Characterization of a Supercluster of SnoRNA Genes from Rice Genome

Small nucleolar RNAs (snoRNAs) are mainly involved in rRNA processing and modification, including the maturation of precursor ribosomal RNAs (pre-rRNA), and methylation and pseudouridy nation of rRNA bases. These moleclules are transcripted independly, along with host gene as an intron or as polycistron, reflecting the different pathways for processing of precursor snoRNAs (pre-snoRNAs) into mature snoRNAs. Analysis ofsnoRNA gene organizations and sequences will enable us to explore their evolutions. Previously, we have briefly mentioned a surprisingly larg cluster from rice, consisting of 5 duplictions of a cluster. It provides a good opportunity to reveal the evolution machanism of the snoRNA genes. Here detailed examination were performed and the processs of snoRNA gene loss, insertion and tranfer and cluster duplication are highlighted.

[1]  Zhong Ling,et al.  Two snoRNAs are encoded in the first intron of the rice hsp70 gene , 1997 .

[2]  T. Kiss.  Small Nucleolar RNAs An Abundant Group of Noncoding RNAs with Diverse Cellular Functions , 2002, Cell.

[3]  J. Bachellerie,et al.  Processing of fibrillarin-associated snoRNAs from pre-mRNA introns: an exonucleolytic process exclusively directed by the common stem-box terminal structure. , 1996, Biochimie.

[4]  N Selvamurugan,et al.  Genes for E1, E2, and E3 small nucleolar RNAs. , 1993, Proceedings of the National Academy of Sciences of the United States of America.

[5]  Tamás Kiss,et al.  Site-Specific Pseudouridine Formation in Preribosomal RNA Is Guided by Small Nucleolar RNAs , 1997, Cell.

[6]  S. Eddy,et al.  A computational screen for methylation guide snoRNAs in yeast. , 1999, Science.

[7]  J. Bachellerie,et al.  Guiding ribose methylation of rRNA. , 1997, Trends in biochemical sciences.

[8]  D. Tollervey,et al.  Ribosome synthesis in Saccharomyces cerevisiae. , 1999, Annual review of genetics.

[9]  L. Qu,et al.  Identification of 10 novel snoRNA gene clusters from Arabidopsis thaliana. , 2001, Nucleic acids research.

[10]  E. Maxwell,et al.  Elements essential for processing intronic U14 snoRNA are located at the termini of the mature snoRNA sequence and include conserved nucleotide boxes C and D. , 1996, RNA.

[11]  P J Shaw,et al.  Clusters of multiple different small nucleolar RNA genes in plants are expressed as and processed from polycistronic pre‐snoRNAs , 1997, The EMBO journal.

[12]  Laurie Smith,et al.  The RNA World of the Nucleolus: Two Major Families of Small RNAs Defined by Different Box Elements with Related Functions , 1996, Cell.

[13]  M. Fournier,et al.  The small nucleolar RNAs. , 1995, Annual review of biochemistry.

[14]  Tamás Kiss,et al.  Site-Specific Ribose Methylation of Preribosomal RNA: A Novel Function for Small Nucleolar RNAs , 1996, Cell.

[15]  T. Lowe,et al.  Multiple snoRNA gene clusters from Arabidopsis. , 2001, RNA.

[16]  Raghvendra Kumar Mishra,et al.  Three small nucleolar RNAs that are involved in ribosomal RNA precursor processing. , 1997, Proceedings of the National Academy of Sciences of the United States of America.

[17]  Liang-Hu Qu,et al.  The high diversity of snoRNAs in plants: identification and comparative study of 120 snoRNA genes from Oryza sativa. , 2003, Nucleic acids research.

[18]  Liang-Hu Qu,et al.  Seven Novel Methylation Guide Small Nucleolar RNAs Are Processed from a Common Polycistronic Transcript by Rat1p and RNase III in Yeast , 1999, Molecular and Cellular Biology.

[19]  J. Steitz,et al.  Guided tours: from precursor snoRNA to functional snoRNP. , 1999, Current opinion in cell biology.

[20]  C Gaspin,et al.  Box C/D RNA guides for the ribose methylation of archaeal tRNAs. The tRNATrp intron guides the formation of two ribose-methylated nucleosides in the mature tRNATrp. , 2001, Nucleic acids research.

[21]  J. Steitz,et al.  Sno Storm in the Nucleolus: New Roles for Myriad Small RNPs , 1997, Cell.

[22]  J. Steitz,et al.  A small nucleolar RNA requirement for site-specific ribose methylation of rRNA in Xenopus. , 1996, Proceedings of the National Academy of Sciences of the United States of America.

[23]  W. Filipowicz,et al.  Exonucleolytic processing of small nucleolar RNAs from pre-mRNA introns. , 1995, Genes & development.

[24]  T. Kiss,et al.  The family of box ACA small nucleolar RNAs is defined by an evolutionarily conserved secondary structure and ubiquitous sequence elements essential for RNA accumulation. , 1997, Genes & development.

[25]  J. Gilley,et al.  Evolution of U24 and U36 snoRNAs encoded within introns of vertebrate rpL7a gene homologs: unique features of mammalian U36 variants. , 1998, DNA and cell biology.

[26]  Meng Qing,et al.  Identification of 10 novel snoRNA gene clusters from Arabidopsis thaliana , 2001 .

[27]  A. Hüttenhofer,et al.  Identification of brain-specific and imprinted small nucleolar RNA genes exhibiting an unusual genomic organization. , 2000, Proceedings of the National Academy of Sciences of the United States of America.

[28]  Liang-Hu Qu,et al.  Nucleotide Modifications of Eukaryotic rRNAs: the World of Small Nucleolar RNA Guides Revisited , 2000 .

[29]  J. Bachellerie,et al.  Intron-encoded, antisense small nucleolar RNAs: the characterization of nine novel species points to their direct role as guides for the 2'-O-ribose methylation of rRNAs. , 1996, Journal of molecular biology.

[30]  S. Gerbi,et al.  Nucleolar localization elements in U8 snoRNA differ from sequences required for rRNA processing. , 1998, RNA.

[31]  Liang-Hu Qu,et al.  A novel gene organization: intronic snoRNA gene clusters from Oryza sativa. , 2002, Nucleic acids research.

[32]  W. Filipowicz,et al.  Biogenesis of small nucleolar ribonucleoproteins. , 2002, Current opinion in cell biology.

[33]  D. Tollervey,et al.  Function and synthesis of small nucleolar RNAs. , 1997, Current opinion in cell biology.

[34]  J. Ni,et al.  Small Nucleolar RNAs Direct Site-Specific Synthesis of Pseudouridine in Ribosomal RNA , 1997, Cell.

[35]  D. Tollervey,et al.  Trans-acting factors in yeast pre-rRNA and pre-snoRNA processing. , 1995, Biochemistry and cell biology = Biochimie et biologie cellulaire.

[36]  W. Filipowicz,et al.  The Host Gene for Intronic U17 Small Nucleolar RNAs in Mammals Has No Protein-Coding Potential and Is a Member of the 5′-Terminal Oligopyrimidine Gene Family , 1998, Molecular and Cellular Biology.

[37]  Roger A. Garrett,et al.  The Ribosome, Structure, Function, Antibiotics, and Cellular Interactions , 2000 .