Comprehensive Annotation and Expression Profiling of C2H2 Zinc Finger Transcription Factors across Chicken Tissues

Area of Science:

• Genomics
• Evolutionary Biology
• Developmental Biology

Background:

• C2H2-type zinc finger proteins (C2H2-ZFPs) are abundant eukaryotic transcription factors with crucial roles.
• While well-studied in mammals, C2H2-ZFPs are poorly characterized in avian species.
• Recent multi-omics data in chickens allows for genome-wide investigation.

Purpose of the Study:

• To identify and characterize chicken C2H2-ZFPs.
• To investigate their evolutionary signatures and genomic distribution.
• To profile their expression patterns across various chicken tissues.

Main Methods:

• Genome-wide annotation of C2H2-ZFPs in the chicken genome.
• Analysis of effector domains (KRAB, BTB, HOMEO, PHD, SCAN, SET).
• Integration of 101 RNA-seq datasets from 32 chicken tissues for expression profiling.

Main Results:

• 301 C2H2-ZFPs were identified, featuring diverse effector domains.
• Many KRAB-ZFPs lack mammalian orthologs, suggesting rapid avian evolution via duplication.
• A novel, lineage-specific SCAN-ZFP highly expressed in gonads was discovered.
• Most C2H2-ZFPs exhibit tissue-specific expression, with 74 showing blastoderm enrichment, indicating roles in early development.

Conclusions:

• This study provides a comprehensive catalog of chicken C2H2-ZFPs.
• Findings highlight unique evolutionary paths and tissue-specific functions of avian C2H2-ZFPs.
• The results offer new insights into the evolution and function of these transcription factors in birds, particularly in early development.