The distribution of RNA motifs in natural sequences

被引:38
作者
Bourdeau, V [1 ]
Ferbeyre, G [1 ]
Pageau, M [1 ]
Paquin, B [1 ]
Cedergren, R [1 ]
机构
[1] Univ Montreal, Dept Biochim, Montreal, PQ H3C 3J7, Canada
基金
加拿大自然科学与工程研究理事会;
关键词
D O I
10.1093/nar/27.22.4457
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
Functional analysis of genome sequences has largely ignored RNA genes and their structures. We introduce here the notion of 'ribonomics' to describe the search for the distribution of and eventually the determination of the physiological roles of these RNA structures found in the sequence databases. The utility of this approach is illustrated here by the identification in the GenBank database of RNA motifs having known binding or chemical activity. The frequency of these motifs indicates that most have originated from evolutionary drift and are selectively neutral. On the other hand, their distribution among species and their location within genes suggest that the destiny of these motifs may be more elaborate. For example, the hammerhead motif has a skewed organismal presence, is phylogenetically stable and recent work on a schistosome version confirms its in vivo biological activity. The under-representation of the valine-binding motif and the Rev-binding element in GenBank hints at a detrimental effect on cell growth or viability. Data on the presence and the location of these motifs may provide critical guidance in the design of experiments directed towards the understanding and the manipulation of RNA complexes and activities in vivo.
引用
收藏
页码:4457 / 4467
页数:11
相关论文
共 59 条
  • [41] TAR RNA-BINDING PROTEIN IS AN INHIBITOR OF THE INTERFERON-INDUCED PROTEIN-KINASE PKR
    PARK, HS
    DAVIES, MV
    LANGLAND, JO
    CHANG, HW
    NAM, YS
    TARTAGLIA, J
    PAOLETTI, E
    JACOBS, BL
    KAUFMAN, RJ
    VENKATESAN, S
    [J]. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 1994, 91 (11) : 4713 - 4717
  • [42] CONFORMATION OF THE TAR RNA-ARGININE COMPLEX BY NMR-SPECTROSCOPY
    PUGLISI, JD
    TAN, RY
    CALNAN, BJ
    FRANKEL, AD
    WILLIAMSON, JR
    [J]. SCIENCE, 1992, 257 (5066) : 76 - 80
  • [43] RNA sequence determinants for aminoglycoside binding to an A-site rRNA model oligonucleotide
    Recht, MI
    Fourmy, D
    Blanchard, SC
    Dahlquist, KD
    Puglisi, JD
    [J]. JOURNAL OF MOLECULAR BIOLOGY, 1996, 262 (04) : 421 - 436
  • [44] Generic properties of combinatory maps: Neutral networks of RNA secondary structures
    Reidys, C
    Stadler, PF
    Schuster, P
    [J]. BULLETIN OF MATHEMATICAL BIOLOGY, 1997, 59 (02) : 339 - 397
  • [45] HIGH-AFFINITY RNA LIGANDS TO ESCHERICHIA-COLI RIBOSOMES AND RIBOSOMAL-PROTEIN S1 - COMPARISON OF NATURAL AND UNNATURAL BINDING-SITES
    RINGQUIST, S
    JONES, T
    SNYDER, EE
    GIBSON, T
    BONI, I
    GOLD, L
    [J]. BIOCHEMISTRY, 1995, 34 (11) : 3640 - 3648
  • [46] A general purpose RNA-cleaving DNA enzyme
    Santoro, SW
    Joyce, GF
    [J]. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 1997, 94 (09) : 4262 - 4266
  • [47] AN RNA MOTIF THAT BINDS ATP
    SASSANFAR, M
    SZOSTAK, JW
    [J]. NATURE, 1993, 364 (6437) : 550 - 553
  • [48] FROM SEQUENCES TO SHAPES AND BACK - A CASE-STUDY IN RNA SECONDARY STRUCTURES
    SCHUSTER, P
    FONTANA, W
    STADLER, PF
    HOFACKER, IL
    [J]. PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES, 1994, 255 (1344) : 279 - 284
  • [49] Getting closer to efficient gene discovery, in silico
    Segovia, L
    [J]. NATURE BIOTECHNOLOGY, 1998, 16 (01) : 25 - 25
  • [50] TRANS-ACTING TRANSCRIPTIONAL REGULATION OF HUMAN T-CELL LEUKEMIA-VIRUS TYPE-III LONG TERMINAL REPEAT
    SODROSKI, J
    ROSEN, C
    WONGSTAAL, F
    SALAHUDDIN, SZ
    POPOVIC, M
    ARYA, S
    GALLO, RC
    HASELTINE, WA
    [J]. SCIENCE, 1985, 227 (4683) : 171 - 173