26G endo-siRNAs regulate spermatogenic and zygotic gene expression
Ontology highlight
ABSTRACT:
ORGANISM(S): Caenorhabditis elegans
PROVIDER: GSE20341 | GEO | 2010/05/25
REPOSITORIES: GEO
Similar Datasets
Project description:Analysis of small RNAs with 5'p, 3'OH Small RNAs (18-32nt) expressed in purified male sperm, hermaphrodite oocytes, embryos, N2, glp-4(bn2), and eri-1(mg366) were cloned and sequenced by 454 and Illumina high-throughput sequencing.
2010-05-24 | E-GEOD-20341 | biostudies-arrayexpress
Project description:p53 and NF-kB are important transcription factors involved in the pathogenesis of cardiac hypertrophy and the progression to heart failure/dilatation. We report the genome-wide empirical binding sites co-occupied by the transcription factors in human dilated hearts. p53-NF-kB sequential chromatin immunoprecipitation and high-throughput sequencing were performed using tissues from control and diseased hearts. These data may facilitate the discovery of mechanisms by which transcription factors cooperate in close proximity or a multi-molecular complex at a cis-regulatory element to control gene expression. Raw data (qseq format) files are available on the following FTP site: ftp://ftp.ncbi.nlm.nih.gov/pub/geosup/Series/GSE21356
2011-01-01 | GSE21356 | GEO
Project description:The 3' untranslated region (3'UTR) constitutes a major site of post-transcriptional regulation of gene expression. Sequence elements in the 3'UTR interact with trans-acting regulators such as microRNAs that affect translation and stability. The overall aim is to use a 3'RACE cloning-sequencing stragety to identify the 3'UTRs of C. elegans transcripts and explore their heterogeneity in different developmental stages and tissues. Keywords: Transcriptome analysis For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf Raw data files are available on our FTP site: ftp://ftp.ncbi.nlm.nih.gov/pub/geosup/Series/GSE17781
2009-09-02 | GSE17781 | GEO
Project description:Endogenous small interfering RNAs (endo-siRNAs) regulate diverse gene expression programs in eukaryotes by either binding and cleaving mRNA targets or mediating heterochromatin formation; however, the mechanisms of endo-siRNA biogenesis, sorting, and target regulation remain poorly understood. Here we report the identification and function of a specific class of germline-generated endo-siRNAs in Caenorhabditis elegans that are 26 nt in length and contain a guanine at the first nucleotide position (i.e., 26G RNAs). 26G RNAs regulate gene expression during spermatogenesis and zygotic development, and their biogenesis requires the ERI-1 exonuclease and the RRF-3 RNA-dependent RNA polymerase (RdRP). Remarkably, we identified two nonoverlapping subclasses of 26G RNAs that sort into specific RNA-induced silencing complexes (RISCs) and differentially regulate distinct mRNA targets. Class I 26G RNAs target genes are expressed during spermatogenesis, whereas class II 26G RNAs are maternally inherited and silence gene expression during zygotic development. These findings implicate a class of endo-siRNAs in the global regulation of transcriptional programs required for fertility and development.
| S-EPMC2765456 | biostudies-literature
Project description:The 3' untranslated region (3'UTR) constitutes a major site of post-transcriptional regulation of gene expression. Sequence elements in the 3'UTR interact with trans-acting regulators such as microRNAs that affect translation and stability. The overall aim is to use a 3'RACE cloning-sequencing stragety to identify the 3'UTRs of C. elegans transcripts and explore their heterogeneity in different developmental stages and tissues. Keywords: Transcriptome analysis For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf Raw data files are available on our FTP site: ftp://ftp.ncbi.nlm.nih.gov/pub/geosup/Series/GSE17781 pilot study [GSM443959..GSM443964]: N2 wildtype worms staged at embryo, L1, L2, L3, L4, and adult full experiment [GSM446651..GSM446661]: N2 wildtype worms staged at embryo, L1, L2, L3, L4, dauer, and adult. Illumina Genome Analyzer sequencing of isolated clones [GSM469439] 454 sequencing of RACE clones [GSM469976]
2009-09-01 | E-GEOD-17781 | biostudies-arrayexpress
Project description:Genome-wide chromatin state maps of murine embryonic stem (ES) cells, ES-derived neural progenitor cells and whole brain tissue. The data were generated to examine the correlation between histone and DNA methylation during lineage-commitment. Keywords: High-throughput ChIP-sequencing, Illumina, cell type comparison H3K4me3, H3K4me2 and/or H3K4me1 ChIP-Seq in singlicate from mouse embryonic stem (ES) cells, ES-derived neural progenitor cells and whole brain tissue suspensions Raw sequence data files for this study are available for download from the SRA FTP site at ftp://ftp.ncbi.nlm.nih.gov/sra/Studies/SRP000/SRP000230
