Identification of mammalian microRNA host genes and transcription units.

To derive a global perspective on the transcription of microRNAs (miRNAs) in mammals, we annotated the genomic position and context of this class of noncoding RNAs (ncRNAs) in the human and mouse genomes. Of the 232 known mammalian miRNAs, we found that 161 overlap with 123 defined transcription units (TUs). We identified miRNAs within introns of 90 protein-coding genes with a broad spectrum of molecular functions, and in both introns and exons of 66 mRNA-like noncoding RNAs (mlncRNAs). In addition, novel families of miRNAs based on host gene identity were identified. The transcription patterns of all miRNA host genes were curated from a variety of sources illustrating spatial, temporal, and physiological regulation of miRNA expression. These findings strongly suggest that miRNAs are transcribed in parallel with their host transcripts, and that the two different transcription classes of miRNAs ('exonic' and 'intronic') identified here may require slightly different mechanisms of biogenesis.

[1]  Lin He,et al.  MicroRNAs: small RNAs with a big role in gene regulation , 2004, Nature Reviews Genetics.

[2]  Lin He,et al.  MicroRNAs: small RNAs with a big role in gene regulation , 2004, Nature Reviews Genetics.

[3]  D. Haussler,et al.  Ultraconserved Elements in the Human Genome , 2004, Science.

[4]  Joaquín Dopazo,et al.  FatiGO: a web tool for finding significant associations of Gene Ontology terms with groups of genes , 2004, Bioinform..

[5]  D. Bartel.  MicroRNAs Genomics, Biogenesis, Mechanism, and Function , 2004, Cell.

[6]  Sam Griffiths-Jones,et al.  The microRNA Registry , 2004, Nucleic Acids Res..

[7]  N. Nomura,et al.  Complete sequencing and characterization of 21,243 full-length human cDNAs , 2004, Nature Genetics.

[8]  V. Ambros,et al.  Expression profiling of mammalian microRNAs uncovers a subset of brain-expressed microRNAs with possible roles in murine and human neuronal differentiation , 2004, Genome Biology.

[9]  Gary Ruvkun,et al.  Identification of many microRNAs that copurify with polyribosomes in mammalian neurons , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[10]  Michael Z Michael,et al.  Reduced accumulation of specific microRNAs in colorectal neoplasia. , 2003, Molecular cancer research : MCR.

[11]  J. Mattick.  Challenging the dogma: the hidden layer of non-protein-coding RNAs in complex organisms. , 2003, BioEssays : news and reviews in molecular, cellular and developmental biology.

[12]  V. Kim,et al.  The nuclear RNase III Drosha initiates microRNA processing , 2003, Nature.

[13]  P. Sharp,et al.  Embryonic stem cell-specific MicroRNAs. , 2003, Developmental cell.

[14]  V. Ambros,et al.  Role of MicroRNAs in Plant and Animal Development , 2003, Science.

[15]  Y. Hayashizaki,et al.  Systematic expression profiling of the mouse transcriptome using RIKEN cDNA microarrays. , 2003, Genome research.

[16]  M. Tomita,et al.  Identification of putative noncoding RNAs among the RIKEN mouse full-length cDNA collection. , 2003, Genome research.

[17]  Bruce A. Hay,et al.  The Drosophila MicroRNA Mir-14 Suppresses Cell Death and Is Required for Normal Fat Metabolism , 2003, Current Biology.

[18]  C. Burge,et al.  Vertebrate MicroRNA Genes , 2003, Science.

[19]  G. Dreyfuss,et al.  Numerous microRNPs in neuronal cells containing novel microRNAs. , 2003, RNA.

[20]  T. Tuschl,et al.  New microRNAs from mouse and human. , 2003, RNA.

[21]  E. Birney,et al.  Analysis of the mouse transcriptome based on functional annotation of 60,770 full-length cDNAs , 2002, Nature.

[22]  V. Kim,et al.  MicroRNA maturation: stepwise processing and subcellular localization , 2002, The EMBO journal.

[23]  J. Squire,et al.  Identification of a novel gene NCRMS on chromosome 12q21 with differential expression between Rhabdomyosarcoma subtypes , 2002, Oncogene.

[24]  T. Tuschl,et al.  Identification of Tissue-Specific MicroRNAs from Mouse , 2002, Current Biology.

[25]  A. Orth,et al.  Large-scale analysis of the human and mouse transcriptomes , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[26]  M. Mann,et al.  miRNPs: a novel class of ribonucleoproteins containing numerous microRNAs. , 2002, Genes & development.

[27]  D. Barlow,et al.  Quantitative genetics: Turning up the heat on QTL mapping , 2002, Nature Reviews Genetics.

[28]  S. Kawamoto,et al.  Expression profile of active genes in the human pituitary gland. , 2002, Journal of molecular endocrinology.

[29]  T. Bliss,et al.  Ntab, a novel non-coding RNA abundantly expressed in rat brain , 2001, Neuroscience.

[30]  T. Tuschl,et al.  Identification of Novel Genes Coding for Small Expressed RNAs , 2001, Science.

[31]  W. Tam.  Identification and characterization of human BIC, a gene on chromosome 21 that encodes a noncoding RNA. , 2001, Gene.

[32]  Minchen Chien,et al.  Nucleotide sequence, transcription map, and mutation analysis of the 13q14 chromosomal region deleted in B-cell chronic lymphocytic leukemia. , 2001, Blood.

[33]  J. Blake,et al.  Creating the Gene Ontology Resource : Design and Implementation The Gene Ontology Consortium 2 , 2001 .

[34]  T. Friedrich,et al.  Characterization of renal chloride channel (CLCN5) mutations in Dent's disease. , 2000, Journal of the American Society of Nephrology : JASN.

[35]  V. Ambros,et al.  Control of developmental timing in Caenorhabditis elegans. , 2000, Current opinion in genetics & development.

[36]  Maciej Szymanski,et al.  Non-coding, mRNA-like RNAs database Y2K , 2000, Nucleic Acids Res..

[37]  C. Chen,et al.  A new structure for the murine Xist gene and its relationship to chromosome choice/counting during X-chromosome inactivation. , 1999, Proceedings of the National Academy of Sciences of the United States of America.

[38]  P. Legrain,et al.  Yeast RNase III as a key processing enzyme in small nucleolar RNAs metabolism. , 1998, Journal of molecular biology.

[39]  Tatsuhiko Kodama,et al.  Sterol-dependent Transcriptional Regulation of Sterol Regulatory Element-binding Protein-2* , 1996, The Journal of Biological Chemistry.

[40]  M. Fujita,et al.  hCDC47, a Human Member of the MCM Family , 1996, The Journal of Biological Chemistry.

[41]  J. Steitz,et al.  A mammalian gene with introns instead of exons generating stable RNA products , 1996, Nature.

[42]  J. Bachellerie,et al.  U24, a novel intron-encoded small nucleolar RNA with two 12 nt long, phylogenetically conserved complementarities to 28S rRNA. , 1995, Nucleic acids research.

[43]  J. Merlie,et al.  A novel synapse-associated noncoding RNA , 1994, Molecular and cellular biology.

[44]  J. Steitz,et al.  A small nucleolar RNA is processed from an intron of the human gene encoding ribosomal protein S3. , 1993, Genes & development.