IsopiRBank: a research resource for tracking piRNA isoforms

Zhang, Huan; Ali, Asim; Gao, Jianing; Ban, Rongjun; Jiang, Xiaohua; Zhang, Yuanwei; Shi, Qinghua

doi:10.1093/database/bay059

Cited by 20 publications

(10 citation statements)

References 56 publications

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“…Recently, different length variations of piRNAs have been discovered in several studies, and several exonucleases have been found to be required for piRNA end trimming in different species [51][52][53]. To our knowledge, no bioinformatic resource is yet available for the detection and annotation of piRNA isoforms, with the exception of IsopiRBank [54], which unfortunately does not cover the bovine species. However, consistent with statistics from IsopiRBank and general mechanisms of RNA editing, we found that length variations at the 3′ end were the most frequent changes affecting piRNA isoforms.…”

Section: The Overall Small Rna Content Of Bull Spermmentioning

confidence: 99%

A comprehensive overview of bull sperm-borne small non-coding RNAs and their diversity across breeds

Sellem¹,

Marthey

Rau

et al. 2020

Epigenetics & Chromatin

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Background: Mature sperm carry thousands of RNAs, including mRNAs, lncRNAs, tRNAs, rRNAs and sncRNAs, though their functional significance is still a matter of debate. Growing evidence suggests that sperm RNAs, especially sncR-NAs, are selectively retained during spermiogenesis or specifically transferred during epididymis maturation, and are thus delivered to the oocyte at fertilization, providing resources for embryo development. However , a deep characterization of the sncRNA content of bull sperm and its expression profile across breeds is currently lacking. To fill this gap, we optimized a guanidinium-Trizol total RNA extraction protocol to prepare high-quality RNA from frozen bull sperm collected from 40 representative bulls from six breeds. Deep sequencing was performed (40 M single 50-bp reads per sample) to establish a comprehensive repertoire of cattle sperm sncRNA. Results: Our study showed that it comprises mostly piRNAs (26%), rRNA fragments (25%), miRNAs (20%) and tRNA fragments (tsRNA, 14%). We identified 5p-halves as the predominant tsRNA subgroup in bull sperm, originating mostly from Gly and Glu isoacceptors. Our study also increased by ~ 50% the sperm repertoire of known miRNAs and identified 2022 predicted miRNAs. About 20% of sperm miRNAs were located within genomic clusters, expanding the list of known polycistronic pri-miRNA clusters and defining several networks of co-expressed miRNAs. Strikingly, our study highlighted the great diversity of isomiRs, resulting mainly from deletions and non-templated additions (A and U) at the 3p end. Substitutions within miRNA sequence accounted for 40% of isomiRs, with G>A, U>C and C>U substitutions being the most frequent variations. In addition, many sncRNAs were found to be differentially expressed across breeds. Conclusions: Our study provides a comprehensive overview of cattle sperm sncRNA, and these findings will pave the way for future work on the role of sncRNAs in embryo development and their relevance as biomarkers of semen fertility.

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Section: The Overall Small Rna Content Of Bull Spermmentioning

confidence: 99%

A comprehensive overview of bull sperm-borne small non-coding RNAs and their diversity across breeds

Sellem¹,

Marthey

Rau

et al. 2020

Epigenetics & Chromatin

View full text Add to dashboard Cite

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“…Many piRNAs are believed to have isoforms bearing both variations at their 5′ and 3′ ends with reliable evidence . End variations of piRNA family members identified in this study were analyzed.…”

Section: Resultsmentioning

confidence: 99%

Differential expression of piRNAs in reprogrammed pluripotent stem cells from mouse embryonic fibroblasts

