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Scientific Reports Mar 2020To investigate the genetic diversity, spatiotemporal dynamics, and transmission networks of HIV-1 CRF55_01B epidemic in China. A total of 209 partial pol gene sequences...
To investigate the genetic diversity, spatiotemporal dynamics, and transmission networks of HIV-1 CRF55_01B epidemic in China. A total of 209 partial pol gene sequences of HIV-1 CRF55_01B were sampled during 2007-2015 from 7 provinces of China. Phylogenetic analyses and trait diffusion process of these sequences were performed using Bayesian methods. Distance-based molecular network analyses were performed to infer putative relationships. Characteristics of genetically linked individuals were analyzed. Our study identified that HIV-1 CRF55_01B likely originated among men who have sex with men (MSM) in Guangdong province in January 2003 (April 2000-April 2005), and that Guangdong province and MSM are major hubs for the spread of the HIV-1 CRF55_01B epidemic in China. A Bayesian Skygrid plot revealed that the effective population size of HIV-1 CRF55_01B experienced increased phase followed by a plateau. All sequences from persons of unknown risk clustered within groups who reported MSM risk. This could be because Chinese MSM may not report such risk due to HIV/AIDS-related stigmatization and discrimination. This study inferred the transmission dynamics of the HIV-1 CRF55_01B epidemic in China at high resolution. The methods developed in this study may be critical for designing effective HIV prevention strategies in China and beyond.
Topics: China; Female; Genetic Linkage; Genome, Viral; HIV Infections; HIV-1; Homosexuality, Male; Humans; Male; Phylogeny; pol Gene Products, Human Immunodeficiency Virus
PubMed: 32198405
DOI: 10.1038/s41598-020-61870-x -
Open Biology Feb 2017RNA polymerase III (Pol III) transcribes a limited set of short genes in eukaryotes producing abundant small RNAs, mostly tRNA. The originally defined yeast Pol III... (Review)
Review
RNA polymerase III (Pol III) transcribes a limited set of short genes in eukaryotes producing abundant small RNAs, mostly tRNA. The originally defined yeast Pol III transcriptome appears to be expanding owing to the application of new methods. Also, several factors required for assembly and nuclear import of Pol III complex have been identified recently. Models of Pol III based on cryo-electron microscopy reconstructions of distinct Pol III conformations reveal unique features distinguishing Pol III from other polymerases. Novel concepts concerning Pol III functioning involve recruitment of general Pol III-specific transcription factors and distinctive mechanisms of transcription initiation, elongation and termination. Despite the short length of Pol III transcription units, mapping of transcriptionally active Pol III with nucleotide resolution has revealed strikingly uneven polymerase distribution along all genes. This may be related, at least in part, to the transcription factors bound at the internal promoter regions. Pol III uses also a specific negative regulator, Maf1, which binds to polymerase under stress conditions; however, a subset of Pol III genes is not controlled by Maf1. Among other RNA polymerases, Pol III machinery represents unique features related to a short transcript length and high transcription efficiency.
Topics: Eukaryota; Protein Conformation; RNA Polymerase III; RNA, Transfer; Repressor Proteins; Transcription, Genetic
PubMed: 28228471
DOI: 10.1098/rsob.170001 -
Viruses May 2022Interferon is a marker of host antiviral immunity, which is disordered in COVID-19 patients. ERV can affect the secretion of interferon through the cGAS-STING pathway....
Interferon is a marker of host antiviral immunity, which is disordered in COVID-19 patients. ERV can affect the secretion of interferon through the cGAS-STING pathway. In this study, we explored whether IFN-I and HERV-K (HML-2) were activated in COVID-19 patients and whether there was an interaction between them. We collected blood samples from COVID-19 patients and healthy controls. We first detected the expression of HERV-K (HML-2) , , and genes and IFN-I-related genes between patients and healthy people by qPCR, synchronously detected VERO cells infected with SARS-CoV-2. Then, the chromosome distributions of highly expressed HERV-K (HML-2) , , and genes were mapped by the next-generation sequencing results, and GO analysis was performed on the related genes. We found that the HERV-K (HML-2) , , and genes were highly expressed in COVID-19 patients and VERO cells infected with SARS-CoV-2. The interferon-related genes , and were also activated in COVID-19 patients, and GO analysis showed that HERV-K (HML-2) can regulate the secretion of interferon. The high expression of HERV-K (HML-2) might activate the increase of interferon in COVID-19 patients, proving that HERV-K does not only play a negative role in the human body.
Topics: Animals; Antiviral Agents; COVID-19; Chlorocebus aethiops; Endogenous Retroviruses; Genes, Viral; Humans; Interferons; SARS-CoV-2; Vero Cells
PubMed: 35632738
DOI: 10.3390/v14050996 -
RNA (New York, N.Y.) Feb 2022Widespread cotranscriptional splicing has been demonstrated from yeast to human. However, most studies to date addressing the kinetics of splicing relative to...
