Sense-antisense pairs in mammals: functional and evolutionary considerations

被引：52

作者：

Galante, Pedro A. F.

Vidal, Daniel O.

de Souza, Jorge E.

Camargo, Anamaria A.

de Souza, Sandro J.

机构：

[1] Hosp Alemao Oswaldo Cruz, Ludwig Inst Canc Res, Sao Paulo Branch, BR-01323903 Sao Paulo, Brazil

[2] Univ Sao Paulo, Dept Biochem, BR-05508900 Sao Paulo, Brazil

来源：

GENOME BIOLOGY | 2007年 / 8卷 / 03期

关键词：

D O I：

10.1186/gb-2007-8-3-r40

中图分类号：

Q81 [生物工程学（生物技术）]; Q93 [微生物学];

学科分类号：

071005 ; 0836 ; 090102 ; 100705 ;

摘要：

Background: A significant number of genes in mammalian genomes are being found to have natural antisense transcripts (NATs). These sense-antisense (S-AS) pairs are believed to be involved in several cellular phenomena. Results: Here, we generated a catalog of S-AS pairs occurring in the human and mouse genomes by analyzing different sources of expressed sequences available in the public domain plus 122 massively parallel signature sequencing (MPSS) libraries from a variety of human and mouse tissues. Using this dataset of almost 20,000 S-AS pairs in both genomes we investigated, in a computational and experimental way, several putative roles that have been assigned to NATs, including gene expression regulation. Furthermore, these global analyses allowed us to better dissect and propose new roles for NATs. Surprisingly, we found that a significant fraction of NATs are artifacts produced by genomic priming during cDNA library construction. Conclusion: We propose an evolutionary and functional model in which alternative polyadenylation and retroposition account for the origin of a significant number of functional S-AS pairs in mammalian genomes.

引用

页数：14

共 56 条

[11] Extensive gene traffic on the mammalian X chromosome [J].

Emerson, JJ ;

Kaessmann, H ;

Betrán, E ;

Long, MY .

SCIENCE, 2004, 303 (5657) :537-540

[12] Complex loci in human and mouse genomes [J].

Engstrom, Par G. ;

Suzuki, Harukazu ;

Ninomiya, Noriko ;

Akalin, Altuna ;

Sessa, Luca ;

Lavorgna, Giovanni ;

Brozzi, Alessandro ;

Luzi, Lucilla ;

Tan, Sin Lam ;

Yang, Liang ;

Kunarso, Galih ;

ng, Edwin Lian-Cho Ng ;

Batalov, Serge ;

Wahlestedt, Claes ;

Kai, Chikatoshi ;

Kawai, Jun ;

Carninci, Piero ;

Hayashizaki, Yoshihide ;

Wells, Christine ;

Bajic, Vladimir B. ;

Orlando, Valerio ;

Reid, James F. ;

Lenhard, Boris ;

Lipovich, Leonard .

PLOS GENETICS, 2006, 2 (04) :564-577

[13] Overlapping antisense transcription in the human genome [J].

Fahey, ME ;

Moore, TF ;

Higgins, DG .

COMPARATIVE AND FUNCTIONAL GENOMICS, 2002, 3 (03) :244-253

[14] PSEUDOGENES IN YEAST [J].

FINK, GR .

CELL, 1987, 49 (01) :5-6

[15] A computer program for aligning a cDNA sequence with a genomic DNA sequence [J].

Florea, L ;

Hartzell, G ;

Zhang, Z ;

Rubin, GM ;

Miller, W .

GENOME RESEARCH, 1998, 8 (09) :967-974

[16] Detection and evaluation of intron retention events in the human transcriptome [J].

Galante, PAF ;

Sakabe, NJ ;

Kirschbaum-Slager, N ;

De Souza, SJ .

RNA, 2004, 10 (05) :757-765

[17] Post-transcriptional regulation of thyroid hormone receptor expression by cis-acting sequences and a naturally occurring antisense RNA [J].

Hastings, ML ;

Ingle, HA ;

Lazar, MA ;

Munroe, SH .

JOURNAL OF BIOLOGICAL CHEMISTRY, 2000, 275 (15) :11507-11513

[18]

HENDURE J, 2002, GENOME BIOL, V3, pR44

[19] Long-range heterogeneity at the 3′ ends of human mRNAs [J].

Iseli, C ;

Stevenson, BJ ;

de Souza, SJ ;

Samaia, HB ;

Camargo, AA ;

Buetow, KH ;

Strausberg, RL ;

Simpson, AJG ;

Bucher, P ;

Jongeneel, CV .

GENOME RESEARCH, 2002, 12 (07) :1068-1074

[20] Natural antisense transcripts with coding capacity in Arabidopsis may have a regulatory role that is not linked to double-stranded RNA degradation -: art. no. R51 [J].

Jen, CH ;

Michalopoulos, I ;

Westhead, DR ;

Meyer, P .

GENOME BIOLOGY, 2005, 6 (06)

← 1 2 3 4 5 6 →