A panel of induced pluripotent stem cells from chimpanzees: a resource for comparative functional genomics

被引：88

作者：

Romero, Irene Gallego ^{[1
]}

Pavlovic, Bryan J. ^{[1
]}

Hernando-Herraez, Irene ^{[2
]}

Zhou, Xiang ^{[3
]}

Ward, Michelle C. ^{[1
]}

Banovich, Nicholas E. ^{[1
]}

Kagan, Courtney L. ^{[1
]}

Burnett, Jonathan E. ^{[1
]}

Huang, Constance H. ^{[1
]}

Mitrano, Amy ^{[1
]}

Chavarria, Claudia I. ^{[1
]}

Ben-Nun, Inbar Friedrich ^{[4
,9
]}

Li, Yingchun ^{[5
,6
]}

Sabatini, Karen ^{[4
,6
,7
]}

Leonardo, Trevor R. ^{[4
,6
,7
]}

Parast, Mana ^{[5
,6
]}

Marques-Bonet, Tomas ^{[2
,8
]}

Laurent, Louise C. ^{[6
,7
]}

Loring, Jeanne F. ^{[4
]}

Gilad, Yoav ^{[1
]}

机构：

[1] Univ Chicago, Dept Human Genet, Chicago, IL 60637 USA

[2] Inst Biol Evolut CSIC UPF, Parc Recerca Biomed Barcelona, Barcelona, Spain

[3] Univ Michigan, Dept Biostat, Ann Arbor, MI 48109 USA

[4] Scripps Res Inst, Dept Physiol Chem, Ctr Regenerat Med, La Jolla, CA 92037 USA

[5] Univ Calif San Diego, Dept Pathol, San Diego, CA 92103 USA

[6] Sanford Consortium Regenerat Med, La Jolla, CA USA

[7] Univ Calif San Diego, Dept Reprod Med, San Diego, CA 92103 USA

[8] Ctr Nacl Anal Genom CNAG CRG, Barcelona, Spain

[9] Lonza Walkersville Inc, Walkersville, MD USA

来源：

ELIFE | 2015年 / 4卷

基金：

欧洲研究理事会; 美国国家卫生研究院; 英国惠康基金;

关键词：

GENE-EXPRESSION; DNA METHYLATION; EVOLUTION; NORMALIZATION; GENERATION; REGULATORS; DERIVATION; INDUCTION; ALIGNMENT; DISEASE;

D O I：

10.7554/eLife.07103

中图分类号：

Q [生物科学];

学科分类号：

07 ; 0710 ; 09 ;

摘要：

Comparative genomics studies in primates are restricted due to our limited access to samples. In order to gain better insight into the genetic processes that underlie variation in complex phenotypes in primates, we must have access to faithful model systems for a wide range of cell types. To facilitate this, we generated a panel of 7 fully characterized chimpanzee induced pluripotent stem cell (iPSC) lines derived from healthy donors. To demonstrate the utility of comparative iPSC panels, we collected RNA-sequencing and DNA methylation data from the chimpanzee iPSCs and the corresponding fibroblast lines, as well as from 7 human iPSCs and their source lines, which encompass multiple populations and cell types. We observe much less within-species variation in iPSCs than in somatic cells, indicating the reprogramming process erases many inter-individual differences. The low within-species regulatory variation in iPSCs allowed us to identify many novel inter-species regulatory differences of small magnitude.

引用

页数：29

共 92 条

[21] Turning straw into gold: directing cell fate for regenerative medicine [J].

Cohen, Dena E. ;

Melton, Douglas .

NATURE REVIEWS GENETICS, 2011, 12 (04) :243-252

[22] The Evolution of Lineage-Specific Regulatory Activities in the Human Embryonic Limb [J].

Cotney, Justin ;

Leng, Jing ;

Yin, Jun ;

Reilly, Steven K. ;

DeMare, Laura E. ;

Emera, Deena ;

Ayoub, Albert E. ;

Rakic, Pasko ;

Noonan, James P. .

CELL, 2013, 154 (01) :185-196

[23] Development of Histocompatible Primate-Induced Pluripotent Stem Cells for Neural Transplantation [J].

