Expression profile analysis of C. elegans intermediate sized non-coding transcriptome
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ABSTRACT:
ORGANISM(S): Caenorhabditis elegans
PROVIDER: GSE24023 | GEO | 2010/10/01
SECONDARY ACCESSION(S): PRJNA130269
REPOSITORIES: GEO
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Project description:We detected 32230 transfrags by Tiling array Analysis Software, of which 5866 were transfrags with unknown function (TUF). These TUFs exhibited distinct chromosome location, expression and conservation patterns. Six developmental and two conditional stages of C. elegans 70~500nt transcriptome. L1~L4, mature adult (MA), male (ML), dauer (DU), heat shocked (HS). GSM591423_CB2007199-L4-1.CEL is Ce25b_MF, GPL5634 is Ce25b_MR, CEL file is okay using GPL5634's cdf.
2010-09-30 | E-GEOD-24023 | biostudies-arrayexpress
Project description:We utilized high-throughput RNA-seq to uncover the intermediate-sized noncoding RNAs invovled in UV-DNA Damage Responses in C. elegans. 450 novel transfrags were discovered, some of which show dramatic expression change between the UV irradiation and control. This study should lead to a better understanding of the role of is-ncRNAs invovled in UV-DDR.
2012-05-01 | GSE37063 | GEO
Project description:We utilized high-throughput RNA-seq to uncover the intermediate-sized noncoding RNAs invovled in UV-DNA Damage Responses in C. elegans. 450 novel transfrags were discovered, some of which show dramatic expression change between the UV irradiation and control. This study should lead to a better understanding of the role of is-ncRNAs invovled in UV-DDR. Examination of intermediate-sized transcripts (70-500nt) in L4 larvae of C. elegans strains, including wild-type (N2), UV-irradiated (N2-UV100J/m2) and NER-deficient mutant (xpa-1) strains.
2012-05-01 | E-GEOD-37063 | biostudies-arrayexpress
Project description:Accumulating evidence suggests that non-coding RNAs (ncRNAs) are both widespread and functionally important in many eukaryotic organisms. In this study, we employed a special size fractionation and cDNA library construction method followed by 454 deep sequencing to systematically profile rice intermediate-size ncRNAs. Our analysis resulted in the identification of 1349 ncRNAs in total, including 754 novel ncRNAs of an unknown functional category. Chromosome distribution of all identified ncRNAs showed no strand bias, and displayed a pattern similar to that observed in protein-coding genes with few chromosome dependencies. More than half of the ncRNAs were centered around the plus-strand of the 5' and 3' termini of the coding regions. The majority of the novel ncRNAs were rice specific, while 78% of the small nucleolar RNAs (snoRNAs) were conserved. Tandem duplication drove the expansion of over half of the snoRNA gene families. Furthermore, 90% of the snoRNA candidates were shown to produce small RNAs between 20-30 nt, 80% of which were associated with ARGONAUT proteins generally, and AGO1b in particular. Overall, our findings provide a comprehensive view of an intermediate-size non-coding transcriptome in a monocot species, which will serve as a useful platform for an in-depth analysis of ncRNA functions.
| S-EPMC3716300 | biostudies-literature
Project description:BackgroundA network of DNA damage response (DDR) mechanisms functions coordinately to maintain genome integrity and prevent disease. The Nucleotide Excision Repair (NER) pathway is known to function in the response to UV-induced DNA damage. Although numbers of coding genes and miRNAs have been identified and reported to participate in UV-induced DNA damage response (UV-DDR), the precise role of non-coding RNAs (ncRNAs) in UV-DDR remains largely unknown.Methodology/principal findingsWe used high-throughput RNA-sequencing (RNA-Seq) to discover intermediate-size (70-500 nt) ncRNAs (is-ncRNAs) in C. elegans, using the strains of L4 larvae of wild-type (N2), UV-irradiated (N2/UV100) and NER-deficient mutant (xpa-1), and 450 novel non-coding transcripts were initially identified. A customized microarray assay was then applied to examine the expression profiles of both novel transcripts and known is-ncRNAs, and 57 UV-DDR-related is-ncRNA candidates showed expression variations at different levels between UV irradiated strains and non- irradiated strains. The top ranked is-ncRNA candidates with expression differences were further validated by qRT-PCR analysis, of them, 8 novel is-ncRNAs were significantly up-regulated after UV irradiation. Knockdown of two novel is-ncRNAs, ncRNA317 and ncRNA415, by RNA interference, resulted in higher UV sensitivity and significantly decreased expression of NER-related genes in C. elegans.Conclusions/significanceThe discovery of above two novel is-ncRNAs in this study indicated the functional roles of is-ncRNAs in the regulation of UV-DDR network, and aided our understanding of the significance of ncRNA involvement in the UV-induced DNA damage response.
