Identification of mammalian microRNA host genes and transcription units.

By Antony Rodríguez, Sam Griffiths-Jones, J. Ashurst, A. Bradley. Genome Research, 2004

2,185 citations recorded by the source corpus.

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.

Subfields: Cancer Research, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/b686010b6e0ce0f76c1e8703a0f698a977bfe808

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Citations in the corpus

MicroRNAs in cell proliferation, cell death, and tumorigenesis (2006, background): “It is now apparent that abnormal miRNA expression is a common feature of human malignancies.”
The Genetic Signatures of Noncoding RNAs (2009, background): “At least some of these RNAs, including intronic RNAs, are precursors for small regulatory RNAs like microRNAs (miRNAs), small interfering RNAs (siRNAs), piwi-interacting RNAs (piRNAs), and small nucleolar RNAs (snoRNAs) [58–68].”
microPrimer: the biogenesis and function of microRNA (2005, background): “About half of the known mammalian miRNAs are within the introns of protein-coding genes, or within either the introns or exons of non-coding RNAs, rather than in their own unique transcription units (Rodriguez et al., 2004).”
Processing of intronic microRNAs (2007, methodology): “However, a recent study by Rodriguez et al (2004) showed that the majority of the human miRNA loci are in fact located within the intronic regions of either coding or noncoding TUs (Rodriguez et al, 2004).”
Microarray profiling of microRNAs reveals frequent coexpression with neighboring miRNAs and host genes. (2005, result): “Similar findings for two miRNAs were also recently reported (Rodriguez et al. 2004).”
miRBase: tools for microRNA genomics (2007, background): “40–70% of vertebrate miRNAs appear to be expressed from introns of protein- and non-coding transcripts (Table 1) (23).”
Genome-wide transcription and the implications for genomic organization (2007, background): “A sizeable fraction of known miRNAs and almost all snoRNAs are found within annotated genes or non-coding transcriptional unit”
Clustering and conservation patterns of human microRNAs (2005, background): “As the MH miRNAs reside within a defined genomic entity and since most of the hosted clusters of miRNAs tend to reside in the same genomic entity (7), we extracted for MH miRNAs the whole intron, rather than a flanking region of defined length.”
Evolution of microRNA diversity and regulation in animals (2011, background): “Many miRNAs reside in introns of protein-coding gene”
An overview of microRNAs (2015, neutral): “miRNA genes are located throughout the genome[15].”
Bioinformatic discovery of microRNA precursors from human ESTs and introns (2006, methodology): “Only a few miRNAs are derived from protein-coding sequences [12], and therefore we selected TC records from Human Gene Index (HGI release 14) lacking an NP number and those containing singleton ESTs as our raw data for predicting miRNAs.”
Genomics of microRNA. (2006, background): “However, recent analyses of miRNA gene locations showed that the majority (w70%) of mammalian miRNA genes (161 out of 232) are located in defined transcription units (TUs) [ 37 ].”