Deleidi, Michela ;

Hargus, Gunnar ;

Hallett, Penelope ;

Osborn, Teresia ;

Isacson, Ole .

STEM CELLS, 2011, 29 (07) :1052-1063

[24] lumi:: a pipeline for processing Illumina microarray [J].

Du, Pan ;

Kibbe, Warren A. ;

Lin, Simon M. .

BIOINFORMATICS, 2008, 24 (13) :1547-1548

[25] MUSCLE: multiple sequence alignment with high accuracy and high throughput [J].

Edgar, RC .

NUCLEIC ACIDS RESEARCH, 2004, 32 (05) :1792-1797

[26] A Humanized Version of Foxp2 Affects Cortico-Basal Ganglia Circuits in Mice [J].

Enard, Wolfgang ;

Gehre, Sabine ;

Hammerschmidt, Kurt ;

Hoelter, Sabine M. ;

Blass, Torsten ;

Somel, Mehmet ;

Brueckner, Martina K. ;

Schreiweis, Christiane ;

Winter, Christine ;

Sohr, Reinhard ;

Becker, Lore ;

Wiebe, Victor ;

Nickel, Birgit ;

Giger, Thomas ;

Mueller, Uwe ;

Groszer, Matthias ;

Adler, Thure ;

Aguilar, Antonio ;

Bolle, Ines ;

Calzada-Wack, Julia ;

Dalke, Claudia ;

Ehrhardt, Nicole ;

Favor, Jack ;

Fuchs, Helmut ;

Gailus-Durner, Valerie ;

Hans, Wolfgang ;

Hoelzlwimmer, Gabriele ;

Javaheri, Anahita ;

Kalaydjiev, Svetoslav ;

Kallnik, Magdalena ;

Kling, Eva ;

Kunder, Sandra ;

Mossbrugger, Ilona ;

Naton, Beatrix ;

Racz, Ildiko ;

Rathkolb, Birgit ;

Rozman, Jan ;

Schrewe, Anja ;

Busch, Dirk H. ;

Graw, Jochen ;

Ivandic, Boris ;

Klingenspor, Martin ;

Klopstock, Thomas ;

Ollert, Markus ;

Quintanilla-Martinez, Leticia ;

Schulz, Holger ;

Wolf, Eckhard ;

Wurst, Wolfgang ;

Zimmer, Andreas ;

Fisher, Simon E. .

CELL, 2009, 137 (05) :961-971

[27] Derivation of induced pluripotent stem cells from pig somatic cells [J].

Ezashi, Toshihiko ;

Telugu, Bhanu Prakash V. L. ;

Alexenko, Andrei P. ;

Sachdev, Shrikesh ;

Sinha, Sunilima ;

Roberts, R. Michael .

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2009, 106 (27) :10993-10998

[28] Bioconductor: open software development for computational biology and bioinformatics [J].

Gentleman, RC ;

Carey, VJ ;

Bates, DM ;

Bolstad, B ;

Dettling, M ;

Dudoit, S ;

Ellis, B ;

Gautier, L ;

Ge, YC ;

Gentry, J ;

Hornik, K ;

Hothorn, T ;

Huber, W ;

Iacus, S ;

Irizarry, R ;

Leisch, F ;

Li, C ;

Maechler, M ;

Rossini, AJ ;

Sawitzki, G ;

Smith, C ;

Smyth, G ;

Tierney, L ;

Yang, JYH ;

Zhang, JH .

GENOME BIOLOGY, 2004, 5 (10)

[29] Multi-species microarrays reveal the effect of sequence divergence on gene expression profiles [J].

Gilad, Y ;

Rifkin, SA ;

Bertone, P ;

Gerstein, M ;

White, KP .

GENOME RESEARCH, 2005, 15 (05) :674-680

[30] Dynamics of DNA Methylation in Recent Human and Great Ape Evolution [J].

Hernando-Herraez, Irene ;

Prado-Martinez, Javier ;

Garg, Paras ;

Fernandez-Callejo, Marcos ;

Heyn, Holger ;

Hvilsom, Christina ;

Navarro, Arcadi ;

Esteller, Manel ;

Sharp, Andrew J. ;

Marques-Bonet, Tomas .

PLOS GENETICS, 2013, 9 (09)

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