Circular RNAs (circRNAs) are a recently discovered class of RNAs derived from protein-coding genes that have important biological and pathological roles. They are formed through backsplicing during co-transcriptional alternative splicing; however, the unified mechanism that accounts for backsplicing decisions remains unclear. Factors that regulate the transcriptional timing and spatial organization of pre-mRNA, including RNAPII kinetics, the availability of splicing factors, and features of gene architecture, have been shown to influence backsplicing decisions. Poly (ADP-ribose) polymerase I (PARP1) regulates alternative splicing through both its presence on chromatin as well as its PARylation activity. However, no studies have investigated PARP1's possible role in regulating circRNA biogenesis. Here, we hypothesized that PARP1's role in splicing extends to circRNA biogenesis. Our results identify many unique circRNAs in PARP1 depletion and PARylation-inhibited conditions compared to the wild type. We found that while all genes producing circRNAs share gene architecture features common to circRNA host genes, genes producing circRNAs in PARP1 knockdown conditions had longer upstream introns than downstream introns, whereas flanking introns in wild type host genes were symmetrical. Interestingly, we found that the behavior of PARP1 in regulating RNAPII pausing is distinct between these two classes of host genes. We conclude that the PARP1 pausing of RNAPII works within the context of gene architecture to regulate transcriptional kinetics, and therefore circRNA biogenesis. Furthermore, this regulation of PARP1 within host genes acts to fine tune their transcriptional output with implications in gene function.
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http://dx.doi.org/10.3390/cells12081160 | DOI Listing |
Int J Antimicrob Agents
December 2024
Department of Life Sciences, Centre for Functional Ecology, Associate Laboratory TERRA, Faculty of Sciences and Technology, University of Coimbra, 3000-456, Coimbra, Portugal.
Integrons mediate the acquisition and expression of gene cassettes (GCs). The production of beta-lactamases (BLs) is the most relevant mechanism of beta-lactams resistance. To explore the role of integrons in BL genes dissemination, we retrieved sequences and metadata from the INTEGRALL database and performed literature review.
View Article and Find Full Text PDFBMC Res Notes
December 2024
Laboratory of Infectious Diseases, Graduate School of Infection Control Sciences and Ōmura Satoshi Memorial Institute, Kitasato University, 5-9-1 Shirokane, Minato-ku, Tokyo, 108-8641, Japan.
Objective: We aimed to characterize integrative and conjugative elements (ICEs) in antimicrobial resistant Streptococcs uberis isolates from bovine milk in Chiba, Japan, based on whole-genome sequence (WGS) data.
Results: Of the 101 isolates, we found the 36 isolates harboring erm(B)-tet(O), showing resistance to macrolides-lincosamides-tetracyclines. The 22 isolates were randomly selected and subject to WGS determination.
Parasit Vectors
December 2024
Disease Intervention and Prevention Program, Texas Biomedical Research Institute, P.O. Box 760549, San Antonio, TX, 78245, USA.
Background: Genomic analysis has revealed extensive contamination among laboratory-maintained microbes including malaria parasites, Mycobacterium tuberculosis, and Salmonella spp. Here, we provide direct evidence for recent contamination of a laboratory schistosome parasite population, and we investigate its genomic consequences. The Brazilian Schistosoma mansoni population SmBRE has several distinctive phenotypes, showing poor infectivity, reduced sporocyst number, low levels of cercarial shedding and low virulence in the intermediate snail host, and low worm burden and low fecundity in the vertebrate rodent host.
View Article and Find Full Text PDFTuberculosis (Edinb)
December 2024
Shanxi Provincial Key Laboratory for Medical Molecular Cell Biology, Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, and Institutes of Biomedical Sciences, Shanxi University, Taiyuan, 030006, China. Electronic address:
Background: Immune imbalance is crucial in tuberculosis pathogenesis and may be modulated by mesenchymal stem cells (MSCs). However, how MSCs regulate the host's response to Mycobacterium tuberculosis (Mtb) is unclear.
Methods: Human umbilical cord-derived MSCs were co-cultured with Mtb-infected THP-1 macrophages.
Microbiol Immunol
December 2024
Department of Oral Microbiology and Immunology, Showa University Graduate School of Dentistry, Shinagawa-ku, Tokyo, Japan.
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