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122
IntaRNA: efficient prediction of bacterial sRNA targets incorporating target site accessibility and seed regions
- Bioinformatics
, 2008
"... Motivation: During the last few years, several new small regulatory RNAs (sRNAs) have been discovered in bacteria. Most of them act as post-transcriptional regulators by base pairing to a target mRNA, causing translational repression or activation, or mRNA degradation. Numerous sRNAs have already be ..."
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Motivation: During the last few years, several new small regulatory RNAs (sRNAs) have been discovered in bacteria. Most of them act as post-transcriptional regulators by base pairing to a target mRNA, causing translational repression or activation, or mRNA degradation. Numerous sRNAs have already been identified, but the number of experimentally verified targets is considerably lower. Consequently, computational target prediction is in great demand. Many existing tar-get prediction programs neglect the accessibility of target sites and the existence of a seed, while other approaches are either specialized to certain types of RNAs or too slow for genome-wide searches. Results: We introduce INTARNA, a new general and fast approach to the prediction of RNA-RNA interactions incorporating accessibility of target sites as well as the existence of a user-definable seed. We suc-cessfully applied INTARNA to the prediction of bacterial sRNA targets and determined the exact locations of the interactions with a higher accuracy than competing programs.
miRGen: a database for the study of animal microRNA genomic organization and function
- Nucleic Acids Res
, 2007
"... doi:10.1093/nar/gkl904 ..."
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fRNAdb: a platform for mining/annotating functional RNA candidates from non-coding RNA sequences
- Nucleic Acids Res
, 2006
"... candidates from non-coding RNA sequences ..."
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miR-145 and miR-143 regulate smooth muscle cell fate and plasticity
- Nature
, 2009
"... microRNAs are regulators of myriad cellular events, but evidence for a single microRNA that can efficiently differentiate multipotent cells into a specific lineage or regulate direct reprogramming of cells into an alternate cell fate has been elusive. Here, we show that miR-145 and miR-143 are co-tr ..."
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Cited by 18 (0 self)
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microRNAs are regulators of myriad cellular events, but evidence for a single microRNA that can efficiently differentiate multipotent cells into a specific lineage or regulate direct reprogramming of cells into an alternate cell fate has been elusive. Here, we show that miR-145 and miR-143 are co-transcribed in multipotent cardiac progenitors before becoming localized to smooth muscle cells, including neural crest stem cell–derived vascular smooth muscle cells. miR-145 and miR-143 were direct transcriptional targets of serum response factor, myocardin and Nkx2.5, and were downregulated in injured or atherosclerotic vessels containing proliferating, less differentiated smooth muscle cells. miR-145 was necessary for myocardin-induced reprogramming of adult fibroblasts into smooth muscle cells and sufficient to induce differentiation of multipotent neural crest stem cells into vascular smooth muscle. Furthermore, miR-145 and miR-143 cooperatively targeted a network of transcription factors, including Klf4, myocardin, and Elk-1 to promote differentiation and repress proliferation of smooth muscle cells. These findings demonstrate that miR-145 can direct the smooth muscle fate and that miR-145 and miR-143 function to regulate the quiescent versus proliferative phenotype of smooth muscle cells. MicroRNAs (miRNAs) represent a class of small (20–25 nucleotides), non-coding RNAs
Human cellular microRNA hsa-miR-29a interferes with viral nef protein expression and HIV-1 replication
- Retrovirology
, 2008
"... protein expression and HIV-1 replication ..."
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Numerous Conserved and Divergent MicroRNAs Expressed by Herpes Simplex Viruses 1 and 2 �
, 2009
"... Certain viruses use microRNAs (miRNAs) to regulate the expression of their own genes, host genes, or both. Previous studies have identified a limited number of miRNAs expressed by herpes simplex viruses 1 and 2 (HSV-1 and-2), some of which are conserved between these two viruses. To more comprehensi ..."
