Article (Scientific journals)
An organism-wide ATAC-seq peak catalog for the bovine and its use to identify regulatory variants.
Yuan, Can; Tang, Lijing; Lopdell, Thomas et al.
2023In Genome Research, 33 (10), p. 1848 - 1864
Peer Reviewed verified by ORBi
 

Files


Full Text
Genome Res.-2023-Yuan-1848-64.pdf
Author postprint (5.07 MB)
Download

All documents in ORBi are protected by a user license.

Send to



Details



Keywords :
Chromatin; Animals; Cattle/genetics; Sequence Analysis, DNA; Chromatin/genetics; Regulatory Sequences, Nucleic Acid; Chromatin Immunoprecipitation Sequencing; High-Throughput Nucleotide Sequencing; Cattle; Genetics; Genetics (clinical)
Abstract :
[en] We report the generation of an organism-wide catalog of 976,813 cis-acting regulatory elements for the bovine detected by the assay for transposase accessible chromatin using sequencing (ATAC-seq). We regroup these regulatory elements in 16 components by nonnegative matrix factorization. Correlation between the genome-wide density of peaks and transcription start sites, correlation between peak accessibility and expression of neighboring genes, and enrichment in transcription factor binding motifs support their regulatory potential. Using a previously established catalog of 12,736,643 variants, we show that the proportion of single-nucleotide polymorphisms mapping to ATAC-seq peaks is higher than expected and that this is owing to an approximately 1.3-fold higher mutation rate within peaks. Their site frequency spectrum indicates that variants in ATAC-seq peaks are subject to purifying selection. We generate eQTL data sets for liver and blood and show that variants that drive eQTL fall into liver- and blood-specific ATAC-seq peaks more often than expected by chance. We combine ATAC-seq and eQTL data to estimate that the proportion of regulatory variants mapping to ATAC-seq peaks is approximately one in three and that the proportion of variants mapping to ATAC-seq peaks that are regulatory is approximately one in 25. We discuss the implication of these findings on the utility of ATAC-seq information to improve the accuracy of genomic selection.
Disciplines :
Genetics & genetic processes
Author, co-author :
Yuan, Can ;  Université de Liège - ULiège > GIGA > GIGA Medical Genomics - Unit of Animal Genomics
Tang, Lijing ;  Université de Liège - ULiège > GIGA
Lopdell, Thomas  ;  Université de Liège - ULiège > GIGA > GIGA Administration ; Research and Development, Livestock Improvement Corporation, Hamilton 3240, New Zealand
Petrov, Vyacheslav A;  Unit of Animal Genomics, GIGA-R and Faculty of Veterinary Medicine, University of Liège, 4000 Liège, Belgium
Oget-Ebrad, Claire ;  Unit of Animal Genomics, GIGA-R and Faculty of Veterinary Medicine, University of Liège, 4000 Liège, Belgium
Moreira, Gabriel Costa Monteiro;  Unit of Animal Genomics, GIGA-R and Faculty of Veterinary Medicine, University of Liège, 4000 Liège, Belgium
Gualdrón Duarte, José Luis;  Unit of Animal Genomics, GIGA-R and Faculty of Veterinary Medicine, University of Liège, 4000 Liège, Belgium
Sartelet, Arnaud  ;  Université de Liège - ULiège > Département d'Enseignement et de Clinique des animaux de Production (DCP)
Cheng, Zhangrui;  Royal Veterinary College, Hatfield, Herts AL9 7TA, United Kingdom
Salavati, Mazdak;  Royal Veterinary College, Hatfield, Herts AL9 7TA, United Kingdom
Wathes, D Claire;  Royal Veterinary College, Hatfield, Herts AL9 7TA, United Kingdom
Crowe, Mark A;  School of Veterinary Medicine, University College Dublin, Dublin 4, Ireland
GplusE Consortium
Coppieters, Wouter ;  Université de Liège - ULiège > GIGA > GIGA Platform Genomics
Littlejohn, Mathew;  Research and Development, Livestock Improvement Corporation, Hamilton 3240, New Zealand
Charlier, Carole  ;  Université de Liège - ULiège > GIGA > GIGA Medical Genomics
Druet, Tom  ;  Université de Liège - ULiège > Département des sciences de la vie
Georges, Michel   ;  Université de Liège - ULiège > GIGA > GIGA Innovation
Takeda, Haruko   ;  Université de Liège - ULiège > Département de gestion vétérinaire des Ressources Animales (DRA) > Génomique animale
More authors (9 more) Less
 These authors have contributed equally to this work.
Language :
English
Title :
An organism-wide ATAC-seq peak catalog for the bovine and its use to identify regulatory variants.
Publication date :
October 2023
Journal title :
Genome Research
ISSN :
1088-9051
eISSN :
1549-5469
Publisher :
Cold Spring Harbor Laboratory Press, United States
Volume :
33
Issue :
10
Pages :
1848 - 1864
Peer reviewed :
Peer Reviewed verified by ORBi
European Projects :
FP7 - 613689 - GPLUSE - Genotype and Environment contributing to the sustainability of dairy cow production systems through the optimal integration of genomic selection and novel management protocols based on the development
Name of the research project :
Damona
Funders :
ERC - European Research Council [BE]
EU - European Union [BE]
Région wallonne [BE]
F.R.S.-FNRS - Fonds de la Recherche Scientifique [BE]
Funding number :
CAUSEL grant from the Walloon Region (no.1710030)
Funding text :
We thank Calixte Bayrou, Ken Kusakabe, Ruth Appeltant, Anne- Sophie Van Laere, and all members of Michel Georges’ laboratory for their help for sample collections, technical support, and fruitful discussion. We also thank the support provided by the GIGA Genomics and Bioinformatics core facilities. This work was funded by the Damona European Research Council advanced grant from the EU (AdG-GA323030), the GplusE FP7 grant from the EU (no. 613689), the CAUSEL grant from the Walloon Region (no.1710030), and financial support from Inoveo. C.C. and T.D. are senior research associate and research director from the Fonds de la Recherche Scientifique. Computational resources have been provided by the Consortium des Équipements de Calcul Intensif, funded by the Fonds de la Recherche Scientifique de Belgique (no. 2.5020.11) and by the Walloon Region.
Available on ORBi :
since 27 December 2023

Statistics


Number of views
40 (9 by ULiège)
Number of downloads
1 (1 by ULiège)

Scopus citations®
 
1
Scopus citations®
without self-citations
0

Bibliography


Similar publications



Contact ORBi