ArticleGenome research2013
Integrated detection of natural antisense transcripts using strand-specific RNA sequencing data.
Article in Genome research, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 33 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
33 citing papers in PubMed, 66 citations in OpenAlex.
- Identification of Gene Expression and Splicing QTLs in Porcine Muscle Associated with Meat Quality Traits.Animals : an open access journal from MDPI · 2025Article
- RAG-seq: NSR-primed and Transposase Tagmentation-mediated Strand-specific Total RNA Sequencing in Single Cells.Genomics, proteomics & bioinformatics · 2024Article
- Population-level annotation of lncRNAs in Arabidopsis reveals extensive expression variation associated with transposable element-like silencing.The Plant cell · 2023Article
- CCIVR2 facilitates comprehensive identification of both overlapping and non-overlapping antisense transcripts within specified regions.Scientific reports · 2023Article
- The non-coding RNA SVALKA locus produces a cis-natural antisense transcript that negatively regulates the expression of CBF1 and biomass production at normal temperatures.Plant communications · 2023Article
- Article
- Exploitation of epigenetic variation of crop wild relatives for crop improvement and agrobiodiversity preservation.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2022Review
- CCIVR facilitates comprehensive identification of cis-natural antisense transcripts with their structural characteristics and expression profiles.Scientific reports · 2022Article
- Transcriptome-guided annotation and functional classification of long non-coding RNAs in Arabidopsis thaliana.Scientific reports · 2022Article
- Biogenesis, Functions, Interactions, and Resources of Non-Coding RNAs in Plants.International journal of molecular sciences · 2022Review
- Posttranscriptional regulation of cellulose synthase genes by small RNAs derived from cellulose synthase antisense transcripts.Plant direct · 2021Article
- Modern Approaches for Transcriptome Analyses in Plants.Advances in experimental medicine and biology · 2021Article
- Computational tools for plant small RNA detection and categorization.Briefings in bioinformatics · 2019Review
- Article
- Genome-wide identification of oil biosynthesis-related long non-coding RNAs in allopolyploid Brassica napus.BMC genomics · 2018Article
- Widespread antisense transcription of Populus genome under drought.Molecular genetics and genomics : MGG · 2018Article
- Genome-wide gene expression analysis of amphioxus (Branchiostoma belcheri) following lipopolysaccharide challenge using strand-specific RNA-seq.RNA biology · 2017Article
- Cocaine alters Homer1 natural antisense transcript in the nucleus accumbens.Molecular and cellular neurosciences · 2017Article
- Natural antisense transcripts are significantly involved in regulation of drought stress in maize.Nucleic acids research · 2017Article
- Control of Arabidopsis lateral root primordium boundaries by MYB36.The New phytologist · 2017Article
Corrections and comments
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Authors and funding
5 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Pairs of RNA molecules transcribed from partially or entirely complementary loci are called cis-natural antisense transcripts (cis-NATs), and they play key roles in the regulation of gene expression in many organisms. A promising experimental tool for profiling sense and antisense transcription is strand-specific RNA sequencing (ssRNA-seq). To identify cis-NATs using ssRNA-seq, we developed a new computational method based on a model comparison framework that incorporates the inherent variable efficiency of generating perfectly strand-specific libraries. Applying the method to new ssRNA-seq data from whole-root and cell-type-specific Arabidopsis libraries confirmed most of the known cis-NAT pairs and identified 918 additional cis-NAT pairs. Newly identified cis-NAT pairs are supported by polyadenylation data, alternative splicing patterns, and RT-PCR validation. We found 209 cis-NAT pairs that have opposite expression levels in neighboring cell types, implying cell-type-specific roles for cis-NATs. By integrating a genome-wide epigenetic profile of Arabidopsis, we identified a unique chromatin signature of cis-NATs, suggesting a connection between cis-NAT transcription and chromatin modification in plants. An analysis of small-RNA sequencing data showed that ∼4% of cis-NAT pairs produce putative cis-NAT-induced siRNAs. Taken together, our data and analyses illustrate the potential for multifaceted regulatory roles of plant cis-NATs.
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Registered trials
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.