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Certain viruses use microRNAs (miRNAs) to regulate the expression of their own genes, host genes, or both. Previous studies have identified a limited number of miRNAs expressed by herpes simplex viruses 1 and 2 (HSV-1 and-2), some of which are conserved between these two viruses. To more comprehensively analyze the miRNAs expressed by HSV-1 or HSV-2 during productive and latent infection, we applied a massively parallel sequencing approach. We were able to identify 16 and 17 miRNAs expressed by HSV-1 and HSV-2, respectively, including all previously known species, and a number of previously unidentified virus-encoded miRNAs. The genomic positions of most miRNAs encoded by these two viruses are within or proximal to the latencyassociated transcript region. Nine miRNAs are conserved in position and/or sequence, particularly in the seed region, between these two viruses. Interestingly, we did not detect an HSV-2 miRNA homolog of HSV-1 miR-H1, which is highly expressed during productive infection, but we did detect abundant expression of miR-H6, whose seed region is conserved with HSV-1 miR-H1 and might represent a functional analog. We also identified a highly conserved miRNA family arising from the viral origins of replication. In addition, we detected several pairs of complementary miRNAs and we found miRNA-offset RNAs (moRs) arising from the precursors of HSV-1 and HSV-2 miR-H6 and HSV-2 miR-H4. Our results reveal elements of miRNA conservation and
Sequence analysis
"... IntaRNA: efficient prediction of bacterial sRNA targets incorporating target site accessibility and seed regions ..."
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IntaRNA: efficient prediction of bacterial sRNA targets incorporating target site accessibility and seed regions
Site-specific microRNA-92a regulation of Kruppellike factors 4 and 2 in atherosusceptible endothelium. Arterioscler Thromb Vasc Biol
"... Objective—Endothelial transcription factors Krüppel-like factor 4 (KLF4) and KLF2 are implicated in protection against atherogenesis. Steady-state microRNA (miR) regulation of KLFs in vivo is accessible by screening region-specific endothelial miRs and their targets. Methods and Results—A subset of ..."
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Objective—Endothelial transcription factors Krüppel-like factor 4 (KLF4) and KLF2 are implicated in protection against atherogenesis. Steady-state microRNA (miR) regulation of KLFs in vivo is accessible by screening region-specific endothelial miRs and their targets. Methods and Results—A subset of differentially expressed endothelial miRs was identified in atherosusceptible versus protected regions of normal swine aorta. In silico analyses predicted highly conserved binding sites in the 3=-untranslated region (3=UTR) of KLF4 for 5 miRs of the subset (miR-26a,-26b,-29a,-92a, and-103) and a single binding site for a miR-92a complex in the 3=UTR of KLF2. Of these, only miR-92a knockdown and knock-in resulted in responses of KLF4 and KLF2 expression in human arterial endothelial cells. Dual luciferase reporter assays demonstrated functional interactions of miR-92a with full-length 3=UTR sequences of both KLFs and with the specific binding elements therein. Two evolutionarily conserved miR-92a sites in KLF4 3=UTR and 1 site in KLF2 3=UTR were functionally validated. Knockdown of miR-92a in vitro resulted in partial rescue from cytokine-induced proinflamma-tory marker expression (monocyte chemotactic protein 1, vascular cell adhesion molecule-1, E-selectin, and endothelial nitric oxide synthase) that was attributable to enhanced KLF4 expression. Leukocyte-human arterial endothelial cell adhesion experiments supported this conclusion. In swine aortic arch endothelium, a site of atherosusceptibility where miR-92a expression was elevated, both KLFs were expressed at low levels relative to protected thoracic aorta. Conclusion—miR-92a coregulates KLF4 and KLF2 expression in arterial endothelium and contributes to phenotype heterogeneity associated with regional atherosusceptibility and protection in vivo. (Arterioscler Thromb Vasc Biol.
Oncofetal H19-derived miR-675 regulates tumor suppressor RB in human colorectal cancer. Carcinogenesis 31
, 2010
"... D ow nloaded from H19 is an imprinted oncofetal non-coding RNA recently shown to be the precursor of miR-675. The pathophysiologic roles of H19 and its mature product miR-675 to carcinogenesis have however not been defined. By quantitative RT-PCR, both H19 and miR-675 were found to be up-regulated i ..."
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D ow nloaded from H19 is an imprinted oncofetal non-coding RNA recently shown to be the precursor of miR-675. The pathophysiologic roles of H19 and its mature product miR-675 to carcinogenesis have however not been defined. By quantitative RT-PCR, both H19 and miR-675 were found to be up-regulated in human colon cancer cell lines and primary human colorectal cancer (CRC) tissues compared with adjacent non-cancerous tissues. Subsequently, the tumor suppressor RB was confirmed to be a direct target of miR-675 as the miRNA suppressed the activity of the luciferase reporter carrying the 3’UTR of RB mRNA that contains the miR-675 binding site. Suppression of miR-675 by transfection with anti-miR-675 increased RB expression, and at the same time, decreased cell growth and soft agar colony formation in human colon cancer cells. Reciprocally, enhanced miR-675 expression by transfection with miR-675 precursor decreased RB expression, increased tumor cell
Small noncoding RNA GcvB is a novel regulator of acid resistance in Escherichia coli.
- BMC Genomics
, 2009
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