Multiomic atlas with functional stratification and developmental dynamics of zebrafish cis-regulatory elements

Area of Science:

• Developmental Biology
• Genomics
• Comparative Genomics

Background:

• Zebrafish are crucial models for embryonic development and human disease research.
• A lack of systematic functional annotation hindered comprehensive zebrafish genomic studies.
• Existing genomic data required integration for improved functional insights.

Purpose of the Study:

• To establish a central repository for zebrafish developmental functional genomic data.
• To systematically annotate functional genomic elements in zebrafish.
• To enable comparative genomics studies between zebrafish and mammals.

Main Methods:

• Formation of the international DANIO-CODE consortium.
• Creation of a central data coordination center to store and process genomic data.
• Analysis of 1,802 genomic data sets (published and unpublished).
• Identification and characterization of cis-regulatory elements.
• Comparative analysis of regulatory elements and epigenomic landscapes between zebrafish and mouse.

Main Results:

• Over 140,000 cis-regulatory elements identified across zebrafish development.
• Distinct classes of regulatory elements characterized by temporal and spatial activity.
• Delineation of chromatin features and distance topology for regulatory elements active during different developmental stages.
• Successful matching of regulatory elements and epigenomic landscapes between zebrafish and mouse.
• Prediction of functional relationships beyond sequence similarity.

Conclusions:

• The DANIO-CODE repository significantly improves zebrafish functional genomic annotation.
• The identified cis-regulatory elements provide valuable insights into developmental processes.
• Comparative analyses extend the applicability of zebrafish genomics to mammalian systems.
• This resource facilitates improved experimental design in zebrafish research.