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ARS Home » Plains Area » Kerrville, Texas » Knipling-Bushland U.S. Livestock Insects Research Laboratory » Cattle Fever Tick Research Unit » Research » Publications at this Location » Publication #375281
Research Project: Integrated Pest Management of Cattle Fever Ticks

Location: Cattle Fever Tick Research Unit

Title: A comparative analysis of chromatin accessibility in cattle, pig, and mouse tissues

Author
item HALSTEAD, MICHELLE - UNIVERSITY OF CALIFORNIA, DAVIS
item KERN, COLIN - UNIVERSITY OF CALIFORNIA, DAVIS
item Saelao, Perot
item WANG, YING - UNIVERSITY OF CALIFORNIA, DAVIS
item CHANTHAVIXAY, GANREA - UNIVERSITY OF CALIFORNIA, DAVIS
item MEDRANO, JUAN - UNIVERSITY OF CALIFORNIA, DAVIS
item VAN EENENNAAM, ALISON - UNIVERSITY OF CALIFORNIA, DAVIS
item KORF, IAN - UNIVERSITY OF CALIFORNIA, DAVIS
item TUGGLE, CHRISTOPHER - IOWA STATE UNIVERSITY
item ERNST, CATHERINE - MICHIGAN STATE UNIVERSITY
item ZHOU, HUAIJUN - UNIVERSITY OF CALIFORNIA, DAVIS
item ROSS, PABLO - UNIVERSITY OF CALIFORNIA, DAVIS

Submitted to: BMC Genomics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 6/2/2020
Publication Date: 10/7/2020
Citation: Halstead, M., Kern, C., Saelao, P., Wang, Y., Chanthavixay, G., Medrano, J.F., Van Eenennaam, A.L., Korf, I., Tuggle, C.K., Ernst, C.W., Zhou, H., Ross, P.J. 2020. A comparative analysis of chromatin accessibility in cattle, pig, and mouse tissues. BMC Genomics. 21:698. https://doi.org/10.1186/s12864-020-07078-9.
DOI: https://doi.org/10.1186/s12864-020-07078-9

Interpretive Summary: Animal genomes contain noncoding elements that help to regulate the expression of genes. However, very little is known about where these elements may exist in farm animal genomes such as the cow, pig, and chicken. This study uses a novel method called ATAC-Seq to identify these noncoding regions of the genome of these species. Using mouse as an out-species, this study finds that many of these noncoding regions are highly conserved with evolutionary distance. The closer two species are related to one another, the more likely they are to share these noncoding elements. In addition, many of these conserved elements are in the start of the gene, highlighting that regions importance in gene expression. This study provides the first exploration into the regulatory regions of farm animals and provides novel identification for future studies.

Technical Abstract: Despite the economic significance of livestock, functional annotations of their genomes, especially of noncoding regulatory elements, are limited. To address this knowledge gap, we identified 306,304 and 273,594 active regulatory elements in pig and cattle, respectively, by profiling chromatin accessibility in a representative set of eight adult tissues. Of these regions, 71,478 regulatory elements and 47,454 regulatory elements were highly tissue-specific in pigs and cattle, respectively. These regions were correspondingly enriched for known binding motifs of tissue-specific transcription factors. However, the most prominent motif in all open chromatin across tissues was that of the insulating factor CTCF, suggesting pervasive involvement of these loci in 3D chromatin architecture. A comparative analysis of pig and cattle open chromatin with that of published data generated from mouse tissues 1 revealed that open chromatin conservation was consistent with evolutionary distance, and favored conservation of promoter elements, rather than distal elements. The lack of distal element conservation further emphasizes the need for species-specific regulatory element annotations, rather than inferring function from those species with already curated annotations, such as mouse. Although further efforts will refine and classify the active regulatory elements identified in this study, this atlas of chromatin accessibility in cattle and pig tissues constitutes a first step towards dissecting the regulatory link between genome and phenome.