Using reporter gene assays to identify cis regulatory differences between humans and chimpanzees

被引:17
作者
Chabot, Adrien [1 ]
Shrit, Ralla A. [1 ]
Blekhman, Ran [1 ]
Gilad, Yoav [1 ]
机构
[1] Univ Chicago, Dept Human Genet, Chicago, IL 60637 USA
关键词
D O I
10.1534/genetics.107.073429
中图分类号
Q3 [遗传学];
学科分类号
071007 ; 090102 ;
摘要
Most phenotypic differences between human and chimpanzee are likely to result from differences in gene regulation, rather than changes to protein-coding regions. To date, however, only a handful of human-chimpanzee nucleotide differences leading to changes in gene regulation have been identified. To hone in on differences in regulatory elements between human and chimpanzee, we focused on 10 genes that were previously found to be differentially expressed between the two species. We then designed reporter gene assays for the putative human and chimpanzee promoters of the 10 genes. Of seven promoters that we found to be active in human liver cell lines, human and chimpanzee promoters had significantly different activity in four cases, three of which recapitulated the gene expression difference seen in the microarray experiment. For these three genes, we were therefore able to demonstrate that a change in cis influences expression differences between humans and chimpanzees. Moreover, using site-directed mutagenesis on one construct, the promoter for the DDA3 gene, we were able to identify three nucleotides that together lead to a cis regulatory difference between the species. High-throughput application of this approach can provide a map of regulatory element differences between humans and our close evolutionary relatives.
引用
收藏
页码:2069 / 2076
页数:8
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共 54 条
[41]  
2
[42]   A role of Ultrabithorax in morphological differences between Drosophila species [J].
Stern, DL .
NATURE, 1998, 396 (6710) :463-466
[43]   CIS-ACTING SEQUENCES IN THE ALEUTIAN MINK DISEASE PARVOVIRUS LATE PROMOTER IMPORTANT FOR TRANSCRIPTION - COMPARISON TO THE CANINE PARVOVIRUS AND MINUTE VIRUS OF MICE [J].
STORGAARD, T ;
CHRISTENSEN, J ;
AASTED, B ;
ALEXANDERSEN, S .
JOURNAL OF VIROLOGY, 1993, 67 (04) :1887-1895
[44]  
Takahashi H, 1999, DEVELOPMENT, V126, P3725
[45]   BRCA1 mRNA expression levels as an indicator of chemoresistance in lung cancer [J].
Taron, M ;
Rosell, R ;
Felip, E ;
Mendez, P ;
Souglakos, J ;
Ronco, MS ;
Queralt, C ;
Majo, J ;
Sanchez, JM ;
Sanchez, JJ ;
Maestre, J .
HUMAN MOLECULAR GENETICS, 2004, 13 (20) :2443-2449
[46]   Identification and functional analysis of human transcriptional promoters [J].
Trinklein, ND ;
Aldred, SJF ;
Saldanha, AJ ;
Myers, RM .
GENOME RESEARCH, 2003, 13 (02) :308-312
[47]   Prediction of cis-regulatory elements using binding site matrices -: the successes, the failures and the reasons for both [J].
Vavouri, T ;
Elgar, G .
CURRENT OPINION IN GENETICS & DEVELOPMENT, 2005, 15 (04) :395-402
[48]  
WHITTE RJ, 2001, GENE TRANSCRIPTION M
[49]   Evolutionary changes in cis and trans gene regulation [J].
Wittkopp, PJ ;
Haerum, BK ;
Clark, AG .
NATURE, 2004, 430 (6995) :85-88
[50]   Structure and evolution of a pair-rule interaction element:: runt regulatory sequences in D-melanogaster and D-virilis [J].
Wolff, C ;
Pepling, M ;
Gergen, P ;
Klingler, M .
MECHANISMS OF DEVELOPMENT, 1999, 80 (01) :87-99