Unification of miRNA and isomiR research: the mirGFF3 format and the mirtop API

Desvignes, Thomas; Loher, Phillipe; Eilbeck, Karen; Ma, Jeffery; Urgese, Gianvito; Fromm, Bastian; Sydes, Jason; Aparicio‐Puerta, Ernesto; Barrera, Víctor; Espín, Roderic; Thibord, Florian; Ros, Xavier Bofill-De; Londin, Eric; Telonis, Aristeidis G.; Ficarra, Elisa; Friedländer, Marc R.; Postlethwait, John H.; Rigoutsos, Isidore; Hackenberg, Michael; Vlachos, Ioannis S.; Halushka, Marc K.; Pantano, Lorena

doi:10.1093/bioinformatics/btz675

Cited by 34 publications

(34 citation statements)

References 66 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Other ncRNAs are per default quantified without any mismatches and all multi-mapping reads with the lowest number of mismatches are considered. To generate the miRGFF3 isoform format, mirtop 0.4.23 ( 33 ) is run on the aligned files and subsequently filtered to accommodate the user selected number of allowed mismatches.…”

Section: Methodsmentioning

confidence: 99%

miRMaster 2.0: multi-species non-coding RNA sequencing analyses at scale

Fehlmann

Kern

Laham

et al. 2021

Nucleic Acids Research

View full text Add to dashboard Cite

Analyzing all features of small non-coding RNA sequencing data can be demanding and challenging. To facilitate this process, we developed miRMaster. After the analysis of over 125 000 human samples and 1.5 trillion human small RNA reads over 4 years, we present miRMaster 2 with a wide range of updates and new features. We extended our reference data sets so that miRMaster 2 now supports the analysis of eight species (e.g. human, mouse, chicken, dog, cow) and 10 non-coding RNA classes (e.g. microRNAs, piRNAs, tRNAs, rRNAs, circRNAs). We also incorporated new downstream analysis modules such as batch effect analysis or sample embeddings using UMAP, and updated annotation data bases included by default (miRBase, Ensembl, GtRNAdb). To accommodate the increasing popularity of single cell small-RNA sequencing data, we incorporated a module for unique molecular identifier (UMI) processing. Further, the output tables and graphics have been improved based on user feedback and new output formats that emerged in the community are now supported (e.g. miRGFF3). Finally, we integrated differential expression analysis with the miRNA enrichment analysis tool miEAA. miRMaster is freely available at https://www.ccb.uni-saarland.de/mirmaster2.

show abstract

Section: Methodsmentioning

confidence: 99%

miRMaster 2.0: multi-species non-coding RNA sequencing analyses at scale

Fehlmann

Kern

Laham

et al. 2021

Nucleic Acids Research

View full text Add to dashboard Cite

show abstract

“…Each software uses different strategies and might produce different results [ 36 ]. We have included them as they allow following standardization procedures performed by miRTOP software and adopt the miR.gff3 file format [ 37 ]. Again, the pipeline modular implementation would allow adding additional softwares converging and adapting to miRTOP and miR.gff3 format.…”

Section: Methodsmentioning

confidence: 99%

Paired-end small RNA sequencing reveals a possible overestimation in the isomiR sequence repertoire previously reported from conventional single read data analysis

et al. 2021

View full text Add to dashboard Cite

Background Next generation sequencing has allowed the discovery of miRNA isoforms, termed isomiRs. Some isomiRs are derived from imprecise processing of pre-miRNA precursors, leading to length variants. Additional variability is introduced by non-templated addition of bases at the ends or editing of internal bases, resulting in base differences relative to the template DNA sequence. We hypothesized that some component of the isomiR variation reported so far could be due to systematic technical noise and not real. Results We have developed the XICRA pipeline to analyze small RNA sequencing data at the isomiR level. We exploited its ability to use single or merged reads to compare isomiR results derived from paired-end (PE) reads with those from single reads (SR) to address whether detectable sequence differences relative to canonical miRNAs found in isomiRs are true biological variations or the result of errors in sequencing. We have detected non-negligible systematic differences between SR and PE data which primarily affect putative internally edited isomiRs, and at a much smaller frequency terminal length changing isomiRs. This is relevant for the identification of true isomiRs in small RNA sequencing datasets. Conclusions We conclude that potential artifacts derived from sequencing errors and/or data processing could result in an overestimation of abundance and diversity of miRNA isoforms. Efforts in annotating the isomiRnome should take this into account.

show abstract

“…documentation page (https://prost.readt hedocs.io). The miRNA and isomiR nomenclature follow the rules established for zebrafish (Desvignes et al, 2015;Desvignes, Loher, et al, 2019). For expression analysis, only sequences with a minimum of 30 reads were retained.…”

Section: Small Rna Read Analysis and Mirna Annotationmentioning

confidence: 99%

microRNA expression variation as a potential molecular mechanism contributing to adaptation to hydrogen sulphide

Kelley

Desvignes

McGowan

et al. 2020

J of Evolutionary Biology

Self Cite

View full text Add to dashboard Cite

microRNAs (miRNAs) are post‐transcriptional regulators of gene expression and can play an important role in modulating organismal development and physiology in response to environmental stress. However, the role of miRNAs in mediating adaptation to diverse environments in natural study systems remains largely unexplored. Here, we characterized miRNAs and their expression in Poecilia mexicana, a species of small fish that inhabits both normal streams and extreme environments in the form of springs rich in toxic hydrogen sulphide (H2S). We found that P. mexicana has a similar number of miRNA genes as other teleosts. In addition, we identified a large population of mature miRNAs that were differentially expressed between locally adapted populations in contrasting habitats, indicating that miRNAs may contribute to P. mexicana adaptation to sulphidic environments. In silico identification of differentially expressed miRNA‐mRNA pairs revealed, in the sulphidic environment, the downregulation of miRNAs predicted to target mRNAs involved in sulphide detoxification and cellular homeostasis, which are pathways essential for life in H2S‐rich springs. In addition, we found that predicted targets of upregulated miRNAs act in the mitochondria (16.6% of predicted annotated targets), which is the main site of H2S toxicity and detoxification, possibly modulating mitochondrial function. Together, the differential regulation of miRNAs between these natural populations suggests that miRNAs may be involved in H2S adaptation by promoting functions needed for survival and reducing functions affected by H2S. This study lays the groundwork for further research to directly demonstrate the role of miRNAs in adaptation to H2S. Overall, this study provides a critical stepping‐stone towards a comprehensive understanding of the regulatory mechanisms underlying the adaptive variation in gene expression in a natural system.

show abstract

Unification of miRNA and isomiR research: the mirGFF3 format and the mirtop API

Cited by 34 publications

References 66 publications

miRMaster 2.0: multi-species non-coding RNA sequencing analyses at scale

miRMaster 2.0: multi-species non-coding RNA sequencing analyses at scale

Paired-end small RNA sequencing reveals a possible overestimation in the isomiR sequence repertoire previously reported from conventional single read data analysis

microRNA expression variation as a potential molecular mechanism contributing to adaptation to hydrogen sulphide

Contact Info

Product

Resources

About