PIWI-interacting RNAs (piRNAs) are a class of small RNAs abundantly expressed in animal gonads. piRNAs that map to retrotransposons are generated by a "ping-pong" amplification loop to suppress the activity of retrotransposons. However, the biogenesis and function of other categories of piRNAs have yet to be investigated. In this study, we first profiled the expression of small RNAs in type A spermatogonia, pachytene spermatocytes, and round spermatids by deep sequencing. We then focused on the computational analysis of the potential piRNAs generated in the present study as well as other published sets. piRNAs mapping to retrotransposons, mRNAs, and intergenic regions had different length distributions and were differentially regulated in spermatogenesis. piRNA-generating mRNAs (PRMRs), whose expression positively correlated with their piRNA products, constituted one-third of the protein-coding genes and were evolutionarily conserved and enriched with splicing isoforms and antisense transcripts. PRMRs with piRNAs preferentially mapped to CDSs and 3' UTRs partitioned into three clusters differentially expressed during spermatogenesis and enriched with unique sets of functional annotation terms related to housekeeping activities as well as spermatogenesis-specific processes. Intergenic piRNAs were divided into 2992 clusters probably representing novel transcriptional units that have not been reported. The transcripts of a large number of genes involved in spermatogenesis are the precursors of piRNAs, and these genes are intricately regulated by alternative splicing and antisense transcripts. piRNAs, whose regulatory role in gene expression awaits to be identified, are clearly products of a novel regulatory process that needs to be defined.
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http://dx.doi.org/10.1261/rna.2648411 | DOI Listing |
Biomark Res
January 2025
Department of Genomics, Institute of Hematology and Blood Transfusion, Prague, Czech Republic.
Background: Myelodysplastic neoplasms (MDS) are heterogeneous hematopoietic disorders characterized by ineffective hematopoiesis and genome instability. Mobilization of transposable elements (TEs) is an important source of genome instability leading to oncogenesis, whereas small PIWI-interacting RNAs (piRNAs) act as cellular suppressors of TEs. However, the roles of TEs and piRNAs in MDS remain unclear.
View Article and Find Full Text PDFBMC Cancer
January 2025
Department of Thoracic Surgery, The First Affiliated Hospital of Nanjing Medical University, No. 300, Guangzhou Road, Nanjing, 210029, Jiangsu, China.
Background: Esophageal squamous cell carcinoma (ESCC) is a highly aggressive malignancy, and current postoperative prognostic assessment methods remain unsatisfactory, underlining the urgent to develop a reliable approach for precision medicine. Given the similarities with gametogenesis, cancer/testis genes (CTGs) are acknowledged for regulation unrestrained multiplication and immune microenvironment during oncogenic processes. These processes are associated with advanced disease and poorer prognosis, indicating that CTGs could serve as ideal prognostic biomarkers in ESCC.
View Article and Find Full Text PDFJ Biol Chem
January 2025
Department of Biochemistry and Molecular Biology and Hollings Cancer Center, Medical University of South Carolina, Charleston, SC 29425, USA. Electronic address:
Transposable element (TE) silencing in the germline is crucial for preserving genome integrity; its absence results in sterility and diminished developmental robustness. The Piwi-interacting RNA (piRNA) pathway is the primary small non-coding RNA mechanism by which TEs are silenced in the germline. Three piRNA binding proteins promote the piRNA pathway function in the germline- P-element-induced wimpy testis (Piwi), Aubergine (Aub), and Argonaute 3 (Ago3).
View Article and Find Full Text PDFGenomics
January 2025
Reproductive Medicine Center, Zhongnan Hospital of Wuhan University, Wuhan, Hubei 430071, China; Hubei Clinical Research Center for Prenatal Diagnosis and Birth Health, Wuhan, Hubei 430071, China. Electronic address:
Background: Current endometrial receptivity analysis is invasive, preventing embryo transfer during the biopsy cycle. This study aims to screen serum sncRNAs as non-invasive biomarkers for ERA tests.
Methods: The study included 12 infertile patients undergoing IVF-ET and ERA, whose serum samples were collected for high-energy sequencing technology to detect sncRNA expression profiles.
Noncoding RNA
December 2024
Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA 02115, USA.
RNA metabolism is focused on RNA molecules and encompasses all the crucial processes an RNA molecule may or will undergo throughout its life cycle. It is an essential cellular process that allows all cells to function effectively. The transcriptomic landscape of a cell is shaped by the processes such as RNA biosynthesis, maturation (RNA processing, folding, and modification), intra- and inter-cellular transport, transcriptional and post-transcriptional regulation, modification, catabolic decay, and retrograde signaling, all of which are interconnected and are essential for cellular RNA homeostasis.
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