piRNAs Interact with Cold-Shock Domain-Containing RNA Binding Proteins and Regulate Neuronal Gene Expression During Differentiation

Subhramanyam, Charannya Sozheesvari; Cao, Qian; Wang, Cheng; Heng, Zealyn Shi‐Lin; Zhou, Zhihong; Hu, Qidong

doi:10.1007/s12035-021-02678-2

Cited by 3 publications

(3 citation statements)

References 56 publications

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“…piRNAs play critical regulatory roles during development, disease states and other complex biological processes, suggesting their involvement in important tissue-specific functions in addition to transposon silencing in the germline ( 10 , 41–43 ). For instance, piRNAs regulate neuronal differentiation via association with cold-shock domain proteins, cardiac circulatory system regeneration and genomic imprinting in the placenta ( 44–46 ).…”

Section: Discussionmentioning

confidence: 99%

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%

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

Wang,

Perera,

Morgan

et al. 2024

Database

View full text Add to dashboard Cite

show abstract

“…51 Additionally, piRNA's role in regulating neuronal differentiation via interacting with cold shock domain containing RNA binding proteins has been validated in human embryonal carcinoma cells. 52 Furthermore, the same group demonstrated that PIWIL4 modulated neuronal differentiation in NT2 cells. 53 Hence, piRNAs and PIWIL proteins may either work together or independently to mediate the biological processes mentioned above.…”

Section: Enriched Motifs Of Pirnas and Their Associated Functionsmentioning

confidence: 95%

piRNAs in the human retina and retinal pigment epithelium reveal a potential role in intracellular trafficking and oxidative stress

Karpagavalli,

Sivagurunathan,

Panda

et al. 2024

Mol. Omics

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“…During RA-induced neuronal differentiation of NT2 cells, two piRNAs, piR-DQ582359 and piR-DQ596268 , were upregulated ( Subhramanyam et al, 2022 ). Furthermore, these piRNAs potentially downregulated the expression of cold-shock domain-containing RNA-binding proteins, such as DIS3 homolog, exosome endoribonuclease and 3′–5′ exoribonuclease ( DIS3 ), DIS3 like 3′–5′ exoribonuclease 2 ( DIS3L2 ), and Y box-binding protein ( YB-1 ), which likely suppress the expression of MAP2 and TUBB3 ( Subhramanyam et al, 2022 ), suggesting that piRNAs mediate neuronal differentiation by modulating neuronal gene expression ( Figure 1B ).…”

Section: Neuronal Pirna Functionsmentioning

confidence: 99%

Role of piRNA biogenesis and its neuronal function in the development of neurodegenerative diseases

Sato

Takayama

Inoue

2023

Front. Aging Neurosci.

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Neurodegenerative diseases, such as Alzheimer’s disease (AD), Parkinson’s disease (PD), and amyotrophic lateral sclerosis (ALS), are caused by neuronal loss and dysfunction. Despite remarkable improvements in our understanding of these pathogeneses, serious worldwide problems with significant public health burdens are remained. Therefore, new efficient diagnostic and therapeutic strategies are urgently required. PIWI-interacting RNAs (piRNAs) are a major class of small non-coding RNAs that silence gene expression through transcriptional and post-transcriptional processes. Recent studies have demonstrated that piRNAs, originally found in the germ line, are also produced in non-gonadal somatic cells, including neurons, and further revealed the emerging roles of piRNAs, including their roles in neurodevelopment, aging, and neurodegenerative diseases. In this review, we aimed to summarize the current knowledge regarding the piRNA roles in the pathophysiology of neurodegenerative diseases. In this context, we first reviewed on recent updates on neuronal piRNA functions, including biogenesis, axon regeneration, behavior, and memory formation, in humans and mice. We also discuss the aberrant expression and dysregulation of neuronal piRNAs in neurodegenerative diseases, such as AD, PD, and ALS. Moreover, we review pioneering preclinical studies on piRNAs as biomarkers and therapeutic targets. Elucidation of the mechanisms underlying piRNA biogenesis and their functions in the brain would provide new perspectives for the clinical diagnosis and treatment of AD and various neurodegenerative diseases.

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piRNAs Interact with Cold-Shock Domain-Containing RNA Binding Proteins and Regulate Neuronal Gene Expression During Differentiation

Cited by 3 publications

References 56 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

piRNAs in the human retina and retinal pigment epithelium reveal a potential role in intracellular trafficking and oxidative stress

Role of piRNA biogenesis and its neuronal function in the development of neurodegenerative diseases

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