PIWI-Interacting RNA (piRNA) and Epigenetic Editing in Environmental Health Sciences

Perera, Bambarendage P. U.; Morgan, Rachel K.; Polemi, Katelyn M.; Sala-Hamrick, Kimmie E.; Svoboda, Laurie K.; Dolinoy, Dana C.

doi:10.1007/s40572-022-00372-6

Cited by 5 publications

(3 citation statements)

References 175 publications

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“…It is therefore imperative to create a publicly available piRNA database to accurately predict piRNA expression in somatic tissues ( 45 ). Currently available piRNA databases, including piRBase, piRNAQuest, piRNABank and piRNAclusterDB, are predominantly composed of germline tissues, with limited capacity for tissue- and sex-specific piRNA interrogation ( 24 , 27–30 ). They also contain multiple piRNA detection methods such as RNA co-immunoprecipitation and small RNA sequencing approaches based on length, which introduce high sequence heterogeneity due in part to antibody purity and specificity.…”

Section: Discussionmentioning

confidence: 99%

“…Because piRNAs have been associated with human diseases and environmental exposures ( 18–22 ) and there is increasing focus on them, a comprehensive and highly specific database to confidently identify them is paramount. Thus, a piRNA database with detailed information on species, tissue, sex, cell-type, age and rigorous selection criteria is critical to assess disease or exposure-induced piRNA expression differences and develop piRNA-directed therapeutic approaches, including biomarker studies and epigenome editing technology for future biology, medicine and toxicology research ( 23 , 24 ).…”

Section: Introductionmentioning

confidence: 99%

“…Some databases have limited data on tissue-specific piRNA information as well. As more sncRNA transcriptomic data become available for disease-associated biomarker identification, data interpretation and subsequent statistical analyses must be cautious of high heterogeneity and false-positive sequences included within piRNA databases ( 24 ). To address some of these key knowledge gaps, we introduce piOxi DB, a web resource of piRNA sequences and locations in multiple species, tissues and sexes that incorporates a comprehensive, rigorous analysis of piRNAs identified via sodium periodate treatment ( https://pioxidb.dcmb.med.umich.edu/ ).…”

Section: Introductionmentioning

confidence: 99%

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piOxi database: a web resource of germline and somatic tissue piRNAs identified by chemical oxidation

Wang,

Perera,

Morgan

et al. 2024

Database

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PIWI-interacting RNAs (piRNAs) are a class of small non-coding RNAs that are highly expressed and extensively studied from the germline. piRNAs associate with PIWI proteins to maintain DNA methylation for transposon silencing and transcriptional gene regulation for genomic stability. Mature germline piRNAs have distinct characteristics including a 24- to 32-nucleotide length and a 2ʹ-O-methylation signature at the 3ʹ end. Although recent studies have identified piRNAs in somatic tissues, they remain poorly characterized. For example, we recently demonstrated notable expression of piRNA in the murine soma, and while overall expression was lower than that of the germline, unique characteristics suggested tissue-specific functions of this class. While currently available databases commonly use length and association with PIWI proteins to identify piRNA, few have included a chemical oxidation method that detects piRNA based on its 3ʹ modification. This method leads to reproducible and rigorous data processing when coupled with next-generation sequencing and bioinformatics analysis. Here, we introduce piOxi DB, a user-friendly web resource that provides a comprehensive analysis of piRNA, generated exclusively through sodium periodate treatment of small RNA. The current version of piOxi DB includes 435 749 germline and 9828 somatic piRNA sequences robustly identified from M. musculus, M. fascicularis and H. sapiens. The database provides species- and tissue-specific data that are further analyzed according to chromosome location and correspondence to gene and repetitive elements. piOxi DB is an informative tool to assist broad research applications in the fields of RNA biology, cancer biology, environmental toxicology and beyond. Database URL: https://pioxidb.dcmb.med.umich.edu/

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Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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piOxi database: a web resource of germline and somatic tissue piRNAs identified by chemical oxidation

Wang,

Perera,

Morgan

et al. 2024

Database

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Revolutionizing cattle breeding: Gene editing advancements for enhancing economic traits

Liu,

Sheng

et al. 2024

Gene

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Epigenetics and the exposome: DNA methylation as a proxy for health impacts of prenatal environmental exposures

et al. 2023

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The accumulation of every day exposures can impact health across the life course, but our understanding of such exposures is impeded by our ability to delineate the relationship between an individual’s early life exposome and later life health effects. Measuring the exposome is challenging. Exposure assessed at a given time point captures a snapshot of the exposome but does not represent the full spectrum of exposures across the life course. In addition, the assessment of early life exposures and their effects is often further challenged by lack of relevant samples and the time gap between exposures and related health outcomes in later life. Epigenetics, specifically DNA methylation, has the potential to overcome these barriers as environmental epigenetic perturbances can be retained through time. In this review, we describe how DNA methylation can be framed in the world of the exposome. We offer three compelling examples of common environmental exposures, including cigarette smoke, the endocrine active compound bisphenol A (BPA), and the metal lead (Pb), to illustrate the application of DNA methylation as a proxy to measure the exposome. We discuss areas for future explorations and current limitations of this approach. Epigenetic profiling is a promising and rapidly developing tool and field of study, offering us a unique and powerful way to assess the early life exposome and its effects across different life stages.

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PIWI-Interacting RNA (piRNA) and Epigenetic Editing in Environmental Health Sciences

Cited by 5 publications

References 175 publications

piOxi database: a web resource of germline and somatic tissue piRNAs identified by chemical oxidation

piOxi database: a web resource of germline and somatic tissue piRNAs identified by chemical oxidation

Revolutionizing cattle breeding: Gene editing advancements for enhancing economic traits

Epigenetics and the exposome: DNA methylation as a proxy for health impacts of prenatal environmental exposures

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