The expression profiles of microRNAs in prostate epithelial cells
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ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE123273 | GEO | 2021/11/29
REPOSITORIES: GEO
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Project description:MicroRNAs (miRNAs) are non-protein-coding small RNAs in the size range 19–25 nucleotides (nt) that are cleaved from 70-100 nt hairpin pre-miRNA precursors.MiRNAs bind to complementary sequences in the 3′-untranslated regions of their target mRNAs and induce mRNA degradation or translational repression. Recent intensive studies have revealed that miRNAs play important roles in a large number of biological processes, including cellular differentiation, proliferation and death. These wide-ranging biological roles suggest that miRNAs may be involved in cancer development. MiRNAs regulate a variety of biological processes, including developmental timing, signal transduction, cell growth, and cell death.Kaposi’s sarcoma (KS) is a multicentric angioproliferative tumor of mesenchymal origin.8, 9 In 1872, the disease was first described by Moritz Kaposi, and it mostly affects elderly men of Italian, Jewish, or Mediterranean origin. In China, more than 90% of KS cases occur in Xinjiang,12-14 which is a multiethnic gathering place where Uyghur (45.7%) and Han (39.7%) are the main ethnic groups; other groups include the Kazakh (7%) and Hui(4.5%). The specific geographical environment and ethnic specificity may characterize some of the specific features of KS in this area, which might also be reflected in the miRNA expression profile in KS tissues. MicroRNAs (miRNAs) are non-protein-coding small RNAs in the size range 19–25 nucleotides (nt) that are cleaved from 70-100 nt hairpin pre-miRNA precursors.MiRNAs bind to complementary sequences in the 3′-untranslated regions of their target mRNAs and induce mRNA degradation or translational repression. Recent intensive studies have revealed that miRNAs play important roles in a large number of biological processes, including cellular differentiation, proliferation and death. These wide-ranging biological roles suggest that miRNAs may be involved in cancer development. MiRNAs regulate a variety of biological processes, including developmental timing, signal transduction, cell growth, and cell death.Kaposi’s sarcoma (KS) is a multicentric angioproliferative tumor of mesenchymal origin.8, 9 In 1872, the disease was first described by Moritz Kaposi, and it mostly affects elderly men of Italian, Jewish, or Mediterranean origin. In China, more than 90% of KS cases occur in Xinjiang,12-14 which is a multiethnic gathering place where Uyghur (45.7%) and Han (39.7%) are the main ethnic groups; other groups include the Kazakh (7%) and Hui(4.5%). The specific geographical environment and ethnic specificity may characterize some of the specific features of KS in this area, which might also be reflected in the miRNA expression profile in KS tissues.
2017-03-05 | GSE55625 | GEO
Project description:MicroRNAs (miRNAs) are endogenous small RNAs that play important roles in various biological and metabolic processes in plants. Caragana intermedia is an important ecological and economic tree species that is prominent in the desert environment of west and northwest China. To date, no investigation into C. intermedia miRNAs has been reported. In this study, high-throughput sequencing of small RNAs was performed to identify both conserved and novel miRNAs, and also their target mRNA genes in C. intermedia. Based on sequence similarity and hairpin structure prediction, 132 putative conserved miRNAs (12 of which were confirmed to form hairpin precursors) belonging to 31 known miRNA families were identified. Ten novel miRNAs (including the miRNA* sequences of three novel miRNAs) were also discovered. The expression of 12 miRNAs was validated in different tissues, and the 12 miRNAs were further assessed by qRT-PCR after salt treatment. Furthermore, 36 potential target genes of 17 known miRNA families and two potential target genes of one novel miRNA were predicted, and some target genes were also assessed by qRT-PCR after salt treatment. Our study provides a basic catalog of miRNAs and their targets, which will promote further understanding of the important roles of miRNAs in C. intermedia and in other species of the leguminous genus, Caragana.
