ArticleNucleic acids research2006
Profiling Caenorhabditis elegans non-coding RNA expression with a combined microarray.
Article in Nucleic acids research, 2006. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
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Who cites it
18 citing papers in PubMed, 32 citations in OpenAlex.
- Expression profiling of snoRNAs in normal hematopoiesis and AML.Blood advances · 2018Article
- Transcriptional regulation of snRNAs and its significance for plant development.Journal of plant research · 2017Review
- Article
- Regulatory elements of Caenorhabditis elegans ribosomal protein genes.BMC genomics · 2012Article
- Family size and turnover rates among several classes of small non-protein-coding RNA genes in Caenorhabditis nematodes.Genome biology and evolution · 2012Article
- Identification of intermediate-size non-coding RNAs involved in the UV-induced DNA damage response in C. elegans.PloS one · 2012Article
- The Caenorhabditis elegans intermediate-size transcriptome shows high degree of stage-specific expression.Nucleic acids research · 2011Article
- Identification and characterization of wheat long non-protein coding RNAs responsive to powdery mildew infection and heat stress by using microarray analysis and SBS sequencing.BMC plant biology · 2011Article
- A comparative genome-wide study of ncRNAs in trypanosomatids.BMC genomics · 2010Article
- Computational prediction of Caenorhabditis box H/ACA snoRNAs using genomic properties of their host genes.RNA (New York, N.Y.) · 2010Article
- Novel long non-protein coding RNAs involved in Arabidopsis differentiation and stress responses.Genome research · 2009Article
- In vivo analysis of Caenorhabditis elegans noncoding RNA promoter motifs.BMC molecular biology · 2008Article
- Microarray analysis of ncRNA expression patterns in Caenorhabditis elegans after RNAi against snoRNA associated proteins.BMC genomics · 2008Article
- Bioinformatics in China: a personal perspective.PLoS computational biology · 2008Review
- Elucidating the role of C/D snoRNA in rRNA processing and modification in Trypanosoma brucei.Eukaryotic cell · 2008Article
- Mapping the C. elegans noncoding transcriptome with a whole-genome tiling microarray.Genome research · 2007Article
- Systematic identification of non-coding RNA 2,2,7-trimethylguanosine cap structures in Caenorhabditis elegans.BMC molecular biology · 2007Article
- A novel family of C. elegans snRNPs contains proteins associated with trans-splicing.RNA (New York, N.Y.) · 2007Article
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Authors and funding
15 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Small non-coding RNAs (ncRNAs) are encoded by genes that function at the RNA level, and several hundred ncRNAs have been identified in various organisms. Here we describe an analysis of the small non-coding transcriptome of Caenorhabditis elegans, microRNAs excepted. As a substantial fraction of the ncRNAs is located in introns of protein-coding genes in C.elegans, we also analysed the relationship between ncRNA and host gene expression. To this end, we designed a combined microarray, which included probes against ncRNA as well as host gene mRNA transcripts. The microarray revealed pronounced differences in expression profiles, even among ncRNAs with housekeeping functions (e.g. snRNAs and snoRNAs), indicating distinct developmental regulation and stage-specific functions of a number of novel transcripts. Analysis of ncRNA-host mRNA relations showed that the expression of intronic ncRNA loci with conserved upstream motifs was not correlated to (and much higher than) expression levels of their host genes. Even promoter-less intronic ncRNA loci, though showing a clear correlation to host gene expression, appeared to have a surprising amount of 'expressional freedom', depending on host gene function. Taken together, our microarray analysis presents a more complete and detailed picture of a non-coding transcriptome than hitherto has been presented for any other multicellular organism.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.