Pig Matrix: a matched multi-omics 3D regulatory genomics database for evolutionary and comparative analyses in pigs

Area of Science:

• Genomics
• Bioinformatics
• Comparative Genomics

Background:

• Current pig functional genomic resources are limited, hindering the study of regulatory region-gene relationships.
• Systematic resolution of distal regulatory elements and their target genes in pigs is challenging.

Purpose of the Study:

• To present Pig Matrix, a comprehensive 3D regulatory genomics database for pigs (Sus scrofa).
• To integrate multi-omics datasets for improved interpretation of non-coding variants and genomic signals.
• To provide a platform for regulatory interpretation, evolutionary analysis, and comparative genomics in pigs.

Main Methods:

• Integration of matched multi-omics datasets (genomic, transcriptomic, epigenomic, 3D genome) across tissues, developmental stages, and cell lines.
• Development of modules for genes, cis-regulatory elements, 3D genome architecture, and genome browsing.
• Inclusion of Evolution and Comparative resources and Genome Annotation and LiftOver tools.

Main Results:

• The Pig Matrix database integrates 7 omics layers and 7,959 processed files from 1,170 libraries.
• It links cis-regulatory elements to proximal and distal target genes using epigenomic and 3D genome information.
• A use case demonstrated extended interpretation of domestication-related signals, identifying additional candidate genes like KIT.

Conclusions:

• Pig Matrix provides an integrated platform for detailed regulatory genomics in pigs.
• The database facilitates the interpretation of non-coding variants and supports evolutionary and comparative genomic studies.
• It offers valuable resources for xenotransplantation research and benchmarking AI models in regulatory genomics.