IsomiR Bank: a research resource for tracking IsomiRs

Zhang, Yuanwei; Zang, Qiguang; Xu, Bo; Zheng, Wei; Ban, Rongjun; Zhang, Huan; Yang, Yifan; Hao, Qiaomei; Iqbal, Furhan; Li, Ao; Shi, Qinghua

doi:10.1093/bioinformatics/btw070

Cited by 53 publications

(37 citation statements)

References 18 publications

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“…There are two mature important miRNAs, 5‐p and 3‐p of the precursors. Evidence has shown extra short reads on miRNA namely “isomiR” related to the same miRNA precursor (Zhang, Yang, et al, ). Any specific miRNA can target hundreds of different mRNA by attaching to them in a sequence‐specific manner.…”

Section: Dna Methylation and Demethylationmentioning

confidence: 99%

Aberrant miRNA promoter methylation and EMT‐involving miRNAs in breast cancer metastasis: Diagnosis and therapeutic implications

Zare

Bastami

Solali

et al. 2017

Journal Cellular Physiology

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Breast cancer (BC) is the most prevalent cancer in women worldwide. Although extensive studies are ongoing concerning its intricate molecular mechanisms, development of novel therapies and more accurate diagnostic and prognostic approaches is still a challenge. Epithelial-mesenchymal transition (EMT) enables the invasion of metastatic cancer cells and has recently been highlighted in a Cancer Stem Cell (CSC) model of BC. Epigenetic events as well as miRNA expression are the master regulators of tumorigenesis and add a further layer to the complexity of BC pathogenesis. The miRNAs are related to epigenetic event and additionally affect epigenetic pathways. Recent evidence demonstrates that epigenetic mechanisms such as DNA methylation may control miRNA expression. Because each miRNA may regulate several target genes, dysregulation of miRNA caused by aberrant DNA methylation patterns of the locus may influence important downstream pathways. Furthermore, some miRNAs is believed to regulate important DNA methylator factors. Any disruption or modification of this intricate network can contribute to the disease process; thus, it is essential to understand these changes. Advancements in new sequencing technologies to detect DNA methylation patterns has provided the opportunity to determine differentially methylated regions (DMRs) of the miRNA locus and their effect on expression profiles to improve BC diagnosis and treatment. The current review examines the interplay of DNA methylation mechanisms and miRNA function in invasive tumorigenesis, specifically EMT and CSC of BC, to highlight its potential for advancements on BC etiology, diagnosis, and therapy.

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Section: Dna Methylation and Demethylationmentioning

confidence: 99%

Aberrant miRNA promoter methylation and EMT‐involving miRNAs in breast cancer metastasis: Diagnosis and therapeutic implications

Zare

Bastami

Solali

et al. 2017

Journal Cellular Physiology

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“…Many tools have appeared to search and recognize isomiRs. 28,29 We also found several features of miR-21-3p isoforms in CRC based on TCGA data. Previously, there were several independent studies described MSIassociated candidate miRNAs, but only part of the candidates overlapped with each other.…”

Section: Discussionmentioning

confidence: 68%

“…We suppose SMAD7 may be strongly involved in miR-21-3p-induced EMT, as reported previously. 28,29 We also found several features of miR-21-3p isoforms in CRC based on TCGA data. 27 MiRNA isoforms an emerging concept proposed by bioinformatics researchers.…”

Section: Discussionmentioning

confidence: 99%

Different miR‐21‐3p isoforms and their different features in colorectal cancer

Jiao

Leng

Zhou

et al. 2017

Intl Journal of Cancer

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MiR-21, the only microRNA (miRNA) found to be overexpressed in any type of solid tumor, its guide stand, miR-21-5p, has been studied a lot in colorectal cancer (CRC); however, few researchers focused on its passenger strand, miR-21-3p. In our study, based on The Cancer Genome Atlas (TCGA) data, we found that there were more varieties and quantities of miR-21-3p isoforms in microsatellite instability (MSI)-type CRC. We further examined the role of miR-21-3p by in vitro and in vivo studies. MiR-21-3p may be an oncogene in CRC by promoting cellular mobility through epithelial-mesenchymal transition. However, different isoforms, especially miR-21-3p 0 | 2, may be a favorable prognostic marker for CRC survival, probably due to increased complementary effect of miR-21-5p and/or target genes. Further study investigating the underlying mechanism of miRNA isoforms is needed.

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“…The use of BLASTn-short (local installation in Galaxy) for sequence comparison to all available sequences for RNA molecules of the target species and the inclusion of ortholog information derived from well annotated species from different annotation sources significantly improves the annotation of identified sequences found in the small RNA-Seq results to 80-90%, depending on the species and the sample type (Jochen Bick, 2016;ETH Zurich;personal communication). The consideration of the frequent occurrence of sequences representing isoforms of miRNAs (isomiRs; Krawczynski et al, 2015a;Zhang et al, 2016) can further improve sequence annotation. IsomiRs result from imprecise and alternative cleavage during the premiRNA processing and post-transcriptional modifications.…”

Section: Analysis Of Small Rna-seq Data Sets With Special Adaptation mentioning

confidence: 99%

“…IsomiRs result from imprecise and alternative cleavage during the premiRNA processing and post-transcriptional modifications. The isomiRs show different miRNA stability, sub-cellular localization, and target selection (Zhang et al, 2016). Since post-transcriptional modification during miRNA processing also leads to the addition of nucleotides not matching to the genome sequence those isomiRs cannot be easily mapped using BWA and/or miRDeep2.…”

Section: Analysis Of Small Rna-seq Data Sets With Special Adaptation mentioning

confidence: 99%

Strategies to avoid drowning in the deep sequencing data flood

Bauersachs¹

2016

Anim Reprod

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The enormous technological progress in the field of functional genomics during the last 15 years had a significant impact on animal sciences. With the development of Next Generation Sequencing it became feasible to analyze genomes and transcriptomes within short time frames and affordable costs. One major challenge of this rapid development is to manage the data flood and to perform data analysis and integration in an optimal manner. This review provides some information about a typical analysis pipeline for RNASequencing (RNA-Seq) data and a strategy for the analysis of small RNA-Seq data derived from species with poor annotation for non-coding RNA genes. Furthermore, problems regarding gene annotation in livestock species and their possible implications for data analysis and interpretation are discussed. Despite of not yet solved problems and challenges with respect to data analysis and integration the approaches in the field of functional genome analysis opened up new ways to try to understand the complex trait fertility.

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IsomiR Bank: a research resource for tracking IsomiRs

Abstract: Supplementary data are available at Bioinformatics online.

Cited by 53 publications

References 18 publications

Aberrant miRNA promoter methylation and EMT‐involving miRNAs in breast cancer metastasis: Diagnosis and therapeutic implications

Aberrant miRNA promoter methylation and EMT‐involving miRNAs in breast cancer metastasis: Diagnosis and therapeutic implications

Different miR‐21‐3p isoforms and their different features in colorectal cancer

Strategies to avoid drowning in the deep sequencing data flood

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