2015-12-31 | GSE44819 | GEO
Project description:MicroRNAs (miRNAs) are endogenous small RNAs that play important roles in various biological and metabolic processes in plants. Caragana intermedia is an important ecological and economic tree species that is prominent in the desert environment of west and northwest China. To date, no investigation into C. intermedia miRNAs has been reported. In this study, high-throughput sequencing of small RNAs was performed to identify both conserved and novel miRNAs, and also their target mRNA genes in C. intermedia. Based on sequence similarity and hairpin structure prediction, 132 putative conserved miRNAs (12 of which were confirmed to form hairpin precursors) belonging to 31 known miRNA families were identified. Ten novel miRNAs (including the miRNA* sequences of three novel miRNAs) were also discovered. The expression of 12 miRNAs was validated in different tissues, and the 12 miRNAs were further assessed by qRT-PCR after salt treatment. Furthermore, 36 potential target genes of 17 known miRNA families and two potential target genes of one novel miRNA were predicted, and some target genes were also assessed by qRT-PCR after salt treatment. Our study provides a basic catalog of miRNAs and their targets, which will promote further understanding of the important roles of miRNAs in C. intermedia and in other species of the leguminous genus, Caragana. Examination of small RNA expression profiling in three-weeks-old seedings of Caragana intermedia.
2015-12-31 | E-GEOD-44819 | biostudies-arrayexpress
Project description:Short-hairpin RNA (shRNA)-induced RNAi is used for biological discovery and therapeutics. Dicer, whose normal role is to liberate endogenous miRNAs from their precursors, processes shRNAs into different biologically active siRNAs, affecting their efficacy and potential for off-targeting. We found that in cells, Dicer induced imprecise cleavage events around the expected sites based on the previously described 5'/3'-counting rules. These promiscuous non-canonical cleavages were abrogated when the cleavage site was positioned 2 nt from a bulge or loop. Interestingly, we observed that the ~1/3 of mammalian endogenous pre-miRNAs that contained such structures were more precisely processed by Dicer. Implementing a new "loop-counting rule", we designed potent anti-HCV shRNAs with substantially reduced off-target effects. Our results suggest that Dicer recognizes the loop/bulge structure in addition to the ends of shRNAs/pre-miRNAs for accurate processing. This has important implications for both miRNA processing and future design of shRNAs for RNAi-based genetic screens and therapies.
2012-12-25 | GSE41292 | GEO
Project description:MicroRNAs (miRNAs) are 21-24 nucleotide (nt) small non-coding RNAs that regulate a wide variety of biological processes at the posttranscriptional level. MiRNA expression often exhibits spatial and temporal specificity. However, genome-wide miRNA expression patterns in different Arabidopsis organs during plant development have not yet been fully investigated. In this study, we sequenced 59 small RNA libraries generated from different tissue types at different developmental stages of Arabidopsis. We then re-annotated Arabidopsis miRNAs based on the most recent criteria. Global analysis of miRNA expression patterns showed that most miRNAs are ubiquitously expressed in different organs or tissues. But a small set of miRNAs, either previously annotated or newly identified, show highly specific expression patterns. In addition, the expression of some miRNA members belonging to the same family is strictly regulated spatially and temporally. Unexpectedly, we found that quite a few miRNAs are produced from different arms of their hairpin precursors at different developmental stages, suggesting that arm switching could be a general and important mechanism in developmental regulation.
2017-12-05 | GSE79414 | GEO
Project description:MicroRNAs (miRNAs) are small non-coding RNAs that play a central role in the regulation of gene expression at the post transcriptional and/or translational level thus impacting various biological processes. Dysregulation of miRNAs could affect processes associated with progression of a variety of diseases including cancer. Majority of miRNA targeting in animals involves a 7-nt “seed region” mapping to positions 2-8 at the molecule’s 5' end. The importance of this 7 nt sequence to miRNA function is evidenced by the fact that the seed region sequence of many miRNAs is highly conserved within and between species. In this study, we computationally and experimentally explore the functional significance of sequence variation within the seed region of human miRNAs. Our results indicate that change of a single nt within the 7-nt seed region changes the spectrum of targeted mRNAs significantly meanwhile further nt changes have little to no additional effect. This high functional cost of even a single nucleotide change within the seed region of miRNAs explains why the seed sequence is highly conserved among many miRNA families both within and between species and could help clarify the likely mechanisms underlying the evolution of miRNA regulatory control.
