A Comprehensive Allele Specific Expression Resource for the Equine Transcriptome.
FAANG
RNA-sequencing
epigenetics
haplotype
horse
Journal
Research square
Titre abrégé: Res Sq
Pays: United States
ID NLM: 101768035
Informations de publication
Date de publication:
04 Apr 2024
04 Apr 2024
Historique:
pubmed:
22
4
2024
medline:
22
4
2024
entrez:
22
4
2024
Statut:
epublish
Résumé
Allele-specific expression (ASE) analysis provides a nuanced view of cis-regulatory mechanisms affecting gene expression. An equine ASE analysis was performed, using integrated Iso-seq and short-read RNA sequencing data from four healthy Thoroughbreds (2 mares and 2 stallions) across 9 tissues from the Functional Annotation of Animal Genomes (FAANG) project. Allele expression was quantified by haplotypes from long-read data, with 42,900 allele expression events compared. Within these events, 635 (1.48%) demonstrated ASE, with liver tissue containing the highest proportion. Genetic variants within ASE events were in histone modified regions 64.2% of the time. Validation of allele-specific variants, using a set of 66 equine liver samples from multiple breeds, confirmed that 97% of variants demonstrated ASE. This valuable publicly accessible resource is poised to facilitate investigations into regulatory variation in equine tissues. Our results highlight the tissue-specific nature of allelic imbalance in the equine genome.
Sections du résumé
Background
UNASSIGNED
Allele-specific expression (ASE) analysis provides a nuanced view of cis-regulatory mechanisms affecting gene expression.
Results
UNASSIGNED
An equine ASE analysis was performed, using integrated Iso-seq and short-read RNA sequencing data from four healthy Thoroughbreds (2 mares and 2 stallions) across 9 tissues from the Functional Annotation of Animal Genomes (FAANG) project. Allele expression was quantified by haplotypes from long-read data, with 42,900 allele expression events compared. Within these events, 635 (1.48%) demonstrated ASE, with liver tissue containing the highest proportion. Genetic variants within ASE events were in histone modified regions 64.2% of the time. Validation of allele-specific variants, using a set of 66 equine liver samples from multiple breeds, confirmed that 97% of variants demonstrated ASE.
Conclusions
UNASSIGNED
This valuable publicly accessible resource is poised to facilitate investigations into regulatory variation in equine tissues. Our results highlight the tissue-specific nature of allelic imbalance in the equine genome.
Identifiants
pubmed: 38645140
doi: 10.21203/rs.3.rs-4182812/v1
pmc: PMC11030527
pii:
doi:
Types de publication
Preprint
Langues
eng
Subventions
Organisme : NCATS NIH HHS
ID : L40 TR001136
Pays : United States
Déclaration de conflit d'intérêts
Competing interests The authors declare that they have no competing interests,
Références
Plant Cell. 2008 Feb;20(2):259-76
pubmed: 18263775
Genome Biol. 2020 Sep 11;21(1):234
pubmed: 32912332
Int J Mol Sci. 2020 Dec 01;21(23):
pubmed: 33271988
Nature. 2020 Sep;585(7825):357-362
pubmed: 32939066
Gigascience. 2021 Feb 16;10(2):
pubmed: 33590861
Bioinformatics. 2016 Oct 1;32(19):3047-8
pubmed: 27312411
Genome Biol. 2015 Sep 17;16:195
pubmed: 26381377
Nucleic Acids Res. 2021 Jul 2;49(W1):W317-W325
pubmed: 34086934
PLoS One. 2017 Jun 30;12(6):e0180378
pubmed: 28665992
Genes (Basel). 2019 Dec 18;11(1):
pubmed: 31861495
Genome Biol. 2016 Jun 06;17(1):122
pubmed: 27268795
Anim Genet. 2018 Dec;49(6):564-570
pubmed: 30311254
PLoS Genet. 2023 Mar 2;19(3):e1010468
pubmed: 36862752
Trends Genet. 2018 Jul;34(7):532-544
pubmed: 29680748
Nat Methods. 2020 Mar;17(3):261-272
pubmed: 32015543
Genome Biol. 2022 Jan 12;23(1):21
pubmed: 35022055
Sci Rep. 2021 Feb 3;11(1):2954
pubmed: 33536552
Wiley Interdiscip Rev RNA. 2018 Jul;9(4):e1474
pubmed: 29582564
Bioinformatics. 2013 Jan 1;29(1):15-21
pubmed: 23104886
PLoS Genet. 2020 May 11;16(5):e1008786
pubmed: 32392242