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Related Experiment Video

Updated: Jul 28, 2026

Annotation of Plant Gene Function via Combined Genomics, Metabolomics and Informatics

Annotation of Plant Gene Function via Combined Genomics, Metabolomics and Informatics

Published on: June 17, 2012

Multiple snoRNA gene clusters from Arabidopsis.

J W Brown¹, G P Clark, D J Leader

¹Unit of Gene Expression, Genetics Division, Scottish Crop Research Institute, Dundee, United Kingdom. lowe@soe.ucsc.edu

RNA (New York, N.Y.)

|January 10, 2002

Summary

Small nucleolar RNAs (snoRNAs) in plants are commonly organized in polycistronic clusters, with many novel genes and methylation sites discovered. This organization differs from vertebrates and highlights snoRNA evolution in plants.

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Area of Science:

Molecular Biology
Genetics
Plant Science

Background:

Small nucleolar RNAs (snoRNAs) are crucial for ribosomal RNA (rRNA) processing and modification.
Gene organization for snoRNAs varies across eukaryotes, with vertebrates primarily using intronic encoding, while maize and yeast utilize polycistronic transcripts.

Purpose of the Study:

To identify and characterize small nucleolar RNA (snoRNA) gene clusters and novel snoRNA genes in plants.
To map 2'-O-ribose methylation sites in plant ribosomal RNAs (rRNAs).
To investigate the gene organization and evolutionary mechanisms of snoRNAs in plants.

Main Methods:

Bioinformatic searches and gene cloning were used to identify snoRNA gene copies and clusters.
Primer extension analysis was employed to map 2'-O-ribose methylation sites in plant rRNAs.
Isolation and characterization of specific snoRNA gene clusters from Arabidopsis.

Main Results:

Identified 43 snoRNA gene clusters, 1 intronic snoRNA, and 10 single genes, totaling 136 copies of 71 different snoRNAs, with 31 novel to plants.
Characterized Arabidopsis snoRNA clusters, including novel box C/D (snoR4) and box H/ACA (snoR5) genes.
Mapped 42 putative 2'-O-ribose methylation sites in plant rRNAs, with eight sites novel to plants.

Conclusions:

The predominant snoRNA gene organization in plants is polycistronic.
A significant portion of predicted and mapped methylation sites in plant rRNAs are novel.
Variations in gene cluster organization suggest diverse mechanisms driving snoRNA evolution in plants.