Results 1 - 10
of
491
A mammalian microRNA expression atlas based on small RNA library sequencing.
- Cell,
, 2007
"... SUMMARY MicroRNAs (miRNAs) are small noncoding regulatory RNAs that reduce stability and/or translation of fully or partially sequencecomplementary target mRNAs. In order to identify miRNAs and to assess their expression patterns, we sequenced over 250 small RNA libraries from 26 different organ sy ..."
Abstract
-
Cited by 418 (4 self)
- Add to MetaCart
(Show Context)
SUMMARY MicroRNAs (miRNAs) are small noncoding regulatory RNAs that reduce stability and/or translation of fully or partially sequencecomplementary target mRNAs. In order to identify miRNAs and to assess their expression patterns, we sequenced over 250 small RNA libraries from 26 different organ systems and cell types of human and rodents that were enriched in neuronal as well as normal and malignant hematopoietic cells and tissues. We present expression profiles derived from clone count data and provide computational tools for their analysis. Unexpectedly, a relatively small set of miRNAs, many of which are ubiquitously expressed, account for most of the differences in miRNA profiles between cell lineages and tissues. This broad survey also provides detailed and accurate information about mature sequences, precursors, genome locations, maturation processes, inferred transcriptional units, and conservation patterns. We also propose a subclassification scheme for miRNAs for assisting future experimental and computational functional analyses.
The Drosha-DGCR8 complex in primary microRNA processing
- Genes Dev
, 2004
"... RNase III proteins play key roles in microRNA (miRNA) biogenesis. The nuclear RNase III Drosha cleaves primary miRNAs (pri-miRNAs) to release hairpin-shaped pre-miRNAs that are subsequently cut by the cytoplasmic RNase III Dicer to generate mature miRNAs. While Dicer (class III) and other simple RNa ..."
Abstract
-
Cited by 220 (4 self)
- Add to MetaCart
RNase III proteins play key roles in microRNA (miRNA) biogenesis. The nuclear RNase III Drosha cleaves primary miRNAs (pri-miRNAs) to release hairpin-shaped pre-miRNAs that are subsequently cut by the cytoplasmic RNase III Dicer to generate mature miRNAs. While Dicer (class III) and other simple RNase III proteins (class I) have been studied intensively, the class II enzyme Drosha remains to be characterized. Here we dissected the action mechanism of human Drosha by generating mutants and by characterizing its new interacting partner, DGCR8. The basic action mechanism of Drosha was found to be similar to that of human Dicer; the RNase III domains A and B form an intramolecular dimer and cleave the 3 and 5 strands of the stem, respectively. Human Drosha fractionates at ∼650 kDa, indicating that Drosha functions as a large complex. In this complex, Drosha interacts with DGCR8, which contains two double-stranded RNA (dsRNA)-binding domains. By RNAi and biochemical reconstitution, we show that DGCR8 may be an essential component of the pri-miRNA processing complex, along with Drosha. Based on these results, we propose a model for the action mechanism of class II RNase III proteins. [Keywords: microRNA; Drosha; DGCR8; processing] Supplemental material is available at
RNA polymerase III transcribes human microRNAs.
- Nature Struct. Mol. Biol.
, 2006
"... Prior work demonstrates that mammalian microRNA (miRNA or miR) expression requires RNA polymerase II (Pol II). However, the transcriptional requirements of many miRNAs remain untested. Our genomic analysis of miRNAs in the human chromosome 19 miRNA cluster (C19MC) revealed that they are intersperse ..."