2019

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piRNAs are a large class of small noncoding RNA that interact with an animal-specific class of Argonaute proteins, P-element induced wimpy proteins. piRNAs were initially discovered in mouse testes to be a fundamental component of spermatogenesis. Outside of the germline, piRNAs were found to function in embryogenesis, development, regeneration and cancer cells. However, despite a decade of scrutiny, functional understanding of this class of small RNAs remains very limited. To determine whether there are piRNAs present and involved in the cellular reprogramming process, we extracted piwi-interacting RNA (piRNA) signatures from a small RNA deep sequencing data set of mouse embryonic fibroblasts (MEFs), mouse embryonic stem cells (mESCs) and reprogrammed stem cells by three different technologies. We successfully identified three piRNA families specifically expressed in these reprogrammed stem cells. Meanwhile, there were almost no piRNAs observed in MEFs and mESCs. Further analysis indicated that these piRNAs may associate with the reprogramming process but not cellular pluripotency. Target gene prediction suggested that at least one of piRNAs, piR-mmu-64162, may take part in the reprogramming process by regulating cell senescence. Overall, we firstly identified the potential reprogramming associated piRNAs, shedding new light on piRNA functions.iPS cells, piRNA, Piwi protein, reprogrammed pluripotent stem cells 1 | INTRODUCTION P-element induced wimpy (Piwi)-interacting RNAs (piRNAs) are a class of small 21-30 nucleotide (nt) RNAs that were recognized about a decade ago in mouse testes. 1-3 piRNAs are transcribed by RNA polymerase II as long single-stranded precursors from specific genomic loci or clusters in animals. [4][5][6] Unlike miRNAs and siRNAs, piRNAs derive from singlestranded, rather than double-stranded RNA (dsRNA), precursors by two distinct steps: primary processing and "ping-pong" amplification. 4,7 In mice, mature piwi-interacting RNA (piRNA) is loaded to PIWI protein after primary processing to cleave its target transcripts to generate second piRNA. In turn, second piRNA can further interact with PIWI protein to give rise to the original piRNA. Through this "ping-pong" cycle, piRNA achieves a high expression level. 8 PIWI are highly conserved RNA-binding proteins and belong to the Argonaute/Piwi family. The RNA silencing activity of PIWI proteins are required for the "ping-pong" amplification. Among three murine PIWI proteins, Miwi and Mili associate with primary piRNAs and Abbreviations: GSCs, germline stem cells; iPS cells, pluripotent stem cells; MEFs, mouse embryonic fibroblasts; mESCs, mouse embryonic stem cells; miRNA, microRNA; piRNA, piwi-interacting RNA; PIWI, P-element induced wimpy. † Yanye Zhu and Chunsun Fan contributed equally to this study.

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“…Another database, piRNAQuest, also contains information about all possible piRNA clusters [ 145 ]. Detailed classifications of piRNA isoforms detected by small RNA sequencing data are included in IsopiRBank [ 146 ]. This database can be used to reveal the role of piRNA isomers in some biological processes through target analysis and enrichment analysis.…”

Section: Databases For Pirnas and Functional Predictionsmentioning

confidence: 99%

The biogenesis and biological function of PIWI-interacting RNA in cancer

et al. 2021

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Small non-coding RNAs (ncRNAs) are vital regulators of biological activities, and aberrant levels of small ncRNAs are commonly found in precancerous lesions and cancer. PIWI-interacting RNAs (piRNAs) are a novel type of small ncRNA initially discovered in germ cells that have a specific length (24–31 nucleotides), bind to PIWI proteins, and show 2′-O-methyl modification at the 3′-end. Numerous studies have revealed that piRNAs can play important roles in tumorigenesis via multiple biological regulatory mechanisms, including silencing transcriptional and posttranscriptional gene processes and accelerating multiprotein interactions. piRNAs are emerging players in the malignant transformation of normal cells and participate in the regulation of cancer hallmarks. Most of the specific cancer hallmarks regulated by piRNAs are involved in sustaining proliferative signaling, resistance to cell death or apoptosis, and activation of invasion and metastasis. Additionally, piRNAs have been used as biomarkers for cancer diagnosis and prognosis and have great potential for clinical utility. However, research on the underlying mechanisms of piRNAs in cancer is limited. Here, we systematically reviewed recent advances in the biogenesis and biological functions of piRNAs and relevant bioinformatics databases with the aim of providing insights into cancer diagnosis and clinical applications. We also focused on some cancer hallmarks rarely reported to be related to piRNAs, which can promote in-depth research of piRNAs in molecular biology and facilitate their clinical translation into cancer treatment.

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IsopiRBank: a research resource for tracking piRNA isoforms

Cited by 20 publications

References 56 publications

A comprehensive overview of bull sperm-borne small non-coding RNAs and their diversity across breeds

A comprehensive overview of bull sperm-borne small non-coding RNAs and their diversity across breeds

Differential expression of piRNAs in reprogrammed pluripotent stem cells from mouse embryonic fibroblasts

The biogenesis and biological function of PIWI-interacting RNA in cancer

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