Genome-wide analyses of two families of snoRNA genes from Drosophila melanogaster, demonstrating the extensive utilization of introns for coding of snoRNAs

被引:58
作者
Huang, ZP [1 ]
Zhou, H [1 ]
He, HL [1 ]
Chen, CL [1 ]
Liang, D [1 ]
Qu, LH [1 ]
机构
[1] Zhongshan Univ, Key Lab Gene Engn Minist Educ, State Key Lab Bioconrol, Guangzhou 510275, Peoples R China
关键词
snoRNA; ncRNA; intron; RNA modification; Drosophila melanogaster;
D O I
10.1261/rna.2380905
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
Small nucleolar RNAs (snoRNAs) are an abundant group of noncoding RNAs mainly involved in the post-transcriptional modifications of rRNAs in eukaryotes. In this study, a large-scale genome-wide analysis of the two major families of snoRNA genes in the fruit fly Drosophila melanogaster has been performed using experimental and computational RNomics methods. Two hundred and twelve gene variants, encoding 56 box H/ACA and 63 box C/D snoRNAs, were identified, of which 57 novel snoRNAs have been reported for the first time. These snoRNAs were predicted to guide a total of 147 methylations and pseudouridylations on rRNAs and snRNAs, showing a more comprehensive pattern of rRNA modification in the fruit fly. With the exception of nine, all the snoRNAs identified to date in D. melanogaster are intron encoded. Remarkably, the genomic organization of the snoRNAs is characteristic of 8 dUhg genes and 17 intronic gene clusters, demonstrating that distinct organizations dominate the expression of the two families of snoRNAs in the fruit fly. Of the 267 introns in the host genes, more than half have been identified as host introns for coding of snoRNAs. In contrast to mammals, the variation in size of the host introns is mainly due to differences in the number of snoRNAs they contain. These results demonstrate the extensive utilization of introns for coding of snoRNAs in the host genes and shed light on further research of other noncoding RNA genes in the large introns of the Drosophila genome.
引用
收藏
页码:1303 / 1316
页数:14
相关论文
共 46 条
[1]   A computational search for box C/D snoRNA genes in the Drosophila melanogaster genome [J].
Accardo, MC ;
Giordano, E ;
Riccardo, S ;
Digilio, FA ;
Iazzetti, G ;
Calogero, RA ;
Furia, M .
BIOINFORMATICS, 2004, 20 (18) :3293-3301
[2]   BASIC LOCAL ALIGNMENT SEARCH TOOL [J].
ALTSCHUL, SF ;
GISH, W ;
MILLER, W ;
MYERS, EW ;
LIPMAN, DJ .
JOURNAL OF MOLECULAR BIOLOGY, 1990, 215 (03) :403-410
[3]  
[Anonymous], 2004, SCIENCE, V306, P2013
[4]   Functional characterization of transcriptional regulatory elements in the upstream region and intron 1 of the human S6 ribosomal protein gene [J].
Antoine, M ;
Kiefer, P .
BIOCHEMICAL JOURNAL, 1998, 336 :327-335
[5]   The small RNA profile during Drosophila melanogaster development [J].
Aravin, AA ;
Lagos-Quintana, M ;
Yalcin, A ;
Zavolan, M ;
Marks, D ;
Snyder, B ;
Gaasterland, T ;
Meyer, J ;
Tuschl, T .
DEVELOPMENTAL CELL, 2003, 5 (02) :337-350
[6]  
Bachellerie JP, 2000, RIBOSOME: STRUCTURE, FUNCTION, ANTIBIOTICS, AND CELLULAR INTERACTIONS, P191
[7]   The expanding snoRNA world [J].
Bachellerie, JP ;
Cavaillé, J ;
Hüttenhofer, A .
BIOCHIMIE, 2002, 84 (08) :775-790
[8]   The RNA world of the nucleolus: Two major families of small RNAs defined by different box elements with related functions [J].
Balakin, AG ;
Smith, L ;
Fournier, MJ .
CELL, 1996, 86 (05) :823-834
[9]   Analysis of conserved noncoding DNA in Drosophila reveals similar constraints in intergenic and intronic sequences [J].
Bergman, CM ;
Kreitman, M .
GENOME RESEARCH, 2001, 11 (08) :1335-1345
[10]   Plant snoRNAs: functional evolution and new modes of gene expression [J].
Brown, JWS ;
Echeverria, M ;
Qu, LH .
TRENDS IN PLANT SCIENCE, 2003, 8 (01) :42-49