We are analyzing https://link.springer.com/article/10.1186/gb-2005-6-6-r51.

Title:
Natural antisense transcripts with coding capacity in Arabidopsismay have a regulatory role that is not linked to double-stranded RNA degradation | Genome Biology
Description:
Background Overlapping transcripts in antisense orientation have the potential to form double-stranded RNA (dsRNA), a substrate for a number of different RNA-modification pathways. One prominent route for dsRNA is its breakdown by Dicer enzyme complexes into small RNAs, a pathway that is widely exploited by RNA interference technology to inactivate defined genes in transgenic lines. The significance of this pathway for endogenous gene regulation remains unclear. Results We have examined transcription data for overlapping gene pairs in Arabidopsis thaliana. On the basis of an analysis of transcripts with coding regions, we find the majority of overlapping gene pairs to be convergently overlapping pairs (COPs), with the potential for dsRNA formation. In all tissues, COP transcripts are present at a higher frequency compared to the overall gene pool. The probability that both the sense and antisense copy of a COP are co-transcribed matches the theoretical value for coexpression under the assumption that the expression of one partner does not affect the expression of the other. Among COPs, we observe an over-representation of spliced (intron-containing) genes (90%) and of genes with alternatively spliced transcripts. For loci where antisense transcripts overlap with sense transcript introns, we also find a significant bias in favor of alternative splicing and variation of polyadenylation. Conclusion The results argue against a predominant RNA degradation effect induced by dsRNA formation. Instead, our data support alternative roles for dsRNAs. They suggest that at least for a subgroup of COPs, antisense expression may induce alternative splicing or polyadenylation.
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Keywords {🔍}

genes, antisense, cops, gene, transcript, sense, transcripts, overlapping, data, expression, article, table, pairs, splicing, analysis, pubmed, alternative, additional, file, rna, google, scholar, genome, dsrna, pool, polyadenylation, cas, variation, arabidopsis, spliced, figure, supplement, coding, degradation, regions, members, bias, region, cop, size, group, role, alternatively, database, microarray, total, intronexon, boundary, full, proteins,

Topics {✒️}

org/pub/data/eukaryotic_projects/o_sativa/annotation_dbs/pseudomolecules/version_3 org/tdb/e2k1/osa1/expression/alt_spliced double-stranded rna-mediated silencing form double-stranded rna double-stranded rna degradation article number r51 article download pdf org/maps/seqviewer_data/sv_gene_feature double-stranded rna substrate induce site-specific cleavage high-density oligonucleotide arrays multiple zinc-finger protein dsrna-dependent adenosine deaminases full size image open reading frame central nervous system double-stranded rna cis-natural antisense transcripts sense intron-exon boundary antisense transcript-mediated effects dsrna-mediated transcript degradation testis-expressed stellate gene genome-wide prediction ioannis michalopoulos & david dsrna-based silencing mechanism dsrna-based transcript degradation privacy choices/manage cookies 1186/gb-2005-6-4-r30 sense-antisense transcript pairs expression profiles authors’ original file full access exon position coordinates intron-exon boundary article jen related subjects natural antisense transcripts nat-mediated interference additional data files author information authors rice expression database rna interference technology regulate imprinting states fgf-2 mrna translation overlapping gene pairs antisense rna levels induce alternative splicing transcript degradation depends rice genome data microarray data generated

Questions {❓}

Vanhee-Brossollet C, Vaquero C: Do natural antisense transcripts make sense in eukaryotes?
Wagner EGH, Flardh K: Antisense RNAs everywhere?

Schema {🗺️}

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