epigenetic regulation clues.

Conclusions:

  • GLEANER is the first web server specifically designed for analyzing and visualizing mammalian germline cycle multiomics data.
  • The tool facilitates a deeper understanding of epigenetic mechanisms in germline development and information transmission.
  • GLEANER is freely accessible for research purposes.