YM500v2: a small RNA sequencing (smRNA-seq) database for human cancer miRNome research

Cheng, Wei‐Chung; Chung, I‐Fang; Tsai, Chun‐Kuang; Huang, Tse‐Shun; Chen, Chen-Yang; Wang, Shao-Chuan; Chang, Ting‐Yu; Sun, Hsin‐Yun; Chao, Jung; Cheng, Cheng-Chung; Wu, Cheng‐Wen; Wang, Hsei‐Wei

doi:10.1093/nar/gku1156

Cited by 48 publications

(39 citation statements)

References 36 publications

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“…From an integrated miRNA-seq database YM500v2 [27], we observed a highly expressed miR-92b-3p in human ovaries and brains ( Figure 1a). Since miRNA sequences are highly conserved between species, we next validated the online array expression findings in various tissues of adult mice.…”

Section: Resultsmentioning

confidence: 99%

microRNA 92b-3p regulates primordial follicle assembly by targeting TSC1 in neonatal mouse ovaries

Liu

Gong

et al. 2019

Cell Cycle

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The primordial follicle pool, providing all oocytes available to a female throughout her reproductive life, is established perinatally. The formation of primordial follicle pool is regulated by precise transcriptional and post-transcriptional mechanisms. Recent studies have identified several microRNAs as post-transcriptional regulatory factors in the process of primordial follicle assembly.Here, we showed that miR-92b-3p was significantly upregulated in the stage of primordial follicle assembly in newborn mouse ovaries. Inhibiting miR-92b-3p suppressed the formation of primordial follicles, while overexpression of miR-92b-3p accelerated the processes of cyst breakdown and the following primordial follicle assembly. Accordingly, the expression of follicular developmentrelated genes was reduced upon inhibiting of miR-92b-3p and increased under miR-92b-3p overexpression. Mechanistic studies identified TSC1 as a direct target of miR-92b-3p. miR-92b-3p could activate mTOR/Rps6 signaling through targeting and inhibiting TSC1 expression. In addition, knockdown of TSC1 showed an identical phenotype with that of miR-92b-3p overexpression in accelerating processes of cyst breakdown and primordial follicle formation. Thus, our work demonstrates that miR-92b-3p is a novel regulator of primordial follicle assembly by negatively regulating TSC1 in mTOR/Rps6 signaling. ARTICLE HISTORY

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Section: Resultsmentioning

confidence: 99%

microRNA 92b-3p regulates primordial follicle assembly by targeting TSC1 in neonatal mouse ovaries

Liu

Gong

et al. 2019

Cell Cycle

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“…The new smRNA-seq and RNA-seq data sets and clinical data in TCGA were downloaded from CGHub (https://cghub.ucsc.edu/) and pre-processed as described in our previous studies (22–24). In brief, all sequencing data were pre-processed by in-house scripts.…”

Section: Data Collection and Small Rna Annotationmentioning

confidence: 99%

“…Previously, we developed the YM500 database (21,22), a database that contains more than 8000 cancer-related smRNA data sets and includes analysis pipelines for novel miRNA prediction, arm switching discovery, isomiR identification and miRNA quantification from smRNA-seq. The previous version of this database focused only on miRNAs.…”

Section: Introductionmentioning

confidence: 99%

YM500v3: a database for small RNA sequencing in human cancer research

Chung¹,

Chang

Chen³

et al. 2016

Nucleic Acids Res

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We previously presented the YM500 database, which contains >8000 small RNA sequencing (smRNA-seq) data sets and integrated analysis results for various cancer miRNome studies. In the updated YM500v3 database (http://ngs.ym.edu.tw/ym500/) presented herein, we not only focus on miRNAs but also on other functional small non-coding RNAs (sncRNAs), such as PIWI-interacting RNAs (piRNAs), tRNA-derived fragments (tRFs), small nuclear RNAs (snRNAs) and small nucleolar RNAs (snoRNAs). There is growing knowledge of the role of sncRNAs in gene regulation and tumorigenesis. We have also incorporated >10 000 cancer-related RNA-seq and >3000 more smRNA-seq data sets into the YM500v3 database. Furthermore, there are two main new sections, ‘Survival' and ‘Cancer', in this updated version. The ‘Survival’ section provides the survival analysis results in all cancer types or in a user-defined group of samples for a specific sncRNA. The ‘Cancer’ section provides the results of differential expression analyses, miRNA–gene interactions and cancer miRNA-related pathways. In the ‘Expression’ section, sncRNA expression profiles across cancer and sample types are newly provided. Cancer-related sncRNAs hold potential for both biotech applications and basic research.

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“…But this nascent effort sequenced only ~1,200 reads per library (Landgraf et al 2007). While providing valuable insights into the relationship of microRNA expression and disease (Lu et al 2005), these and subsequent studies (Cheng et al 2015;Ludwig et al 2016) have not unraveled cellular microRNA expression. Because all tissues are composed of multiple, unique cell types, it is essential to understand from which cell the microRNA signal is obtained.…”

Section: Introductionmentioning

confidence: 99%