The landscape of chromatin accessibility in skeletal muscle during embryonic development in pigs.
Chromatin accessibility
Embryo
Pig
Skeletal muscle
Transcriptome
Journal
Journal of animal science and biotechnology
ISSN: 1674-9782
Titre abrégé: J Anim Sci Biotechnol
Pays: England
ID NLM: 101581293
Informations de publication
Date de publication:
03 May 2021
03 May 2021
Historique:
received:
15
10
2020
accepted:
01
03
2021
entrez:
3
5
2021
pubmed:
4
5
2021
medline:
4
5
2021
Statut:
epublish
Résumé
The development of skeletal muscle in pigs during the embryonic stage is precisely regulated by transcriptional mechanisms, which depend on chromatin accessibility. However, how chromatin accessibility plays a regulatory role during embryonic skeletal muscle development in pigs has not been reported. To gain insight into the landscape of chromatin accessibility and the associated genome-wide transcriptome during embryonic muscle development, we performed ATAC-seq and RNA-seq analyses of skeletal muscle from pig embryos at 45, 70 and 100 days post coitus (dpc). In total, 21,638, 35,447 and 60,181 unique regions (or peaks) were found across the embryos at 45 dpc (LW45), 70 dpc (LW70) and 100 dpc (LW100), respectively. More than 91% of the peaks were annotated within - 1 kb to 100 bp of transcription start sites (TSSs). First, widespread increases in specific accessible chromatin regions (ACRs) from embryos at 45 to 100 dpc suggested that the regulatory mechanisms became increasingly complicated during embryonic development. Second, the findings from integrated ATAC-seq and RNA-seq analyses showed that not only the numbers but also the intensities of ACRs could control the expression of associated genes. Moreover, the motif screening of stage-specific ACRs revealed some transcription factors that regulate muscle development-related genes, such as MyoG, Mef2c, and Mef2d. Several potential transcriptional repressors, including E2F6, OTX2 and CTCF, were identified among the genes that exhibited different regulation trends between the ATAC-seq and RNA-seq data. This work indicates that chromatin accessibility plays an important regulatory role in the embryonic muscle development of pigs and regulates the temporal and spatial expression patterns of key genes in muscle development by influencing the binding of transcription factors. Our results contribute to a better understanding of the regulatory dynamics of genes involved in pig embryonic skeletal muscle development.
Sections du résumé
BACKGROUND
BACKGROUND
The development of skeletal muscle in pigs during the embryonic stage is precisely regulated by transcriptional mechanisms, which depend on chromatin accessibility. However, how chromatin accessibility plays a regulatory role during embryonic skeletal muscle development in pigs has not been reported. To gain insight into the landscape of chromatin accessibility and the associated genome-wide transcriptome during embryonic muscle development, we performed ATAC-seq and RNA-seq analyses of skeletal muscle from pig embryos at 45, 70 and 100 days post coitus (dpc).
RESULTS
RESULTS
In total, 21,638, 35,447 and 60,181 unique regions (or peaks) were found across the embryos at 45 dpc (LW45), 70 dpc (LW70) and 100 dpc (LW100), respectively. More than 91% of the peaks were annotated within - 1 kb to 100 bp of transcription start sites (TSSs). First, widespread increases in specific accessible chromatin regions (ACRs) from embryos at 45 to 100 dpc suggested that the regulatory mechanisms became increasingly complicated during embryonic development. Second, the findings from integrated ATAC-seq and RNA-seq analyses showed that not only the numbers but also the intensities of ACRs could control the expression of associated genes. Moreover, the motif screening of stage-specific ACRs revealed some transcription factors that regulate muscle development-related genes, such as MyoG, Mef2c, and Mef2d. Several potential transcriptional repressors, including E2F6, OTX2 and CTCF, were identified among the genes that exhibited different regulation trends between the ATAC-seq and RNA-seq data.
CONCLUSIONS
CONCLUSIONS
This work indicates that chromatin accessibility plays an important regulatory role in the embryonic muscle development of pigs and regulates the temporal and spatial expression patterns of key genes in muscle development by influencing the binding of transcription factors. Our results contribute to a better understanding of the regulatory dynamics of genes involved in pig embryonic skeletal muscle development.