| S-EPMC3492359 | biostudies-literature
Project description:The 1 Mb tiling array was used to represent the 10.0 Mb to 11.0 Mb region of japonica rice Chromosome 10. A tile path was designed with 36-mer probes at a step of 5 nt. All 388,994 probes were retained and synthesized into a single array. This array was hybridized to the cDNA target used for the full-genome tiling array as well as targets prepared from non-coding RNA sample I and II. Keywords: noncoding RNA
2007-02-06 | GSE6922 | GEO
Project description:We sequenced 188 tissue samples comprising 35 organ types retrieved from six humans. To demonstrate evolutionary conservation we sequenced in addition 58 samples from 6 tissues of mice.
2021-12-19 | GSE163534 | GEO
Project description:The number of annotated protein coding genes in the genome of Caenorhabditis elegans is similar to that of other animals, but the extent of its non-protein coding transcriptome remains unknown. Expression profiling on whole genome tiling microarrays applied to a mixed stage C. elegans population verified the expression of 71% of all annotated exons. Only a small fraction (11 %) of the polyadenylated transcription is non-annotated, and appears to consist of approximately 3200 missed or alternative exons and 7800 small transcripts of unknown function (TUFs). Almost half (44%) of the detected transcriptional output is non-polyadenylated and probably not protein coding, and of this 70% overlap the boundaries of protein coding genes in a complex manner. Specific analysis of small non-polyadenylated transcripts verified 98% of all annotated small ncRNAs, and suggested that the transcriptome contains about 1,200 small (<500 nt) unannoted non-coding loci. After combining overlapping transcripts, we estimate that at least 70% of the total C. elegans genome is transcribed. Keywords: RNA fractions
2007-09-07 | GSE8543 | GEO
Project description:Thousands of small open reading frames (smORFs, <100 aa) located on lncRNAs potentially might be translated into peptides or small proteins. We report a comprehensive analysis of the conservation and evolutionary trajectories of smORFs across different plant taxa. For thousands of smORFs, we demonstrate remarkable conservation and significant purifying selection, indicative of their functionality. The expression of the lncRNAs and translation of the smORFs are validated by RNA-sequencing and proteomics, respectively.
2021-10-05 | PXD025267 | Pride
Project description:BackgroundFunctional characterisation of the compact genome of the model organism Caenorhabditis elegans remains incomplete despite its sequencing 20 years ago. The last decade of research has seen a tremendous increase in the number of non-coding RNAs identified in various organisms. While we have mechanistic understandings of small non-coding RNA pathways, long non-coding RNAs represent a diverse class of active transcripts whose function remains less well characterised.ResultsBy analysing hundreds of published transcriptome datasets, we annotated 3392 potential lncRNAs including 143 multi-exonic loci that showed increased nucleotide conservation and GC content relative to other non-coding regions. Using CRISPR/Cas9 genome editing, we generated deletion mutants for ten long non-coding RNA loci. Using automated microscopy for in-depth phenotyping, we show that six of the long non-coding RNA loci are required for normal development and fertility. Using RNA interference-mediated gene knock-down, we provide evidence that for two of the long non-coding RNA loci, the observed phenotypes are dependent on the corresponding RNA transcripts.ConclusionsOur results highlight that a large section of the non-coding regions of the C. elegans genome remains unexplored. Based on our in vivo analysis of a selection of high-confidence lncRNA loci, we expect that a significant proportion of these high-confidence regions is likely to have a biological function at either the genomic or the transcript level.
| S-EPMC6378714 | biostudies-literature