Striking nucleotide frequency pattern at the borders of highly conserved vertebrate non-coding sequences

被引：24

作者：

Walter, K

Abnizova, I

Elgar, G

Gilks, WR

机构：

[1] Univ Forvie Site, Inst Publ Hlth, MRC, Biostat Unit, Cambridge CB2 2SR, England

[2] MRC, Rosalind Franklin Ctr Genom Res, Cambridge CB10 1SB, England

来源：

TRENDS IN GENETICS | 2005年 / 21卷 / 08期

关键词：

D O I：

10.1016/j.tig.2005.06.003

中图分类号：

Q3 [遗传学];

学科分类号：

071007 ; 090102 ;

摘要：

In a recent study, 1373 highly conserved non-coding elements (CNEs) were detected by aligning the human and Takifugu rubripes (Fugu) genomes. The remarkable degree of sequence conservation in CNEs compared with their surroundings suggested comparing the base composition within CNEs with their 5' and 3' flanking regions. The analysis reveals a novel, sharp and distinct signal of nucleotide frequency bias precisely at the border between CNEs and flanking regions.

引用

页码：436 / 440

页数：5

共 17 条

[1] Whole-genome shotgun assembly and analysis of the genome of Fugu rubripes [J].

Aparicio, S ;

Chapman, J ;

Stupka, E ;

Putnam, N ;

Chia, J ;

Dehal, P ;

Christoffels, A ;

Rash, S ;

Hoon, S ;

Smit, A ;

Gelpke, MDS ;

Roach, J ;

Oh, T ;

Ho, IY ;

Wong, M ;

Detter, C ;

Verhoef, F ;

Predki, P ;

Tay, A ;

Lucas, S ;

Richardson, P ;

Smith, SF ;

Clark, MS ;

Edwards, YJK ;

Doggett, N ;

Zharkikh, A ;

Tavtigian, SV ;

Pruss, D ;

Barnstead, M ;

Evans, C ;

Baden, H ;

Powell, J ;

Glusman, G ;

Rowen, L ;

Hood, L ;

Tan, YH ;

Elgar, G ;

Hawkins, T ;

Venkatesh, B ;

Rokhsar, D ;

Brenner, S .

SCIENCE, 2002, 297 (5585) :1301-1310

[2] Ensembl 2004 [J].

Birney, E ;

Andrews, D ;

Bevan, P ;

Caccamo, M ;

Cameron, G ;

Chen, Y ;

Clarke, L ;

Coates, G ;

Cox, T ;

Cuff, J ;

Curwen, V ;

Cutts, T ;

Down, T ;

Durbin, R ;

Eyras, E ;

Fernandez-Suarez, XM ;

Gane, P ;

Gibbins, B ;

Gilbert, J ;

Hammond, M ;

Hotz, H ;

Iyer, V ;

Kahari, A ;

Jekosch, K ;

Kasprzyk, A ;

Keefe, D ;

Keenan, S ;

Lehvaslaiho, H ;

McVicker, G ;

Melsopp, C ;

Meidl, P ;

Mongin, E ;

Pettett, R ;

Potter, S ;

Proctor, G ;

Rae, M ;

Searle, S ;

Slater, G ;

Smedley, D ;

Smith, J ;

Spooner, W ;

Stabenau, A ;

Stalker, J ;

Storey, R ;

Ureta-Vidal, A ;

Woodwark, C ;

Clamp, M ;

Hubbard, T .

NUCLEIC ACIDS RESEARCH, 2004, 32 :D468-D470

[3] CHARACTERIZATION OF THE PUFFERFISH (FUGU) GENOME AS A COMPACT MODEL VERTEBRATE GENOME [J].

BRENNER, S ;

ELGAR, G ;

SANDFORD, R ;

MACRAE, A ;

VENKATESH, B ;

APARICIO, S .

NATURE, 1993, 366 (6452) :265-268

[4]

Calladine C.R., 2004, UNDERSTANDING DNA

[5] Finishing the euchromatic sequence of the human genome [J].

Collins, FS ;

Lander, ES ;

Rogers, J ;

Waterston, RH .

NATURE, 2004, 431 (7011) :931-945

[6] WebLogo: A sequence logo generator [J].

Crooks, GE ;

Hon, G ;

Chandonia, JM ;

Brenner, SE .

GENOME RESEARCH, 2004, 14 (06) :1188-1190

[7] Clustering of DNA sequences in human promoters [J].

FitzGerald, PC ;

Shlyakhtenko, A ;

Mir, AA ;

Vinson, C .

GENOME RESEARCH, 2004, 14 (08) :1562-1574

[8] The Ensembl genome database project [J].

Hubbard, T ;

Barker, D ;

Birney, E ;

Cameron, G ;

Chen, Y ;

Clark, L ;

Cox, T ;

Cuff, J ;

Curwen, V ;

Down, T ;

Durbin, R ;

Eyras, E ;

Gilbert, J ;

Hammond, M ;

Huminiecki, L ;

Kasprzyk, A ;

Lehvaslaiho, H ;

Lijnzaad, P ;

Melsopp, C ;

Mongin, E ;

Pettett, R ;

Pocock, M ;

Potter, S ;

Rust, A ;

Schmidt, E ;

Searle, S ;

Slater, G ;

Smith, J ;

Spooner, W ;

Stabenau, A ;

Stalker, J ;

Stupka, E ;

Ureta-Vidal, A ;

Vastrik, I ;

Clamp, M .

NUCLEIC ACIDS RESEARCH, 2002, 30 (01) :38-41

[9] A molecular timescale for vertebrate evolution [J].

Kumar, S ;

Hedges, SB .

NATURE, 1998, 392 (6679) :917-920

[10] Nucleotide frequency variation across human genes [J].

Louie, E ;

Ott, J ;

Majewski, J .

GENOME RESEARCH, 2003, 13 (12) :2594-2601

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