dbEmbryo multi-omics database for analyses of synergistic regulation in early mammalian embryo development [RESOURCES]

Xin Huang1,2,6, Xiaohan Tang3,6, Xuemei Bai1,3,6, Honglei Li4, Huan Tao1,2, Junting Wang1,3, Yaru Li1, Yu Sun1, Yang Zheng1, Xiang Xu1, Longteng Wang5, Yang Ding1, Meisong Lu3, Pingkun Zhou2, Xiaochen Bo1, Hao Li1 and Hebing Chen1 1Institute of Health Service and Transfusion Medicine, Beijing 100850, China; 2Beijing Institute of Radiation Medicine, Beijing 100850, China; 3Department of Obstetrics and Gynecology, The First Affiliated Hospital of Harbin Medical University, Harbin 150001, China; 4Beijing Cloudna Technology Company, Limited, Beijing 100029, China; 5Center for Statistical Science, Center for Bioinformatics, School of Life Sciences, Peking University, Beijing 100871, China

6 These authors contributed equally to this work.

Corresponding authors: chenhbbmi.ac.cn, lihao_thu163.com, boxcbmi.ac.cn, zhoupkbmi.ac.cn Abstract

During early mammalian embryo development, different epigenetic marks undergo reprogramming and play crucial roles in the mediation of gene expression. Currently, several databases provide multi-omics information on early embryos. However, how interconnected epigenetic markers function together to coordinate the expression of the genetic code in a spatiotemporal manner remains difficult to analyze, markedly limiting scientific and clinical research. Here, we present dbEmbryo, an integrated and interactive multi-omics database for human and mouse early embryos. dbEmbryo integrates data on gene expression, DNA methylation, histone modifications, chromatin accessibility, and higher-order chromatin structure profiles for human and mouse early embryos. It incorporates customized analysis tools, such as “multi-omics visualization,” “Gene&Peak annotation,” “ZGA gene cluster,” “cis-regulation,” “synergistic regulation,” “promoter signal enrichment,” and “3D genome.” Users can retrieve gene expression and epigenetic profile patterns to analyze synergistic changes across different early embryo developmental stages. We showed the uniqueness of dbEmbryo among extant databases containing data on early embryo development and provided an overview. Using dbEmbryo, we obtained a phase-separated model of transcriptional control during early embryo development. dbEmbryo offers web-based analytical tools and a comprehensive resource for biologists and clinicians to decipher molecular regulatory mechanisms of human and mouse early embryo development.

Footnotes

[Supplemental material is available for this article.]

Article published online before print. Article, supplemental material, and publication date are at https://www.genome.org/cgi/doi/10.1101/gr.276744.122.

Freely available online through the Genome Research Open Access option.

Received March 10, 2022. Accepted July 15, 2022.

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