2019-12-10 | GSE56970 | GEO
Project description:MicroRNAs (miRNAs) are small non-coding RNAs that play a central role in the regulation of gene expression at the post transcriptional and/or translational level thus impacting various biological processes. Dysregulation of miRNAs could affect processes associated with progression of a variety of diseases including cancer. Majority of miRNA targeting in animals involves a 7-nt “seed region” mapping to positions 2-8 at the molecule’s 5' end. The importance of this 7 nt sequence to miRNA function is evidenced by the fact that the seed region sequence of many miRNAs is highly conserved within and between species. In this study, we computationally and experimentally explore the functional significance of sequence variation within the seed region of human miRNAs. Our results indicate that change of a single nt within the 7-nt seed region changes the spectrum of targeted mRNAs significantly meanwhile further nt changes have little to no additional effect. This high functional cost of even a single nucleotide change within the seed region of miRNAs explains why the seed sequence is highly conserved among many miRNA families both within and between species and could help clarify the likely mechanisms underlying the evolution of miRNA regulatory control.
2015-01-30 | GSE56967 | GEO
Project description:MicroRNAs (miRNAs) are small non-coding RNAs that play a central role in the regulation of gene expression at the post transcriptional and/or translational level thus impacting various biological processes. Dysregulation of miRNAs could affect processes associated with progression of a variety of diseases including cancer. Majority of miRNA targeting in animals involves a 7-nt “seed region” mapping to positions 2-8 at the molecule’s 5' end. The importance of this 7 nt sequence to miRNA function is evidenced by the fact that the seed region sequence of many miRNAs is highly conserved within and between species. In this study, we computationally and experimentally explore the functional significance of sequence variation within the seed region of human miRNAs. Our results indicate that change of a single nt within the 7-nt seed region changes the spectrum of targeted mRNAs significantly meanwhile further nt changes have little to no additional effect. This high functional cost of even a single nucleotide change within the seed region of miRNAs explains why the seed sequence is highly conserved among many miRNA families both within and between species and could help clarify the likely mechanisms underlying the evolution of miRNA regulatory control.
2015-01-30 | GSE61230 | GEO
Project description:MicroRNAs (miRNAs) are small non-coding RNAs that play a central role in the regulation of gene expression at the post transcriptional and/or translational level thus impacting various biological processes. Dysregulation of miRNAs could affect processes associated with progression of a variety of diseases including cancer. Majority of miRNA targeting in animals involves a 7-nt “seed region” mapping to positions 2-8 at the molecule’s 5' end. The importance of this 7 nt sequence to miRNA function is evidenced by the fact that the seed region sequence of many miRNAs is highly conserved within and between species. In this study, we computationally and experimentally explore the functional significance of sequence variation within the seed region of human miRNAs. Our results indicate that change of a single nt within the 7-nt seed region changes the spectrum of targeted mRNAs significantly meanwhile further nt changes have little to no additional effect. This high functional cost of even a single nucleotide change within the seed region of miRNAs explains why the seed sequence is highly conserved among many miRNA families both within and between species and could help clarify the likely mechanisms underlying the evolution of miRNA regulatory control.
2015-01-30 | GSE61229 | GEO
Project description:MicroRNAs (miRNAs) are small non-coding RNAs that play a central role in the regulation of gene expression at the post transcriptional and/or translational level thus impacting various biological processes. Dysregulation of miRNAs could affect processes associated with progression of a variety of diseases including cancer. Majority of miRNA targeting in animals involves a 7-nt “seed region” mapping to positions 2-8 at the molecule’s 5' end. The importance of this 7 nt sequence to miRNA function is evidenced by the fact that the seed region sequence of many miRNAs is highly conserved within and between species. In this study, we computationally and experimentally explore the functional significance of sequence variation within the seed region of human miRNAs. Our results indicate that change of a single nt within the 7-nt seed region changes the spectrum of targeted mRNAs significantly meanwhile further nt changes have little to no additional effect. This high functional cost of even a single nucleotide change within the seed region of miRNAs explains why the seed sequence is highly conserved among many miRNA families both within and between species and could help clarify the likely mechanisms underlying the evolution of miRNA regulatory control.
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