The landscape of genomic imprinting across diverse adult human tissues

被引：142

作者：

Baran, Yael ^{[1
]}

Subramaniam, Meena ^{[2
]}

Biton, Anne ^{[2
]}

Tukiainen, Taru ^{[3
,4
]}

Tsang, Emily K. ^{[5
,6
]}

Rivas, Manuel A. ^{[7
]}

Pirinen, Matti ^{[8
]}

Gutierrez-Arcelus, Maria ^{[9
]}

Smith, Kevin S. ^{[5
,10
]}

Kukurba, Kim R. ^{[5
,10
]}

Zhang, Rui ^{[10
]}

Eng, Celeste ^{[2
]}

Torgerson, Dara G. ^{[2
]}

Urbanek, Cydney ^{[11
]}

Li, Jin Billy ^{[10
]}

Rodriguez-Santana, Jose R. ^{[12
]}

Burchard, Esteban G. ^{[2
,13
]}

Seibold, Max A. ^{[11
,14
,15
]}

MacArthur, Daniel G. ^{[3
,4
,16
]}

Montgomery, Stephen B. ^{[5
,10
]}

Zaitlen, Noah A. ^{[2
]}

Lappalainen, Tuuli ^{[17
,18
]}

机构：

[1] Tel Aviv Univ, Blavatnik Sch Comp Sci, IL-69978 Tel Aviv, Israel

[2] Univ Calif San Francisco, Dept Med, San Francisco, CA 94158 USA

[3] Massachusetts Gen Hosp, Analyt & Translat Genet Unit, Boston, MA 02114 USA

[4] Broad Inst Harvard & MIT, Program Med & Populat Genet, Cambridge, MA 02142 USA

[5] Stanford Univ, Dept Pathol, Stanford, CA 94305 USA

[6] Stanford Univ, Biomed Informat Program, Stanford, CA 94305 USA

[7] Univ Oxford, Nuffield Dept Clin Med, Wellcome Trust Ctr Human Genet, Oxford OX3 7BN, England

[8] Univ Helsinki, Inst Mol Med Finland, FIN-00014 Helsinki, Finland

[9] Univ Geneva, Dept Genet Med & Dev, CH-1211 Geneva, Switzerland

[10] Stanford Univ, Dept Genet, Stanford, CA 94305 USA

[11] Natl Jewish Hlth, Integrated Ctr Genes Environm & Hlth, Denver, CO 80206 USA

[12] Ctr Neumol Pediat, San Juan, PR 00917 USA

[13] Univ Calif San Francisco, Dept Bioengn & Therapeut Sci, San Francisco, CA 94158 USA

[14] Natl Jewish Hlth, Dept Pediat, Denver, CO 80206 USA

[15] Univ Colorado, Dept Med, Div Pulm Sci & Crit Care Med, Denver, CO 80045 USA

[16] Harvard Univ, Sch Med, Dept Genet, Boston, MA 02115 USA

[17] New York Genome Ctr, New York, NY 10013 USA

[18] Columbia Univ, Dept Syst Biol, New York, NY 10032 USA

来源：

GENOME RESEARCH | 2015年 / 25卷 / 07期

基金：

美国国家卫生研究院; 以色列科学基金会;

关键词：

ALLELE-SPECIFIC EXPRESSION; GENE-EXPRESSION; MONOALLELIC EXPRESSION; HUMAN GRB10; ORIGIN; IDENTIFICATION; DISEASE; TRANSCRIPTOME; MECHANISMS; RESOLUTION;

D O I：

10.1101/gr.192278.115

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：

Genomic imprinting is an important regulatory mechanism that silences one of the parental copies of a gene. To systematically characterize this phenomenon, we analyze tissue specificity of imprinting from allelic expression data in 1582 primary tissue samples from 178 individuals from the Genotype-Tissue Expression (GTEx) project. We characterize imprinting in 42 genes, including both novel and previously identified genes. Tissue specificity of imprinting is widespread, and gender. specific effects are revealed in a small number of genes in muscle with stronger imprinting in males. IGF2 shows maternal expression in the brain instead of the canonical paternal expression elsewhere. Imprinting appears to have only a subtle impact on tissue-specific expression levels, with genes lacking a systematic expression difference between tissues with imprinted and biallelic expression. In summary, our systematic characterization of imprinting in adult tissues highlights variation in imprinting between genes, individuals, and tissues.

引用

页码：927 / 936

页数：10

共 55 条

[1] An integrated map of genetic variation from 1,092 human genomes [J].

Altshuler, David M. ;

Durbin, Richard M. ;

Abecasis, Goncalo R. ;

Bentley, David R. ;

Chakravarti, Aravinda ;

Clark, Andrew G. ;

Donnelly, Peter ;

Eichler, Evan E. ;

Flicek, Paul ;

Gabriel, Stacey B. ;

Gibbs, Richard A. ;

Green, Eric D. ;

Hurles, Matthew E. ;

Knoppers, Bartha M. ;

Korbel, Jan O. ;

Lander, Eric S. ;

Lee, Charles ;

Lehrach, Hans ;

Mardis, Elaine R. ;

Marth, Gabor T. ;

McVean, Gil A. ;

Nickerson, Deborah A. ;

Schmidt, Jeanette P. ;

Sherry, Stephen T. ;

Wang, Jun ;

Wilson, Richard K. ;

Gibbs, Richard A. ;

Dinh, Huyen ;

Kovar, Christie ;

Lee, Sandra ;

Lewis, Lora ;

Muzny, Donna ;

Reid, Jeff ;

Wang, Min ;

Wang, Jun ;

Fang, Xiaodong ;

Guo, Xiaosen ;

Jian, Min ;

Jiang, Hui ;

Jin, Xin ;

Li, Guoqing ;

Li, Jingxiang ;

Li, Yingrui ;

Li, Zhuo ;

Liu, Xiao ;

Lu, Yao ;

Ma, Xuedi ;

Su, Zhe ;

Tai, Shuaishuai ;

Tang, Meifang .

