piRNAQuest: searching the piRNAome for silencers

Sarkar, Arijita; Maji, Ranjan Kumar; Saha, Sudipto; Ghosh, Zhumur

doi:10.1186/1471-2164-15-555

Cited by 55 publications

(51 citation statements)

References 50 publications

(90 reference statements)

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“…1 miR-NAs (18-22 nts), the best-characterized sncRNA among all regulates 60% of the total human protein-coding genes (PCGs), and thus, aberrant expression of the same has been implicated in various diseases. 7,8 The total number of piRNAs identified till now is similar to that of PCGs according to a recent estimate. 7,8 The total number of piRNAs identified till now is similar to that of PCGs according to a recent estimate.…”

Section: Introductionsupporting

confidence: 62%

Investigating piwi‐interacting RNA regulome in human neuroblastoma

Roy

Mallick

2018

Genes Chromosomes & Cancer

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Remarkable attempts have been exercised in recent years using high-throughput technologies to identify and decipher the functions of piRNAs in various abnormalities like cancer. However, piRNAs in the oncogenesis of neuroblastoma (NB) has not been reported yet even after their illustrated roles in neurological processes. Therefore, we investigated the piRNA transcriptome in IMR-32 and SH-SY-5Y NB cell lines by employing high-throughput next-generation sequencing after confirming the expression of three associated PIWILs both at mRNAs and protein level by qRT-PCR and immunofluroscence, respectively. We identified a common pool of 525 piRNAs of 26-32 nts long expressed in both the cell lines. The possible functions of these piRNAs were charted by predicting their targeting on retrotransposon-containing 1769 mRNAs differentially expressed in 39 NB cell lines followed by network and pathway analysis. The analysis revealed that majority of the target binding sites in NB fall within retrotransposons residing within the 3'UTR of target mRNA transcripts like miRNA-targets. Further, we validated the expression of key piRNAs and their target genes enriched in cancer-related networks, pathways and biological processes which are hypothesized to play crucial roles in neoplastic events of NB. We believe that the evidence of piRNAs in human NB and their possible contribution to its pathogenesis reported in this work will open up new exciting possibilities for piRNA-mediated therapeutics for this malignancy.

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Section: Introductionsupporting

confidence: 62%

Investigating piwi‐interacting RNA regulome in human neuroblastoma

Roy

Mallick

2018

Genes Chromosomes & Cancer

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“…piRNAs were initially reported in germ lines regulating the TEs, but now they have been reported in somatic and cancer cells as well . In germlines, piRNAs maintain genome stability by regulating transposons at different levels that include degradation of transposons in association with PIWI‐proteins and regulation of transposon expression by histone‐modification and DNA‐methylation …”

Section: Introductionmentioning

confidence: 99%

“…piRNAs were initially reported in germ lines regulating the TEs, but now they have been reported in somatic and cancer cells as well. 11 In germlines, piRNAs maintain genome stability by regulating transposons at different levels that include degradation of transposons in association with PIWI-proteins [15][16][17] and regulation of transposon expression by histone-modification and DNA-methylation. 18 Besides their germline functions, piRNAs are now reported in several somatic cells such as human saliva with unknown functions, axis and eye formation in Drosophila, long-term memory retention in Aplysia neurons, multigenerational epigenetic memory in C elegans, and spine morphogenesis in mouse hippocampus.…”

mentioning

confidence: 99%

Tumor suppressive activity of PIWI‐interacting RNA in human fibrosarcoma mediated through repression of RRM2

Das

Roy

Jain

et al. 2018

Molecular Carcinogenesis

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P‐element induced wimpy testis (PIWI)‐interacting RNAs (piRNAs) are a promising class of small regulatory RNAs, earlier believed to control transposable elements (TEs) activity in germlines are now reported in somatic and cancer cells. The aberrant expression of piRNAs has been documented in various cancers wherein they modulate tumorigenesis either as oncogenes or tumor suppressors by curbing target gene expression. However, there is no report yet on the association of piRNAs in fibrosarcoma, an early metastatic lethal tumor. For the first time, we reported a piRNA, piR‐39980 in fibrosarcoma and investigated its potential role in malignancy by employing several methods such as qRT‐PCR, MTT assay, transwell invasion and migration assay, wound healing assay, flow cytometric cell cycle analysis, Annexin V‐PE apoptosis assay, AO/EB dual staining assay, and chromatin condensation assay. We observed that piR‐39980 significantly attenuated proliferation, migration, invasion, and colony forming ability as well as induced apoptotic cell death of HT1080 fibrosarcoma cells when transiently overexpressed with its piRNA mimics. The dual luciferase reporter assay confirmed that piR‐39980 promotes apoptosis and inhibits proliferation in fibrosarcoma by repressing RRM2 through direct targeting at its 3′UTR through extensive sequence complementary binding, unlike microRNA targeting. In summary, this study revealed that piR‐39980 has a strong anti‐tumor effect and hence could be a promising RNA‐based therapeutic agent for the malignancy of fibrosarcoma.

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“…proTRAC detects piRNA clusters based on a probabilistic analysis with assumption of a uniform distribution while piClust uses a density based clustering approach for the detection of piRNAs. piRNAQuest allows a search of the piRNome for silencers [154]. Another notable framework is SeqCluster [155], a python pipeline for the annotation and classiication of non-miRNA small ncRNAs.…”

Section: Tools For Identiication Of Other Non-coding Rnamentioning

confidence: 99%

“…The popular tools for piRNA identiication include ProTRAC [152], piClust [153], piRNAQuest [154], etc. (Table 5).…”

Section: Tools For Identiication Of Other Non-coding Rnamentioning

confidence: 99%

Transcriptome Analysis of Non‐Coding RNAs in Livestock Species: Elucidating the Ambiguity

Ngoc¹,

Dudemaine²,

Fomenky³

et al. 2017

Applications of RNA-Seq and Omics Strategies - From Microorganisms to Human Health

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The recent remarkable development of transcriptomics technologies, especially next generation sequencing technologies, allows deeper exploration of the hidden landscapes of complex traits and creates great opportunities to improve livestock productivity and welfare. Non-coding RNAs (ncRNAs), RNA molecules that are not translated into proteins, are key transcriptional regulators of health and production traits, thus, transcriptomics analyses of ncRNAs are important for a beter understanding of the regulatory architecture of livestock phenotypes. In this chapter, we present an overview of common frameworks for generating and processing RNA sequence data to obtain ncRNA transcripts. Then, we review common approaches for analyzing ncRNA transcriptome data and present current state of the art methods for identiication of ncRNAs and functional inference of identiied ncRNAs, with emphasis on tools for livestock species. We also discuss future challenges and perspectives for ncRNA transcriptome data analysis in livestock species.

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piRNAQuest: searching the piRNAome for silencers

Cited by 55 publications

References 50 publications

Investigating piwi‐interacting RNA regulome in human neuroblastoma

Investigating piwi‐interacting RNA regulome in human neuroblastoma

Tumor suppressive activity of PIWI‐interacting RNA in human fibrosarcoma mediated through repression of RRM2

Transcriptome Analysis of Non‐Coding RNAs in Livestock Species: Elucidating the Ambiguity

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