|Baldwin, Cynthia -|
|Chen, Chuang -|
|Herzig, Carolyn Ta -|
|Teifer, Janice -|
Submitted to: BioMed Central (BMC) Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: October 10, 2012
Publication Date: N/A
Interpretive Summary: WC1 genes have multiple copies that vary in different organisms. These genes are involved the immune response to combat bacteria and viruses. During the assembly of the bovine genome there were a number of errors introduced in the organization of this gene family. The research conducted here resolved these errors and provides information on the structure of the bovine WC1 gene family.
Technical Abstract: Background WC1 co-receptors belong to the scavenger receptor cysteine-rich superfamily and are encoded by a multi-gene family. Expression of particular WC1 genes defines functional subpopulations of WC1+ '' T cells. Our previous study identified partial sequences for 13 different WC1 genes by annotation of the bovine genome Btau_3.1 build as well as two additional WC1 transcript sequences from other animals that did not correspond to the genome sequence. Their absence may have reflected gaps in the genome assembly or polymorphisms among animals. Thus the genomic copy number for WC1 and homogeneity of sequences among cattle was unknown. Results By real-time quantitative PCR using DNA from the donor animal of the bovine genome sequencing and annotation (“Dominette”), we determined that the gene copy number for WC1 is 13. This number was confirmed for 8 animals representing 3 breeds of cattle. The complete description of the expressed sequences of those 13 WC1 genes is presented which includes correction of an error in the WC1-2 gene due to mis-assembly in the Btau_3.1 build and filling in sequence gaps by amplifying and sequencing full-length transcripts from Dominette. Transcript sequences were found to agree with the previous annotations of complete or partial genes except for WC1-2. By designing specific primers to preferentially amplify the most variable or A domain of each of the 13 WC1 genes we showed that the sequences are highly conserved among individuals and breeds. Of 160 sequences from 3 breeds of cattle, no additional sequences beyond the 13 described WC1 genes were found. Analysis of the WC1 expressed sequences indicated that 13 WC1 genes represent 3 distinct WC1 molecular forms. Conclusion The bovine WC1 multi-gene family is composed of 13 genes with 3 structural forms whose sequences are conserved among animals and breeds and may act as pattern recognition receptors.