NATURE, 2012, 491 (7422) :56-65

[2] The Genotype-Tissue Expression (GTEx) pilot analysis: Multitissue gene regulation in humans [J].

Ardlie, Kristin G. ;

DeLuca, David S. ;

Segre, Ayellet V. ;

Sullivan, Timothy J. ;

Young, Taylor R. ;

Gelfand, Ellen T. ;

Trowbridge, Casandra A. ;

Maller, Julian B. ;

Tukiainen, Taru ;

Lek, Monkol ;

Ward, Lucas D. ;

Kheradpour, Pouya ;

Iriarte, Benjamin ;

Meng, Yan ;

Palmer, Cameron D. ;

Esko, Tonu ;

Winckler, Wendy ;

Hirschhorn, Joel N. ;

Kellis, Manolis ;

MacArthur, Daniel G. ;

Getz, Gad ;

Shabalin, Andrey A. ;

Li, Gen ;

Zhou, Yi-Hui ;

Nobel, Andrew B. ;

Rusyn, Ivan ;

Wright, Fred A. ;

Lappalainen, Tuuli ;

Ferreira, Pedro G. ;

Ongen, Halit ;

Rivas, Manuel A. ;

Battle, Alexis ;

Mostafavi, Sara ;

Monlong, Jean ;

Sammeth, Michael ;

Mele, Marta ;

Reverter, Ferran ;

Goldmann, Jakob M. ;

Koller, Daphne ;

Guigo, Roderic ;

McCarthy, Mark I. ;

Dermitzakis, Emmanouil T. ;

Gamazon, Eric R. ;

Im, Hae Kyung ;

Konkashbaev, Anuar ;

Nicolae, Dan L. ;

Cox, Nancy J. ;

Flutre, Timothee ;

Wen, Xiaoquan ;

Stephens, Matthew .

SCIENCE, 2015, 348 (6235) :648-660

[3] Global Survey of Genomic Imprinting by Transcriptome Sequencing [J].

Babak, Tomas ;

DeVeale, Brian ;

Armour, Christopher ;

Raymond, Christopher ;

Cleary, Michele A. ;

van der Kooy, Derek ;

Johnson, Jason M. ;

Lim, Lee P. .

CURRENT BIOLOGY, 2008, 18 (22) :1735-1741

[4] A genome-wide approach reveals novel imprinted genes expressed in the human placenta [J].

Barbaux, Sandrine ;

Gascoin-Lachambre, Geraldine ;

Buffat, Christophe ;

Monnier, Paul ;

Mondon, Francoise ;

Tonanny, Marie-Beatrice ;

Pinard, Amelie ;

Auer, Jana ;

Bessieres, Bettina ;

Barlier, Anne ;

Jacques, Sebastien ;

Simeoni, Umberto ;

Dandolo, Luisa ;

Letourneur, Franck ;

Jammes, Helene ;

Vaiman, Daniel .

EPIGENETICS, 2012, 7 (09) :1079-1090

[5] Mammalian Genomic Imprinting [J].

Bartolomei, Marisa S. ;

Ferguson-Smith, Anne C. .

COLD SPRING HARBOR PERSPECTIVES IN BIOLOGY, 2011, 3 (07) :1-17

[6] The GNAS locus:: Quintessential complex gene encoding Gsα, XLαs, and other imprinted transcripts [J].

Bastepe, Murat .

CURRENT GENOMICS, 2007, 8 (06) :398-414

[7] Insulin-Like Growth Factor 2 in Development and Disease: A Mini-Review [J].

Bergman, Daniel ;

Halje, Matilda ;

Nordin, Matilda ;

Engstrom, Wilhelm .

GERONTOLOGY, 2013, 59 (03) :240-249

[8] SNP-specific array-based allele-specific expression analysis [J].

Bjornsson, Hans T. ;

Albert, Thomas J. ;

Ladd-Acosta, Christine M. ;

Green, Roland D. ;

Rongione, Michael A. ;

Middle, Christina M. ;

Irizarry, Rafael A. ;

Broman, Karl W. ;

Feinberg, Andrew P. .

GENOME RESEARCH, 2008, 18 (05) :771-779

[9] Human GRB10 is imprinted and expressed from the paternal and maternal allele in a highly tissue- and isoform-specific fashion [J].

Blagitko, N ;

Mergenthaler, S ;

Schulz, U ;

Wollmann, HA ;

Craigen, W ;

Eggermann, T ;

Ropers, HH ;

Kalscheuer, VM .

HUMAN MOLECULAR GENETICS, 2000, 9 (11) :1587-1595

[10]

Castel SE, 2015, BIORXIV

← 1 2 3 4 5 6 →