ArticleScientific reports2015
Differential and coherent processing patterns from small RNAs.
Article in Scientific reports, 2015. 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.
- Decoding microRNA arm switching: a key to evolutionary innovation and gene regulation.Cellular and molecular life sciences : CMLS · 2025Review
- A comprehensive pan-cancer analysis reveals cancer-associated robust isomiR expression landscapes in miRNA arm switching.Molecular genetics and genomics : MGG · 2023Article
- An Expanded Landscape of Unusually Short RNAs in 11 Samples from Six Eukaryotic Organisms.Non-coding RNA · 2022Article
- DBtRend: A Web-Server of tRNA Expression Profiles from Small RNA Sequencing Data in Humans.Genes · 2021Article
- Extracellular non-coding RNA signatures of the metacestode stage of Echinococcus multilocularis.PLoS neglected tropical diseases · 2020Article
- tRic: a user-friendly data portal to explore the expression landscape of tRNAs in human cancers.RNA biology · 2020Article
- Translational efficiency across healthy and tumor tissues is proliferation-related.Molecular systems biology · 2020Article
- MicroRNAs in Daphnia magna identified and characterized by deep sequencing, genome mapping and manual curation.Scientific reports · 2019Article
- miRNA arm switching identifies novel tumour biomarkers.EBioMedicine · 2018Article
- Article
- Transfer RNA-derived fragments and tRNA halves: biogenesis, biological functions and their roles in diseases.Journal of molecular medicine (Berlin, Germany) · 2018Review
- The discovery potential of RNA processing profiles.Nucleic acids research · 2018Article
- Global analysis of tRNA and translation factor expression reveals a dynamic landscape of translational regulation in human cancers.Communications biology · 2018Article
- RNomic identification and evaluation of npcTB_6715, a non-protein-coding RNA gene as a potential biomarker for the detection of Mycobacterium tuberculosis.Journal of cellular and molecular medicine · 2017Article
- Dissecting miRNA gene repression on single cell level with an advanced fluorescent reporter system.Scientific reports · 2017Article
- SHARAKU: an algorithm for aligning and clustering read mapping profiles of deep sequencing in non-coding RNA processing.Bioinformatics (Oxford, England) · 2016Article
- Peak-valley-peak pattern of histone modifications delineates active regulatory elements and their directionality.Nucleic acids research · 2016Article
- MicroRNA in rectal cancer.World journal of gastrointestinal oncology · 2016Review
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Authors and funding
2 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Post-transcriptional processing events related to short RNAs are often reflected in their read profile patterns emerging from high-throughput sequencing data. MicroRNA arm switching across different tissues is a well-known example of what we define as differential processing. Here, short RNAs from the nine cell lines of the ENCODE project, irrespective of their annotation status, were analyzed for genomic loci representing differential or coherent processing. We observed differential processing predominantly in RNAs annotated as miRNA, snoRNA or tRNA. Four out of five known cases of differentially processed miRNAs that were in the input dataset were recovered and several novel cases were discovered. In contrast to differential processing, coherent processing is observed widespread in both annotated and unannotated regions. While the annotated loci predominantly consist of ~24 nt short RNAs, the unannotated loci comparatively consist of ~17 nt short RNAs. Furthermore, these ~17 nt short RNAs are significantly enriched for overlap to transcription start sites and DNase I hypersensitive sites (p-value < 0.01) that are characteristic features of transcription initiation RNAs. We discuss how the computational pipeline developed in this study has the potential to be applied to other forms of RNA-seq data for further transcriptome-wide studies of differential and coherent processing.
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