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Identification of Hundreds of Conserved and Non-conserved Human MicroRNAs

ABSTRACT: Determining the expression of known and computationally predicted microRNAs by microRNA microarray in several tissues (placenta, testis, thymus, brain and prostate) Keywords: parallel sample microRNAs expression profile

ORGANISM(S): Homo sapiens

SUBMITTER: Eilon Sharon

PROVIDER: E-GEOD-2708 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Identification of hundreds of conserved and nonconserved human microRNAs.

Bentwich Isaac I Avniel Amir A Karov Yael Y Aharonov Ranit R Gilad Shlomit S Barad Omer O Barzilai Adi A Einat Paz P Einav Uri U Meiri Eti E Sharon Eilon E Spector Yael Y Bentwich Zvi Z

Nature genetics 20050619 7

MicroRNAs are noncoding RNAs of approximately 22 nucleotides that suppress translation of target genes by binding to their mRNA and thus have a central role in gene regulation in health and disease. To date, 222 human microRNAs have been identified, 86 by random cloning and sequencing, 43 by computational approaches and the rest as putative microRNAs homologous to microRNAs in other species. To prove our hypothesis that the total number of microRNAs may be much larger and that several have emerg ...[more]

PMID: 15965474

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Identification of Hundreds of Conserved and Non-conserved Human MicroRNAs

Project description:Determining the expression of known and computationally predicted microRNAs by microRNA microarray in several tissues (placenta, testis, thymus, brain and prostate) Keywords: parallel sample

2005-06-19 | GSE2708 | GEO

Computational evidence for hundreds of non-conserved plant microRNAs.

Project description:BackgroundMicroRNAs (miRNA) are small (20-25 nt) non-coding RNA molecules that regulate gene expression through interaction with mRNA in plants and metazoans. A few hundred miRNAs are known or predicted, and most of those are evolutionarily conserved. In general plant miRNA are different from their animal counterpart: most plant miRNAs show near perfect complementarity to their targets. Exploiting this complementarity we have developed a method for identification plant miRNAs that does not rely on phylogenetic conservation.ResultsUsing the presumed targets for the known miRNA as positive controls, we list and filter all segments of the genome of length approximately 20 that are complementary to a target mRNA-transcript. From the positive control we recover 41 (of 92 possible) of the already known miRNA-genes (representing 14 of 16 families) with only four false positives. Applying the procedure to find possible new miRNAs targeting any annotated mRNA, we predict of 592 new miRNA genes, many of which are not conserved in other plant genomes. A subset of our predicted miRNAs is additionally supported by having more than one target that are not homologues.ConclusionThese results indicate that it is possible to reliably predict miRNA-genes without using genome comparisons. Furthermore it suggests that the number of plant miRNAs have been underestimated and points to the existence of recently evolved miRNAs in Arabidopsis.

| S-EPMC1249568 | biostudies-literature

Transgenic overexpression of Pla2g10

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2016-01-29 | E-GEOD-77336 | biostudies-arrayexpress

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Project description:To identify target genes of tumor suppressive microRNAs in human cancer, several cell lines (bladder cancer, prostate cancer, renal cell carcinoma, and head and neck squamous cell carcinoma) were subjected to Agilent whole genome microarrays. miR-517a, miR-218, miR-145, miR-1 and miR-874 function as tumor suppressors. Human cancer cell lines (BOY, T24, A498, PC3, DU145, FaDu, SAS, HSC3, IMC3) were transfected with miRNAs (miR-517a, miR-218, miR-145, miR-1, miR-874). The miRNA-transfected human cancer cell lines were compared to control cell lines.

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Hundreds of conserved non-coding genomic regions are independently lost in mammals.

Project description:Conserved non-protein-coding DNA elements (CNEs) often encode cis-regulatory elements and are rarely lost during evolution. However, CNE losses that do occur can be associated with phenotypic changes, exemplified by pelvic spine loss in sticklebacks. Using a computational strategy to detect complete loss of CNEs in mammalian genomes while strictly controlling for artifacts, we find >600 CNEs that are independently lost in at least two mammalian lineages, including a spinal cord enhancer near GDF11. We observed several genomic regions where multiple independent CNE loss events happened; the most extreme is the DIAPH2 locus. We show that CNE losses often involve deletions and that CNE loss frequencies are non-uniform. Similar to less pleiotropic enhancers, we find that independently lost CNEs are shorter, slightly less constrained and evolutionarily younger than CNEs without detected losses. This suggests that independently lost CNEs are less pleiotropic and that pleiotropic constraints contribute to non-uniform CNE loss frequencies. We also detected 35 CNEs that are independently lost in the human lineage and in other mammals. Our study uncovers an interesting aspect of the evolution of functional DNA in mammalian genomes. Experiments are necessary to test if these independently lost CNEs are associated with parallel phenotype changes in mammals.

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A novel hybrid kinase is essential for regulating the ÏB-mediated stress response of Bacillus cereus.

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2010-06-24 | E-GEOD-14589 | biostudies-arrayexpress

Systematic profiling of human microRNAs in plasma from nasopharyngeal carcinoma patients reveals candidate biomarkers

Project description:We used microarrays to perform systematic profiling of human microRNAs in plasma from nasopharyngeal carcinoma (NPC) patients to find potential biomarkers. By comparing the plasma microRNA profiles of the NPC patients and healthy donors, potential biomarkers for NPC were investigated. A total of 39 microRNAs were aberrantly expressed based on 50 Agilent microarrays containing 887 human microRNAs 50 microarrays containing 887 human microRNAs were used to screen for potential biomarkers with significant differential expression levels between 31 NPC patients and 19 healthy donors.

2013-08-01 | E-GEOD-43329 | biostudies-arrayexpress

Identification of target genes of cancer-related microRNAs in human cancer

Project description:To identify target genes of oncogenic or tumor suppressive microRNAs in human cancer, several cell lines (bladder cancer, prostate cancer, renal cell carcinoma. lung squamous cell carcinoma and head and neck squamous cell carcinoma) were subject to Agilent whole genome microarray. miR-183 and miR-96 function as oncogene. miR-1, miR-133a, miR-135a, miR-145 and miR-375 function as tumor suppressor The miRNA transfected human cancer cell lines (KK47, T24, A498, PC3, DU145, FaDu, SAS, PC10 and H157) were compared to control cell lines.

2012-02-09 | E-GEOD-26032 | biostudies-arrayexpress

Concordant Regulation of Translation and mRNA Abundance for Hundreds of Targets of a Human microRNA

Project description:This SuperSeries is composed of the following subset Series: GSE18834: Human Argonaute Immunoaffinity Purification-associated RNA. GSE18835: mRNA abundance in HEK293T cells mock or miR-124 transfected. GSE18836: Translation Profiling +/- miR-124. GSE18837: Unamplified mRNA abundance in miR-124 and mock-transfected cells. Refer to individual Series

2009-11-09 | E-GEOD-18889 | biostudies-arrayexpress

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