2008-07-05 | E-GEOD-11172 | biostudies-arrayexpress
Project description:Plant virus infection involves the production of viral small RNAs (vsRNAs) with the potential to associate with distinct Argonaute (AGO)-containing silencing complexes and mediate diverse silencing effects on RNA and chromatin. We used multiplexed, high-throughput pyrosequencing to profile populations of vsRNAs from plants infected with viruses from different genera. Sense and antisense vsRNAs of 20 to 24 nucleotides (nts) spread throughout the entire viral genomes in an overlapping configuration; virtually all genomic nucleotide positions were represented in the dataset. We present evidence to suggest that every genomic position could be a putative cleavage site for vsRNA formation, although viral genomes contain specific regions that serve as preferential sources of vsRNA production. Hotspots for vsRNAs of 21-, 22-, and 24-nt usually coincide in the same genomic regions, indicating similar target affinities among Dicer-like (DCL) enzymes. In the light of our results, the overall contribution of perfectly base paired double-stranded RNA and imperfectly base paired structures within single-stranded RNA to vsRNA formation is discussed. Our census of vsRNAs extends the current view of the distribution and composition of vsRNAs in virus-infected plants, and contributes to define a more comprehensive scenario of vsRNA biogenesis and their regulatory functions in plants Raw data files are available on our FTP site: ftp://ftp.ncbi.nlm.nih.gov/pub/geosup/Series/GSE16996
2009-07-10 | GSE16996 | GEO
Project description:Small interfering RNAs (siRNAs) direct RNA interference (RNAi) in eukaryotes. In flies, somatic cells produce siRNAs from exogenous double-stranded RNA as a defense against viral infection. Here, we identify 21-nt long, endogenous siRNAs (endo-siRNAs) corresponding to transposons and heterochromatic sequences in the somatic cells of Drosophila melanogaster. We also detected endo-siRNAs complementary to mRNAs: these siRNAs disproportionately mapped to the complementary regions of overlapping mRNAs predicted to form dsRNA in vivo. Normal accumulation of somatic endo-siRNAs requires the siRNA-generating ribonuclease, Dicer-2, and the RNAi effector protein, Ago2. We propose that endo-siRNAs generated by the fly RNAi pathway silence selfish genetic elements in the soma much as piRNAs do in the germ line. Keywords: Small RNA detection and quantification. Small RNAs (18-30 nt) from fly heads (WT, ago2 mutants, dcr-2 homozygous and heterozygous mutants, and WT expressing an inverted repeat directed against exon 3 of the gene "white") and S2 cells (transgenic for a construct expressing siRNAs against white and GFP) were sequenced using a Solexa Genome Analyzer instrument. Raw sequence data files for this study are available for download from the SRA FTP site at ftp://ftp.ncbi.nlm.nih.gov/sra/Studies/SRP000/SRP000181
2008-04-10 | E-GEOD-11019 | biostudies-arrayexpress
Project description:DNA methylation profiling by D-REAM.<br><br>Additional data files (.BED files and heatmap file) are available in the FTP directory for this experiment <A HREF="ftp://ftp.ebi.ac.uk/pub/databases/microarray/data/experiment/TABM/E-TABM-551/">FTP directory</A>
2008-10-31 | E-TABM-551 | biostudies-arrayexpress
Project description:Significant fractions of eukaryotic genomes give rise to RNA, much of which is unannotated and has reduced protein-coding potential. The genomic origins and the relations of human nuclear and cytosolic polyadenylated RNAs longer than 200 nucleotides and whole-cell RNAs less than 200 nt are investigated in this genome-wide study. Subcellular addresses for nucleotides present in detected RNAs were assigned, and their potential processing into short RNAs was investigated. Taken together, these observations suggest a role for some unannotated RNAs as primary transcripts for the production of short RNAs. Three novel potentially functional classes of RNAs have been identified, two of which are syntenically conserved and correlate with the expression state of protein-coding genes. These data support a highly interleaved organization of the human transcriptome. Processed data files: Graph files at ftp://ftp.ncbi.nih.gov/pub/geo/DATA/projects/GSE7576/graphs/ Transfrag files at ftp://ftp.ncbi.nih.gov/pub/geo/DATA/projects/GSE7576/transfrags/ CEL files available on each Sample record tpmap files available on each Platform record Keywords: tiling, RNA population complexity profiling
2007-05-25 | GSE7576 | GEO