ArticleGenomics2011
Computational dissection of Arabidopsis smRNAome leads to discovery of novel microRNAs and short interfering RNAs associated with transcription start sites.
Article in Genomics, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 7 papers.
What it found
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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
7 citing papers in PubMed, 9 citations in OpenAlex.
- Improved Pre-miRNAs Identification Through Mutual Information of Pre-miRNA Sequences and Structures.Frontiers in genetics · 2019Article
- Article
- Classification of Transcription Boundary-Associated RNAs (TBARs) in Animals and Plants.Frontiers in genetics · 2018Review
- Article
- BP Neural Network Could Help Improve Pre-miRNA Identification in Various Species.BioMed research international · 2016Article
- plantDARIO: web based quantitative and qualitative analysis of small RNA-seq data in plants.Frontiers in plant science · 2014Article
- Computational methods for ab initio detection of microRNAs.Frontiers in genetics · 2012Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
5 authors at 3 institutions in 1 country.
Funding
Abstract
The profiling of small RNAs by high-throughput sequencing (smRNA-Seq) has revealed the complexity of the RNA world. Here, we describe a computational scheme for dissecting the plant smRNAome by integrating smRNA-Seq datasets in Arabidopsis thaliana. Our analytical approach first defines ab initio the genomic loci that produce smRNAs as basic units, then utilizes principal component analysis (PCA) to predict novel miRNAs. Secondary structure prediction of candidates' putative precursors discovered a group of long hairpin double-stranded RNAs (lh-dsRNAs) formed by inverted duplications of decayed coding genes. These gene remnants produce miRNA-like small RNAs which are predominantly 21- and 22-nt long, dependent of DCL1 but independent of RDR2 and DCL2/3/4, and associated with AGO1. Additionally, we found two classes of transcription start site associated (TSSa) RNAs located at sense (+) and antisense (-) approximately 100-200 bp downstream of TSSs, but are differentially incorporated into AGO1 and AGO4, respectively.
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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.