Different measures of "genome-wide" DNA methylation exhibit unique properties in placental and somatic tissues

被引:58
作者
Price, E. Magda [1 ,2 ]
Cotton, Allison M. [1 ]
Penaherrera, Maria S. [1 ]
McFadden, Deborah E. [1 ,4 ]
Kobor, Michael S. [1 ,3 ]
Robinson, Wendy P. [1 ]
机构
[1] Univ British Columbia, Dept Med Genet, Vancouver, BC, Canada
[2] Univ British Columbia, Dept Obstet & Gynaecol, Vancouver, BC V5Z 1M9, Canada
[3] Child & Family Res Inst, Ctr Mol Med & Therapeut, Vancouver, BC, Canada
[4] Univ British Columbia, Dept Pathol, Vancouver, BC, Canada
关键词
L1; Alu; DNA methylation; CpG island; placenta; repetitive elements; epigenetics; ALU REPEATS; CPG ISLANDS; HYPOMETHYLATION; ELEMENTS; AGE; 5-METHYLCYTOSINE; SUBFAMILIES; EXPRESSION; EXPOSURE; LINE-1;
D O I
10.4161/epi.20221
中图分类号
Q5 [生物化学]; Q7 [分子生物学];
学科分类号
071010 ; 081704 ;
摘要
DNA methylation of CpGs located in two types of repetitive elements-LINE1 (L1) and Alu-is used to assess "global" changes in DNA methylation in studies of human disease and environmental exposure. L1 and Alu contribute close to 30% of all base pairs in the human genome and transposition of repetitive elements is repressed through DNA methylation. Few studies have investigated whether repetitive element DNA methylation is associated with DNA methylation at other genomic regions, or the biological and technical factors that influence potential associations. Here, we assess L1 and Alu DNA methylation by Pyrosequencing of consensus sequences and using subsets of probes included in the Illumina Infinium HumanMethylation27 BeadChip array. We show that evolutionary age and assay method affect the assessment of repetitive element DNA methylation. Additionally, we compare Pyrosequencing results for repetitive elements to average DNA methylation of CpG islands, as assessed by array probes classified into strong, weak and non-islands. We demonstrate that each of these dispersed sequences exhibits different patterns of tissue-specific DNA methylation. Correlation of DNA methylation suggests an association between L1 and weak CpG island DNA methylation in some of the tissues examined. We caution, however, that L1, Alu and CpG island DNA methylation are distinct measures of dispersed DNA methylation and one should not be used in lieu of another. Analysis of DNA methylation data is complex and assays may be influenced by environment and pathology in different or complementary ways.
引用
收藏
页码:652 / 663
页数:12
相关论文
共 50 条
[21]   Genome-wide screening of DNA methylation in bovine blastocysts with different kinetics of development [J].
Jessica Ispada ;
Camila Bruna de Lima ;
Marc-André Sirard ;
Patrícia Kubo Fontes ;
Marcelo Fábio Gouveia Nogueira ;
Kelly Annes ;
Marcella Pecora Milazzotto .
Epigenetics & Chromatin, 11
[22]   Technical considerations for placental tissue processing and the subsequent impact on genome-wide DNA methylation analysis [J].
Kocher, Kristen M. ;
Ngwa, Julius ;
Kapse, Kushal J. ;
Bhattacharya, Surajit ;
Rossi, Christopher ;
Delot, Emmanuele ;
duPlessis, Adre ;
Limperopoulos, Catherine ;
Andescavage, Nickie .
CLINICAL EPIGENETICS, 2024, 16 (01)
[23]   Profiling genome-wide DNA methylation [J].
Wai-Shin Yong ;
Fei-Man Hsu ;
Pao-Yang Chen .
Epigenetics & Chromatin, 9
[24]   Profiling genome-wide DNA methylation [J].
Yong, Wai-Shin ;
Hsu, Fei-Man ;
Chen, Pao-Yang .
EPIGENETICS & CHROMATIN, 2016, 9
[25]   GENOME-WIDE DNA METHYLATION PATTERNS IN SUICIDE VICTIMS: IDENTIFICATION OF NEW CANDIDATE GENES [J].
Kouter, Katarina ;
Zupanc, Tomaz ;
Paska, Alja Videtic .
PSYCHIATRIA DANUBINA, 2019, 31 (04) :392-396
[26]   Genome-Wide DNA Methylation Profile in Whole Blood of Patients With Chronic Spontaneous Urticaria [J].
Qi, Yumeng ;
Zhang, Liming ;
Yang, Xiaonan ;
Tang, Biao ;
Xiao, Ting .
FRONTIERS IN IMMUNOLOGY, 2021, 12
[27]   Genome-wide DNA methylation analysis of human brain tissue from schizophrenia patients [J].
Wockner, L. F. ;
Noble, E. P. ;
Lawford, B. R. ;
Young, R. McD ;
Morris, C. P. ;
Whitehall, V. L. J. ;
Voisey, J. .
TRANSLATIONAL PSYCHIATRY, 2014, 4 :e339-e339
[28]   Genome-wide analysis of DNA methylation in pigs using reduced representation bisulfite sequencing [J].
Choi, Minkyeung ;
Lee, Jongin ;
Min Thong Le ;
Dinh Truong Nguyen ;
Park, Suhyun ;
Soundrarajan, Nagasundarapandian ;
Schachtschneider, Kyle M. ;
Kim, Jaebum ;
Park, Jin-Ki ;
Kim, Jin-Hoi ;
Park, Chankyu .
DNA RESEARCH, 2015, 22 (05) :343-355
[29]   The tissue-specific aspect of genome-wide DNA methylation in newborn and placental tissues: implications for epigenetic epidemiologic studies [J].
Herzog, Emilie M. ;
Eggink, Alex J. ;
Willemsen, Sten P. ;
Slieker, Roderick C. ;
Felix, Janine F. ;
Stubbs, Andrew P. ;
van der Spek, Peter J. ;
van Meurs, Joyce B. J. ;
Heijmans, Bastiaan T. ;
Steegers-Theunissen, Regine P. M. .
JOURNAL OF DEVELOPMENTAL ORIGINS OF HEALTH AND DISEASE, 2021, 12 (01) :113-123
[30]   A genome-wide DNA methylation study in colorectal carcinoma [J].
Kibriya, Muhammad G. ;
Raza, Maruf ;
Jasmine, Farzana ;
Roy, Shantanu ;
Paul-Brutus, Rachelle ;
Rahaman, Ronald ;
Dodsworth, Charlotte ;
Rakibuz-Zaman, Muhammad ;
Kamal, Mohammed ;
Ahsan, Habibul .
BMC MEDICAL GENOMICS, 2011, 4