Abstract
-
Cited by 201 (3 self)
- Add to MetaCart
Prior work demonstrates that mammalian microRNA (miRNA or miR) expression requires RNA polymerase II (Pol II). However, the transcriptional requirements of many miRNAs remain untested. Our genomic analysis of miRNAs in the human chromosome 19 miRNA cluster (C19MC) revealed that they are interspersed among Alu repeats. Because Alu transcription occurs through RNA Pol III recruitment, and we found that Alu elements upstream of C19MC miRNAs retain sequences important for Pol III activity, we tested the promoter requirements of C19MC miRNAs. Chromatin immunoprecipitation and cell-free transcription assays showed that Pol III, but not Pol II, is associated with miRNA genomic sequence and sufficient for transcription. Moreover, the mature miRNA sequences of approximately 50 additional human miRNAs lie within Alu and other known repetitive elements. These findings extend the current view of miRNA origins and the transcriptional machinery driving their expression. Over 450 miRNAs have been described in the human genome 1 . miRNAs are important in human development, oncogenesis and immunity, and they have drawn renewed attention to the small noncoding elements of the transcriptome. miRNAs are short (17-25 base pairs (bp)) noncoding RNAs that guide cellular machinery to specific messenger RNAs 2,3 to control expression. Initial miRNA transcripts can be several thousand base pairs in length, and they are processed to produce B70-bp stem-loops (pre-miRNAs) before nuclear export 4 . Upon entering the cytoplasm, the RNA-induced silencing complex (RISC) cleaves and denatures pre-miRNAs to produce the functionally mature, single-stranded miRNAs 4 . Through complementary base pairing to specific protein-coding mRNA transcripts, miRNAs direct mRNA silencing by a variety of mechanisms, including message degradation 5 , deadenylation 6 and translational repression 7 . The evolutionary conservation of miRNAs has been described 8 , as has their use of RNA polymerase II (Pol II) promoters for control of expression 9-11 . A recent study described approximately ten mammalian miRNAs created by a repetitive element transposition and subsequent transcription across two tandem, inverted repetitive elements 12 . In this study, we tested if other miRNAs possess sequences repetitive in origin, and the transcriptional requirements of a dense cluster of human miRNAs interspersed among repetitive Alu elements on chromosome 19. RESULTS miRNAs localize to repeats within the human genome We expanded prior studies by screening sequences flanking all known human miRNAs for repetitive elements (500 bp upstream and down stream) and annotating them using the Censor web server at the Genetic Information Research Institute 13 . Overall, we found that the mature sequences from B50 human miRNAs reside within repetitive elements Upstream Alus express downstream miRNAs We used degenerate primers and thermostable polymerase to first confirm that miRNAs within the C19MC are transcribed in vivo (Supplementary Table 2 online). To discern how the C19MC miRNAs are expressed, we used one of these miRNAs, miR-517a, and sequences immediately upstream, which consist of an Alu We next made reporter constructs to test whether the hairpins expressed from the miR-517a 5¢ Alu had silencing activity. These reporters (517-AS and LacZ-AS) produced Renilla luciferase transcripts with target sequences for miR-517a or shLacZ cloned into the 3¢ UTR
microRNAs as oncogenes and tumor suppressors.
- Dev. Biol.,
, 2007
"... Abstract microRNAs (miRNAs) are a new class of non-protein-coding, endogenous, small RNAs. They are important regulatory molecules in animals and plants. miRNA regulates gene expression by translational repression, mRNA cleavage, and mRNA decay initiated by miRNA-guided rapid deadenylation. Recent ..."
Abstract
-
Cited by 189 (0 self)
- Add to MetaCart
Abstract microRNAs (miRNAs) are a new class of non-protein-coding, endogenous, small RNAs. They are important regulatory molecules in animals and plants. miRNA regulates gene expression by translational repression, mRNA cleavage, and mRNA decay initiated by miRNA-guided rapid deadenylation. Recent studies show that some miRNAs regulate cell proliferation and apoptosis processes that are important in cancer formation. By using multiple molecular techniques, which include Northern blot analysis, real-time PCR, miRNA microarray, up-or down-expression of specific miRNAs, it was found that several miRNAs were directly involved in human cancers, including lung, breast, brain, liver, colon cancer, and leukemia. In addition, some miRNAs may function as oncogenes or tumor suppressors. More than 50% of miRNA genes are located in cancer-associated genomic regions or in fragile sites, suggesting that miRNAs may play a more important role in the pathogenesis of a limited range of human cancers than previously thought. Overexpressed miRNAs in cancers, such as mir-17-92, may function as oncogenes and promote cancer development by negatively regulating tumor suppressor genes and/or genes that control cell differentiation or apoptosis. Underexpressed miRNAs in cancers, such as let-7, function as tumor suppressor genes and may inhibit cancers by regulating oncogenes and/or genes that control cell differentiation or apoptosis. miRNA expression profiles may become useful biomarkers for cancer diagnostics. In addition, miRNA therapy could be a powerful tool for cancer prevention and therapeutics.
Molecular basis for the recognition of primary microRNAs by the Drosha-DGCR8 complex
- Cell
, 2006
"... The Drosha-DGCR8 complex initiates micro-RNA maturation by precise cleavage of the stem loops that are embedded in primary transcripts (pri-miRNAs). Here we propose a model for this process that is based upon evidence from both computational and biochemical analyses. A typical metazoan pri-miRNA con ..."
