Investigation of Gene Expression and DNA Methylation From Seven Different Brain Regions of a Crab-Eating Monkey as Determined by RNA-Seq and Whole-Genome Bisulfite Sequencing.
Macaca fascicularis
RNA-Seq (quantification) analysis
differentially methylated CpG sites
repeat elements
whole genome bisulfite sequencing (WGBS)
Journal
Frontiers in genetics
ISSN: 1664-8021
Titre abrégé: Front Genet
Pays: Switzerland
ID NLM: 101560621
Informations de publication
Date de publication:
2019
2019
Historique:
received:
29
03
2019
accepted:
02
07
2019
entrez:
21
8
2019
pubmed:
21
8
2019
medline:
21
8
2019
Statut:
epublish
Résumé
The crab-eating monkey is widely used in biomedical research for pharmacological experiments. Epigenetic regulation in the brain regions of primates involves complex patterns of DNA methylation. Previous studies of methylated CpG-binding domains using microarray technology or peak identification of sequence reads mostly focused on developmental stages or disease, rather than normal brains. To identify correlations between gene expression and DNA methylation levels that may be related to transcriptional regulation, we generated RNA-seq and whole-genome bisulfite sequencing data from seven different brain regions from a single crab-eating monkey. We identified 92 genes whose expression levels were significantly correlated, positively or negatively, with DNA methylation levels. Among them, 11 genes exhibited brain region-specific characteristics, and their expression patterns were strongly correlated with DNA methylation level. Nine genes (
Identifiants
pubmed: 31428131
doi: 10.3389/fgene.2019.00694
pmc: PMC6690020
doi:
Types de publication
Journal Article
Langues
eng
Pagination
694Références
Oncol Rep. 2001 Sep-Oct;8(5):1063-6
pubmed: 11496317
Hum Genet. 2002 Jan;110(1):64-7
pubmed: 11810298
Biochemistry. 2003 Mar 11;42(9):2493-9
pubmed: 12614143
J Virol. 2003 Apr;77(7):4449-56
pubmed: 12634405
Br Med Bull. 2003;65:49-59
pubmed: 12697616
J Am Chem Soc. 2003 Jun 4;125(22):6612-3
pubmed: 12769553
Philos Trans R Soc Lond B Biol Sci. 1992 Jan 29;335(1273):3-10
pubmed: 1348134
Exp Cell Res. 2004 Feb 1;293(1):31-42
pubmed: 14729055
Dement Geriatr Cogn Disord. 2004;17(3):174-80
pubmed: 14739541
Trends Cogn Sci. 2004 Apr;8(4):170-7
pubmed: 15050513
Brain Res Brain Res Rev. 2005 Feb;48(1):16-42
pubmed: 15708626
Cancer Res. 2005 Apr 1;65(7):2662-7
pubmed: 15805263
Oncogene. 2006 Aug 17;25(36):5018-26
pubmed: 16732332
Cell. 2006 Jul 14;126(1):121-34
pubmed: 16839881
Hum Mol Genet. 2006 Dec 15;15(24):3498-507
pubmed: 17085484
Genomics. 1991 Sep;11(1):103-7
pubmed: 1765368
Am J Hum Genet. 2007 Dec;81(6):1304-15
pubmed: 17999367
Nat Biotechnol. 2008 Jul;26(7):779-85
pubmed: 18612301
CNS Spectr. 2008 Aug;13(8):663-81
pubmed: 18704022
Brain. 2008 Nov;131(Pt 11):3034-50
pubmed: 18819986
Alcohol Clin Exp Res. 2008 Dec;32(12):2117-27
pubmed: 18828801
Behav Brain Res. 2009 Apr 12;199(1):53-60
pubmed: 19059285
J Pharmacol Exp Ther. 2009 May;329(2):558-70
pubmed: 19179540
Neuropsychiatr Dis Treat. 2007 Feb;3(1):87-101
pubmed: 19300540
Cell Death Differ. 2009 Nov;16(11):1469-79
pubmed: 19575017
Bioinformatics. 2010 Mar 15;26(6):841-2
pubmed: 20110278
Hum Mutat. 2010 Apr;31(4):391-406
pubmed: 20127975
Genome Biol. 2010;11(3):R25
pubmed: 20196867
Neuropathol Appl Neurobiol. 2010 Jun;36(4):320-30
pubmed: 20202123
