title: Clustering and conservation patterns of human microRNAs.
abstract: MicroRNAs (miRNAs) are approximately 22 nt-long non-coding RNA molecules, believed to play important roles in gene regulation. We present a comprehensive analysis of the conservation and clustering patterns of known miRNAs in human. We show that human miRNA gene clustering is significantly higher than expected at random. A total of 37% of the known human miRNA genes analyzed in this study appear in clusters of two or more with pairwise chromosomal distances of at most 3000 nt. Comparison of the miRNA sequences with their homologs in four other organisms reveals a typical conservation pattern, persistent throughout the clusters. Furthermore, we show enrichment in the typical conservation patterns and other miRNA-like properties in the vicinity of known miRNA genes, compared with random genomic regions. This may imply that additional, yet unknown, miRNAs reside in these regions, consistent with the current recognition that there are overlooked miRNAs. Indeed, by comparing our predictions with cloning results and with identified miRNA genes in other mammals, we corroborate the predictions of 18 additional human miRNA genes in the vicinity of the previously known ones. Our study raises the proportion of clustered human miRNAs that are <3000 nt apart to 42%. This suggests that the clustering of miRNA genes is higher than currently acknowledged, alluding to its evolutionary and functional implications.
authors.affiliation: Department of Molecular Genetics and Biotechnology, Faculty of Medicine, The Hebrew University PO Box 12272, Jerusalem 91120, Israel.
authors.forename: Yael
authors.initials: Y
authors.lastname: Altuvia
authors.forename: Pablo
authors.initials: P
authors.lastname: Landgraf
authors.forename: Gila
authors.initials: G
authors.lastname: Lithwick
authors.forename: Naama
authors.initials: N
authors.lastname: Elefant
authors.forename: Sébastien
authors.initials: S
authors.lastname: Pfeffer
authors.forename: Alexei
authors.initials: A
authors.lastname: Aravin
authors.forename: Michael J
authors.initials: MJ
authors.lastname: Brownstein
authors.forename: Thomas
authors.initials: T
authors.lastname: Tuschl
authors.forename: Hanah
authors.initials: H
authors.lastname: Margalit
mesh_terms: D001483:Base Sequence; D045744:Cell Line, Tumor; D002874:Chromosome Mapping; D016000:Cluster Analysis; D019143:Evolution, Molecular; D015894:Genome, Human; D006801:Humans; D035683:MicroRNAs / Q000737:chemistry / Q000235:genetics*
chemical_list: D035683:MicroRNAs