Abstract
-
Cited by 133 (1 self)
- Add to MetaCart
The Drosha-DGCR8 complex initiates micro-RNA maturation by precise cleavage of the stem loops that are embedded in primary transcripts (pri-miRNAs). Here we propose a model for this process that is based upon evidence from both computational and biochemical analyses. A typical metazoan pri-miRNA consists of a stem of 33 bp, with a terminal loop and flanking segments. The terminal loop is unessential, whereas the flanking ssRNA segments are critical for processing. The cleavage site is determined mainly by the distance ( 11 bp) from the stem-ssRNA junction. Purified DGCR8, but not Drosha, interacts with pri-miRNAs both directly and specifically, and the flanking ssRNA segments are vital for this binding to occur. Thus, DGCR8 may function as the molecular anchor that measures the distance from the dsRNA-ssRNA junction. Our current study thus facilitates the prediction of novel micro-RNAs and will assist in the rational design of small hairpin RNAs for RNA interference.
Non-coding RNA
- Hum. Mol. Genet., 15(Spec No
, 2006
"... The term non-coding RNA (ncRNA) is commonly employed for RNA that does not encode a protein, but this does not mean that such RNAs do not contain information nor have function. Although it has been generally assumed that most genetic information is transacted by proteins, recent evidence suggests th ..."
Abstract
-
Cited by 75 (2 self)
- Add to MetaCart
(Show Context)
The term non-coding RNA (ncRNA) is commonly employed for RNA that does not encode a protein, but this does not mean that such RNAs do not contain information nor have function. Although it has been generally assumed that most genetic information is transacted by proteins, recent evidence suggests that the majority of the genomes of mammals and other complex organisms is in fact transcribed into ncRNAs, many of which are alternatively spliced and/or processed into smaller products. These ncRNAs include microRNAs and snoRNAs (many if not most of which remain to be identified), as well as likely other classes of yet-to-be-discovered small regulatory RNAs, and tens of thousands of longer transcripts (including complex patterns of interlacing and overlapping sense and antisense transcripts), most of whose functions are unknown. These RNAs (including those derived from introns) appear to comprise a hidden layer of internal signals that control various levels of gene expression in physiology and development, including chromatin architecture/epigenetic memory, transcription, RNA splicing, editing, translation and turnover. RNA regulatory networks may determine most of our complex characteristics, play a significant role in disease and constitute an unexplored world of genetic variation both within and between species.
Mir-17-5p regulates breast cancer cell proliferation by inhibiting translation of AIB1 mRNA
- Mol. Cell Biol
, 2006
"... MicroRNAs are an extensive family of 22-nucleotide-long noncoding RNAs expressed in a wide range of eukaryotes, including humans, and they are important in development and disease. We found that microRNA Mir-17-5p has extensive complementarity to the mRNA of AIB1 (named for “amplified in breast canc ..."
Abstract
-
Cited by 73 (0 self)
- Add to MetaCart
(Show Context)
MicroRNAs are an extensive family of 22-nucleotide-long noncoding RNAs expressed in a wide range of eukaryotes, including humans, and they are important in development and disease. We found that microRNA Mir-17-5p has extensive complementarity to the mRNA of AIB1 (named for “amplified in breast cancer 1”). Cell culture experiments showed that AIB1 expression was downregulated by Mir-17-5p, primarily through trans-lational inhibition. Expression of Mir-17-5p was low in breast cancer cell lines. We also found that downregu-lation of AIB1 by Mir-17-5p resulted in decreased estrogen receptor-mediated, as well as estrogen receptor-independent, gene expression and decreased proliferation of breast cancer cells. Mir-17-5p also completely abrogated the insulin-like growth factor 1-mediated, anchorage-independent growth of breast cancer cells. Our results reveal that Mir-17-5p has a role as a tumor suppressor in breast cancer cells. MicroRNAs (miRNAs) are genomically encoded, 22-nu-cleotide-long noncoding RNAs found in many organisms. miRNAs are produced from primary RNA polymerase II tran-scripts by sequential processing in the nucleus and cytoplasm (26, 27). Nuclear precursor RNAs are cleaved by the endo-nuclease Drosha in a “microprocessor complex ” to release
Characterization and identification of microRNA core promoters in four model species
- PLoS Comput Biol
"... Characterization and identification of microRNA core promoters in four model species ..."
Abstract
-
Cited by 53 (2 self)
- Add to MetaCart
(Show Context)
Characterization and identification of microRNA core promoters in four model species
Processing of pre-microRNAs by the Dicer-1-Loquacious complex in Drosophila cells
- PLoS Biol
, 2005
"... Open access, freely available online ..."
(Show Context)