Identifiants
pubmed: 33934724
doi: 10.1186/s40104-021-00577-z
pii: 10.1186/s40104-021-00577-z
pmc: PMC8091695
doi:
Types de publication
Journal Article
Langues
eng
Pagination
56Subventions
Organisme : Agricultural Science and Technology Innovation Program
ID : ASTIP-IAS02
Références
Proc Natl Acad Sci U S A. 1998 Aug 4;95(16):9190-5
pubmed: 9689056
BMC Bioinformatics. 2015 May 22;16:169
pubmed: 25994840
Nat Commun. 2018 Dec 17;9(1):5345
pubmed: 30559361
Essays Biochem. 2006;42:89-103
pubmed: 17144882
Nat Commun. 2020 Feb 14;11(1):911
pubmed: 32060262
Mol Cell. 2010 May 28;38(4):576-89
pubmed: 20513432
Genome Biol. 2011;12(3):R22
pubmed: 21410973
BMC Genomics. 2005 May 10;6:70
pubmed: 15885146
Genes Dev. 2001 Feb 1;15(3):267-85
pubmed: 11159908
Stem Cell Reports. 2018 Mar 13;10(3):956-969
pubmed: 29478898
Methods Cell Biol. 2019;151:219-235
pubmed: 30948010
Bioinformatics. 2015 Jan 15;31(2):166-9
pubmed: 25260700
Nature. 2016 Jun 30;534(7609):652-7
pubmed: 27309802
PLoS One. 2012;7(7):e41374
pubmed: 22829947
J Clin Invest. 2002 May;109(10):1327-33
pubmed: 12021248
Bioinformatics. 2009 Jul 15;25(14):1754-60
pubmed: 19451168
Nat Commun. 2018 Sep 7;9(1):3647
pubmed: 30194434
Mol Plant. 2016 Aug 1;9(8):1168-1182
pubmed: 27250572
BMC Biol. 2019 Dec 30;17(1):108
pubmed: 31884969
Sci Rep. 2018 Oct 19;8(1):15499
pubmed: 30341348
Elife. 2019 Jan 16;8:
pubmed: 30650056
Nucleic Acids Res. 2016 Jul 8;44(W1):W160-5
pubmed: 27079975
Life Sci. 2020 Feb 1;242:117158
pubmed: 31837328
Annu Rev Biochem. 1988;57:159-97
pubmed: 3052270
Mol Carcinog. 2018 Aug;57(8):978-987
pubmed: 29603380
OMICS. 2012 May;16(5):284-7
pubmed: 22455463
Bioinformatics. 2014 Aug 1;30(15):2114-20
pubmed: 24695404
Genome Biol. 2014;15(12):550
pubmed: 25516281
Development. 2017 Jun 15;144(12):2104-2122
pubmed: 28634270
Cell Discov. 2016 Jan 12;2:15041
pubmed: 27462438
Semin Cell Dev Biol. 2017 Dec;72:33-44
pubmed: 29154822
Nature. 2015 Jul 23;523(7561):486-90
pubmed: 26083756
J Anat. 1983 Sep;137 (Pt 2):235-45
pubmed: 6630038
Mol Metab. 2016 Jan 11;5(3):233-244
pubmed: 26977395
Cancer Res. 2012 Nov 15;72(22):5988-6001
pubmed: 22986744
Nat Commun. 2018 Apr 10;9(1):1364
pubmed: 29636475
Genome Biol. 2010;11(12):R119
pubmed: 21143862
Nature. 2018 Oct;562(7725):76-81
pubmed: 30250250
Front Cell Dev Biol. 2020 Apr 03;8:196
pubmed: 32309280
Int J Biochem Cell Biol. 2020 Jan;118:105661
pubmed: 31805399
Cold Spring Harb Perspect Biol. 2012 Feb 01;4(2):
pubmed: 22300977
Sci Rep. 2018 Jul 31;8(1):11502
pubmed: 30065345
Genome Biol. 2008;9(9):R137
pubmed: 18798982
Nat Rev Genet. 2012 Sep;13(9):613-26
pubmed: 22868264
Reprod Nutr Dev. 2002 Sep-Oct;42(5):415-31
pubmed: 12537254
BMC Genomics. 2020 Oct 7;21(1):698
pubmed: 33028202
Bioinformatics. 2013 Jan 1;29(1):15-21
pubmed: 23104886
Epigenetics Chromatin. 2014 Nov 20;7(1):33
pubmed: 25473421
Epigenetics Chromatin. 2019 Feb 22;12(1):16
pubmed: 30795793
Oncogene. 1999 Jan 14;18(2):467-75
pubmed: 9927203
Proc Natl Acad Sci U S A. 1998 Sep 1;95(18):10716-21
pubmed: 9724770
J Anim Sci. 1973 Jun;36(6):1088-93
pubmed: 4268264
Am J Hum Genet. 2018 Dec 6;103(6):874-892
pubmed: 30503521
Curr Opin Struct Biol. 2016 Jun;38:68-74
pubmed: 27295424
Bioinformatics. 2009 Aug 15;25(16):2078-9
pubmed: 19505943
Trends Microbiol. 2012 Jan;20(1):50-7
pubmed: 22153753
Cell Res. 2017 Feb;27(2):165-183
pubmed: 27824029
Proc Natl Acad Sci U S A. 2008 Feb 5;105(5):1545-50
pubmed: 18230740
Acta Physiol (Oxf). 2010 Aug;199(4):477-87
pubmed: 20345412
Bioinformatics. 2010 Mar 15;26(6):841-2
pubmed: 20110278
Brief Funct Genomics. 2010 May;9(3):259-78
pubmed: 20308039