ICCFGG 2022
#21 Discovery and annotation of Novel Zinc Finger Repeat Elements in the Labrador Retriever assembly ROS_Cfam_1.0 Jeffrey J. Schoenebeck1 , Lel Eory1, Wengang Zhang1, Judit Aguilar1, Melany Jackson1, Derya D. Ozdemir1, Jacqueline Smith1, Emily Clark1, Dominic Kurian1, and Alan L. Archibald1 jeff.schoenebeck@roslin.ed.ac.uk 1The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Midlothian EH25 9RG UK Background Eukaryotic genes are mostly evolutionarily conserved. A notable exception are members of the C2H2 superfamily of transcription factors, that are defined by their zinc finger (ZF) DNA-binding motif(s). Expansion of C2H2 ZF transcription factor genes has created species-specific families. The namesake of C2H2-type ZF transcription factors is its “C-X2-C-X12-H-X3-H” tandem repeat motif. Each ZF is 21 amino acids long coupled with a 7 amino acid spacer that separates flanking ZFs. Underpinned by our improved dog reference genome, ROS_Cfam_1.0, we explored whether Canis lupus ZF transcription factor gene content and gene architecture differs by species and lineage. Results We have found a group of repetitive sequences with repeat periodicities of 84, 168, 252, and 336 base pairs that corresponded with C2H2 ZF motifs. Many of these motifs overlap with the gene annotations of RefSeq, and to a lesser extent, Ensembl. We observed significant enrichment of ZF transcription factors near the telomeres of chromosomes 1, 6, and 20. Even after masking CDS (genic) sites, we observed an unexpected excess of ZF repeat motifs. Our RNA isoform sequence data provide evidence that non-CDS ZF repeats are components of multi-exonic transcripts, indi- cating that the annotation of some ZF genes is incorrect or lacking. In total, we observed 345 zinc finger motifs (coding and noncoding) in ROS_Cfam_1.0. While the overall number of ZF motifs does not differ greatly between dog genome assemblies, we observed structural variation that overlaps with ZF motifs, suggesting that the repeat number of ZF genes can differ between dogs and wolves. Conclusions Discovery and characterization of ZF transcription factors may help to explain the genomic basis of dog diversification
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