Am J Hum Genet. 2010 Mar 12;86(3):411-9
pubmed: 20215007
Nat Biotechnol. 2010 May;28(5):511-5
pubmed: 20436464
PLoS Genet. 2010 May 13;6(5):e1000952
pubmed: 20485568
Cell Cycle. 2010 Oct 1;9(19):3880-3
pubmed: 20890116
Biol Psychiatry. 2011 Jan 15;69(2):188-93
pubmed: 21183010
Nat Rev Genet. 2011 Feb;12(2):123-35
pubmed: 21221116
Brain Res. 2011 May 4;1388:12-21
pubmed: 21382351
Nat Protoc. 2011 Apr;6(4):468-81
pubmed: 21412275
Genome Res. 2011 Aug;21(8):1313-27
pubmed: 21636662
Neurosci Lett. 2012 Mar 28;513(1):106-10
pubmed: 22343310
Nat Protoc. 2012 Mar 01;7(3):562-78
pubmed: 22383036
Nat Protoc. 2012 Mar 08;7(4):617-36
pubmed: 22402632
Cytogenet Genome Res. 2012;136(4):278-87
pubmed: 22456293
Oncogene. 2013 Feb 7;32(6):699-712
pubmed: 22525272
Neuroscientist. 2013 Feb;19(1):43-61
pubmed: 22547530
BMC Genomics. 2012 May 04;13:163
pubmed: 22554259
Epigenetics. 2012 Jun 1;7(6):542-50
pubmed: 22595875
Neuropsychopharmacology. 2013 Jan;38(1):39-54
pubmed: 22669168
Genome Biol. 2012 Jun 15;13(6):R43
pubmed: 22703893
Cephalalgia. 2012 Sep;32(12):924-31
pubmed: 22833613
Am J Hum Genet. 2012 Sep 7;91(3):455-65
pubmed: 22922032
Genome Biol. 2012 Oct 03;13(10):R87
pubmed: 23034086
Nucleic Acids Res. 2013 Jan;41(Database issue):D83-9
pubmed: 23203982
JAMA Psychiatry. 2013 Mar;70(3):325-33
pubmed: 23303482
PLoS One. 2013;8(2):e55761
pubmed: 23437062
Cell Stem Cell. 2013 Sep 5;13(3):360-9
pubmed: 23850244
Mol Psychiatry. 2014 Aug;19(8):862-71
pubmed: 23999529
Bioinformatics. 2014 Feb 15;30(4):523-30
pubmed: 24336805
Bioinformatics. 2014 Aug 1;30(15):2114-20
pubmed: 24695404
Cold Spring Harb Perspect Biol. 2014 May 01;6(5):a019133
pubmed: 24789823
Cell. 2014 May 8;157(4):979-991
pubmed: 24813617
Nat Methods. 2014 Aug;11(8):817-820
pubmed: 25042786
Nature. 2014 Jul 31;511(7511):606-10
pubmed: 25079557
Bipolar Disord. 2014 Dec;16(8):790-9
pubmed: 25243493
Nat Methods. 2015 Mar;12(3):230-2, 1 p following 232
pubmed: 25362363
Biomol Concepts. 2014 May;5(2):95-107
pubmed: 25372745
Proc Natl Acad Sci U S A. 2014 Dec 2;111(48):17224-9
pubmed: 25413365
Nucleic Acids Res. 2015 Jan;43(2):732-44
pubmed: 25572316
Genome Biol Evol. 2015 Jan 09;7(2):567-80
pubmed: 25577199
PLoS Biol. 2015 Jan 26;13(1):e1002045
pubmed: 25621867
Nat Commun. 2015 Mar 23;6:6569
pubmed: 25798578
Nat Genet. 2015 May;47(5):544-9
pubmed: 25848752
Int J Biochem Cell Biol. 2015 Oct;67:58-64
pubmed: 26003740
Neuron. 2015 Jun 17;86(6):1369-84
pubmed: 26087164
Front Cell Neurosci. 2015 Aug 25;9:331
pubmed: 26379502
PLoS One. 2015 Dec 04;10(12):e0143563
pubmed: 26636579
Bioinformatics. 2016 Sep 15;32(18):2847-9
pubmed: 27207943
Epigenetics Chromatin. 2016 Jun 29;9:26
pubmed: 27358654
Front Genet. 2016 Jun 17;7:110
pubmed: 27379160
PLoS One. 2016 Jul 20;11(7):e0159230
pubmed: 27438711
Clin Epigenetics. 2016 Jul 26;8:81
pubmed: 27462375
Bioinformatics. 2017 Feb 15;33(4):471-474
pubmed: 27563026
J Neurosci Res. 2017 Jan 2;95(1-2):587-593
pubmed: 27870430
Blood. 2017 Feb 9;129(6):704-714
pubmed: 28028030
Neuropsychologia. 2017 Feb;96:137-149
pubmed: 28093279
Genome Res. 2017 Jun;27(6):934-946
pubmed: 28348165
J Transl Med. 2017 Dec 29;15(1):269
pubmed: 29287594
BMC Genomics. 2018 Apr 4;19(1):234
pubmed: 29618320
Open Biol. 2018 Oct 31;8(10):
pubmed: 30381360
Gene. 1996 Mar 9;169(2):241-5
pubmed: 8647455
Science. 1997 Nov 14;278(5341):1309-12
pubmed: 9360930