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dc.contributor.author
Goszczynski, Daniel Estanislao
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dc.contributor.author
Halstead, Michelle M.
dc.contributor.author
Islas-Trejo, Alma D.
dc.contributor.author
Zhou, Huaijun
dc.contributor.author
Ross, Pablo J.
dc.date.available
2022-05-24T05:49:04Z
dc.date.issued
2021-04
dc.identifier.citation
Goszczynski, Daniel Estanislao; Halstead, Michelle M.; Islas-Trejo, Alma D.; Zhou, Huaijun; Ross, Pablo J.; Transcription initiation mapping in 31 bovine tissues reveals complex promoter activity, pervasive transcription, and tissue-specific promoter usage; Cold Spring Harbor Laboratory Press; Genome Research; 31; 4; 4-2021; 732-744
dc.identifier.issn
1088-9051
dc.identifier.uri
http://hdl.handle.net/11336/158102
dc.description.abstract
Characterizing transcription start sites is essential for understanding the regulatory mechanisms that control gene expression. Recently, a new bovine genome assembly (ARS-UCD1.2) with high continuity, accuracy, and completeness was released; however, the functional annotation of the bovine genome lacks precise transcription start sites and contains a low number of transcripts in comparison to human and mouse. By using the RAMPAGE approach, this study identified transcription start sites at high resolution in a large collection of bovine tissues. We found several known and novel transcription start sites attributed to promoters of protein-coding and lncRNA genes that were validated through experimental and in silico evidence. With these findings, the annotation of transcription start sites in cattle reached a level comparable to the mouse and human genome annotations. In addition, we identified and characterized transcription start sites for antisense transcripts derived from bidirectional promoters, potential lncRNAs, mRNAs, and pre-miRNAs. We also analyzed the quantitative aspects of RAMPAGE to produce a promoter activity atlas, reaching highly reproducible results comparable to traditional RNA-seq. Coexpression networks revealed considerable use of tissue-specific promoters, especially between brain and testicle, which expressed several genes in common from alternate loci. Furthermore, regions surrounding coexpressed modules were enriched in binding factor motifs representative of each tissue. The comprehensive annotation of promoters in such a large collection of tissues will substantially contribute to our understanding of gene expression in cattle and other mammalian species, shortening the gap between genotypes and phenotypes.
dc.format
application/pdf
dc.language.iso
eng
dc.publisher
Cold Spring Harbor Laboratory Press
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dc.rights
info:eu-repo/semantics/openAccess
dc.rights.uri
https://creativecommons.org/licenses/by-nc-sa/2.5/ar/
dc.subject
RAMPAGE
dc.subject
TRANSCRIPTION START SITE
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GENOME ANNOTATION
dc.subject
CATTLE
dc.subject.classification
Ciencias Veterinarias
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dc.subject.classification
Ciencias Veterinarias
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dc.subject.classification
CIENCIAS AGRÍCOLAS
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dc.title
Transcription initiation mapping in 31 bovine tissues reveals complex promoter activity, pervasive transcription, and tissue-specific promoter usage
dc.type
info:eu-repo/semantics/article
dc.type
info:ar-repo/semantics/artículo
dc.type
info:eu-repo/semantics/publishedVersion
dc.date.updated
2022-05-06T15:41:22Z
dc.journal.volume
31
dc.journal.number
4
dc.journal.pagination
732-744
dc.journal.pais
Estados Unidos
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dc.description.fil
Fil: Goszczynski, Daniel Estanislao. University of California at Davis; Estados Unidos. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico CONICET- La Plata. Instituto de Genética Veterinaria "Ing. Fernando Noel Dulout". Universidad Nacional de La Plata. Facultad de Ciencias Veterinarias. Instituto de Genética Veterinaria; Argentina
dc.description.fil
Fil: Halstead, Michelle M.. University of California at Davis; Estados Unidos
dc.description.fil
Fil: Islas-Trejo, Alma D.. University of California at Davis; Estados Unidos
dc.description.fil
Fil: Zhou, Huaijun. University of California at Davis; Estados Unidos
dc.description.fil
Fil: Ross, Pablo J.. University of California at Davis; Estados Unidos
dc.journal.title
Genome Research
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dc.relation.alternativeid
info:eu-repo/semantics/altIdentifier/doi/http://dx.doi.org/10.1101/GR.267336.120
dc.relation.alternativeid
info:eu-repo/semantics/altIdentifier/url/https://genome.cshlp.org/content/31/4/732
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