title: Fertility and genomics: comparison of gene expression in contrasting reproductive tissues of female cattle.
abstract: To compare gene expression among bovine tissues, large bovine RNA-seq datasets were used, comprising 280 samples from 10 different bovine tissues (uterine endometrium, granulosa cells, theca cells, cervix, embryos, leucocytes, liver, hypothalamus, pituitary, muscle) and generating 260 Gbases of data. Twin approaches were used: an information-theoretic analysis of the existing annotated transcriptome to identify the most tissue-specific genes and a de-novo transcriptome annotation to evaluate general features of the transcription landscape. Expression was detected for 97% of the Ensembl transcriptome with at least one read in one sample and between 28% and 66% at a level of 10 tags per million (TPM) or greater in individual tissues. Over 95% of genes exhibited some level of tissue-specific gene expression. This was mostly due to different levels of expression in different tissues rather than exclusive expression in a single tissue. Less than 1% of annotated genes exhibited a highly restricted tissue-specific expression profile and approximately 2% exhibited classic housekeeping profiles. In conclusion, it is the combined effects of the variable expression of large numbers of genes (73%-93% of the genome) and the specific expression of a small number of genes (<1% of the transcriptome) that contribute to determining the outcome of the function of individual tissues.
authors.affiliation: School of Agriculture and Food Science, University College Dublin, Belfield, Dublin 4, Ireland.
authors.forename: P A
authors.initials: PA
authors.lastname: McGettigan
authors.affiliation: School of Agriculture and Food Science, University College Dublin, Belfield, Dublin 4, Ireland.
authors.forename: J A
authors.initials: JA
authors.lastname: Browne
authors.affiliation: School of Veterinary Medicine, University College Dublin, Belfield, Dublin 4, Ireland.
authors.forename: S D
authors.initials: SD
authors.lastname: Carrington
authors.affiliation: School of Veterinary Medicine, University College Dublin, Belfield, Dublin 4, Ireland.
authors.forename: M A
authors.initials: MA
authors.lastname: Crowe
authors.affiliation: School of Agriculture and Food Science, University College Dublin, Belfield, Dublin 4, Ireland.
authors.forename: T
authors.initials: T
authors.lastname: Fair
authors.affiliation: School of Agriculture and Food Science, University College Dublin, Belfield, Dublin 4, Ireland.
authors.forename: N
authors.initials: N
authors.lastname: Forde
authors.affiliation: School of Medicine and Medical Sciences, University College Dublin, Belfield, Dublin 4, Ireland.
authors.forename: B J
authors.initials: BJ
authors.lastname: Loftus
authors.affiliation: School of Medicine and Medical Sciences, University College Dublin, Belfield, Dublin 4, Ireland.
authors.forename: A
authors.initials: A
authors.lastname: Lohan
authors.affiliation: School of Agriculture and Food Science, University College Dublin, Belfield, Dublin 4, Ireland.
authors.forename: P
authors.initials: P
authors.lastname: Lonergan
authors.affiliation: School of Veterinary Medicine, University College Dublin, Belfield, Dublin 4, Ireland.
authors.forename: K
authors.initials: K
authors.lastname: Pluta
authors.affiliation: School of Agriculture and Food Science, University College Dublin, Belfield, Dublin 4, Ireland.
authors.forename: S
authors.initials: S
authors.lastname: Mamo
authors.affiliation: Conway Institute, University College Dublin, Belfield, Dublin 4, Ireland.
authors.forename: A
authors.initials: A
authors.lastname: Murphy
authors.affiliation: School of Medicine and Medical Sciences, University College Dublin, Belfield, Dublin 4, Ireland.
authors.forename: J
authors.initials: J
authors.lastname: Roche
authors.affiliation: School of Agriculture and Food Science, University College Dublin, Belfield, Dublin 4, Ireland.
authors.forename: S W
authors.initials: SW
authors.lastname: Walsh
authors.affiliation: Animal and Grassland Research and Innovation Centre, Teagasc, Athenry, County Galway, Ireland.
authors.forename: C J
authors.initials: CJ
authors.lastname: Creevey
authors.affiliation: Animal and Grassland Research and Innovation Centre, Teagasc, Athenry, County Galway, Ireland.
authors.forename: B
authors.initials: B
authors.lastname: Earley
authors.affiliation: Animal and Grassland Research and Innovation Centre, Teagasc, Athenry, County Galway, Ireland.
authors.forename: S
authors.initials: S
authors.lastname: Keady
authors.affiliation: Animal and Grassland Research and Innovation Centre, Teagasc, Athenry, County Galway, Ireland.
authors.forename: D A
authors.initials: DA
authors.lastname: Kenny
authors.affiliation: Animal and Grassland Research and Innovation Centre, Teagasc, Athenry, County Galway, Ireland.
authors.forename: D
authors.initials: D
authors.lastname: Matthews
authors.affiliation: Animal and Grassland Research and Innovation Centre, Teagasc, Athenry, County Galway, Ireland.
authors.forename: M
authors.initials: M
authors.lastname: McCabe
authors.affiliation: Animal and Grassland Research and Innovation Centre, Teagasc, Athenry, County Galway, Ireland.
authors.forename: D
authors.initials: D
authors.lastname: Morris
authors.affiliation: Animal and Grassland Research and Innovation Centre, Teagasc, Athenry, County Galway, Ireland.
authors.forename: A
authors.initials: A
authors.lastname: O'Loughlin
authors.affiliation: Animal and Grassland Research and Innovation Centre, Teagasc, Athenry, County Galway, Ireland.
authors.forename: S
authors.initials: S
authors.lastname: Waters
authors.affiliation: Animal and Grassland Research and Innovation Centre, Teagasc, Athenry, County Galway, Ireland.
authors.forename: M G
authors.initials: MG
authors.lastname: Diskin
authors.affiliation: School of Agriculture and Food Science, University College Dublin, Belfield, Dublin 4, Ireland.
authors.forename: A C O
authors.initials: AC
authors.lastname: Evans
mesh_terms: D000818:Animals; D002417:Cattle; D002584:Cervix Uteri / Q000378:metabolism*; D030561:Databases, Nucleic Acid; D004622:Embryo, Mammalian / Q000378:metabolism*; D004717:Endometrium / Q000378:metabolism*; D005260:Female; D005298:Fertility; D020869:Gene Expression Profiling / Q000662:veterinary; D018507:Gene Expression Regulation, Developmental; D015723:Gene Library; D020043:Genes, Essential; D058977:Molecular Sequence Annotation; D009928:Organ Specificity; D006080:Ovarian Follicle / Q000378:metabolism*; D011247:Pregnancy; D025341:Principal Component Analysis; D012333:RNA, Messenger / Q000737:chemistry / Q000378:metabolism; D059467:Transcriptome; D014599:Uterus / Q000378:metabolism*
chemical_list: D012333:RNA, Messenger