Widespread cotranscriptional splicing has been demonstrated from yeast to human. However, most studies to date addressing the kinetics of splicing relative to transcription used either or metazoan cultured cell lines. Here, we adapted native elongating transcript sequencing technology (NET-seq) to measure cotranscriptional splicing dynamics during the early developmental stages of embryos. Our results reveal the position of RNA polymerase II (Pol II) when both canonical and recursive splicing occur. We found heterogeneity in splicing dynamics, with some RNAs spliced immediately after intron transcription, whereas for other transcripts no splicing was observed over the first 100 nt of the downstream exon. Introns that show splicing completion before Pol II has reached the end of the downstream exon are necessarily intron-defined. We studied the splicing dynamics of both nascent pre-mRNAs transcribed in the early embryo, which have few and short introns, as well as pre-mRNAs transcribed later in embryonic development, which contain multiple long introns. As expected, we found a relationship between the proportion of spliced reads and intron size. However, intron definition was observed at all intron sizes. We further observed that genes transcribed in the early embryo tend to be isolated in the genome whereas genes transcribed later are often overlapped by a neighboring convergent gene. In isolated genes, transcription termination occurred soon after the polyadenylation site, while in overlapped genes, Pol II persisted associated with the DNA template after cleavage and polyadenylation of the nascent transcript. Taken together, our data unravel novel dynamic features of Pol II transcription and splicing in the developing embryo.
Topics: Animals; Drosophila Proteins; Drosophila melanogaster; Embryo, Nonmammalian; Introns; Polyadenylation; RNA Polymerase II; RNA Splicing; Transcription Termination, Genetic
PubMed: 34667107
DOI: 10.1261/rna.078933.121 -
Genes & Development Mar 2022RNA polymerase II (Pol II) elongation is a critical step in gene expression. Here we found that NDF, which was identified as a bilaterian nucleosome-destabilizing...
RNA polymerase II (Pol II) elongation is a critical step in gene expression. Here we found that NDF, which was identified as a bilaterian nucleosome-destabilizing factor, is also a Pol II transcription factor that stimulates elongation with plain DNA templates in the absence of nucleosomes. NDF binds directly to Pol II and enhances elongation by a different mechanism than that used by transcription factor TFIIS. Moreover, yeast Pdp3, which is related to NDF, binds to Pol II and stimulates elongation. Thus, NDF is a Pol II binding transcription elongation factor that is localized over gene bodies and is conserved from yeast to humans.
Topics: Humans; Nucleosomes; RNA Polymerase II; Saccharomyces cerevisiae; Transcription Factors; Transcription, Genetic; Transcriptional Elongation Factors
PubMed: 35273076
DOI: 10.1101/gad.349150.121 -
Oxidative Medicine and Cellular... 2021TF IIB-related factor 1 (Brf1) is a key transcription factor of RNA polymerase III (Pol III) genes. Our early studies have demonstrated that Brf1 and Pol III genes are...
TF IIB-related factor 1 (Brf1) is a key transcription factor of RNA polymerase III (Pol III) genes. Our early studies have demonstrated that Brf1 and Pol III genes are epigenetically modulated by histone H3 phosphorylation. Here, we have further investigated the relationship of the abnormal expression of Brf1 with a high level of phosphorylated AMPK (pAMPK) and explored the role and molecular mechanism of pAMPK-mediated dysregulation of Brf1 and Pol III genes in lung cancer. Brf1 is significantly overexpressed in lung cancer cases. The cases with high Brf1 expression display short overall survival times. Elevation of Brf1 expression is accompanied by a high level of pAMPK. Brf1 and pAMPK colocalize in nuclei. Further analysis indicates that the carcinogen MNNG induces pAMPK to upregulate Brf1 expression, resulting in the enhancement of Pol III transcription. In contrast, inhibiting pAMPK decreases cellular levels of Brf1, resulting in the reduction of Pol III gene transcription to attenuate the rates of cell proliferation and colony formation of lung cancer cells. These outcomes demonstrate that high Brf1 expression reveals a worse prognosis in lung cancer patients. pAMPK-mediated dysregulation of Brf1 and Pol III genes plays important roles in cell proliferation, colony formation, and tumor development of lung cancer. Brf1 may be a biomarker for establishing the prognosis of lung cancer. It is a new mechanism that pAMPK mediates dysregulation of Brf1 and Pol III genes to promote lung cancer development.
Topics: Cell Line, Tumor; Female; Humans; Male; Middle Aged; RNA Polymerase III; TATA-Binding Protein Associated Factors; Transcription Factors; Transfection
PubMed: 33995823
DOI: 10.1155/2021/5554932 -
BioRxiv : the Preprint Server For... Feb 2023RNA Polymerase II (Pol II) is a multi-subunit complex that undergoes covalent modifications as transcription proceeds through genes and enhancers. Rate-limiting steps of...
RNA Polymerase II (Pol II) is a multi-subunit complex that undergoes covalent modifications as transcription proceeds through genes and enhancers. Rate-limiting steps of transcription control Pol II recruitment, site and degree of initiation, pausing duration, productive elongation, nascent transcript processing, transcription termination, and Pol II recycling. Here, we developed Precision Run-On coupled to Immuno-Precipitation sequencing (PRO-IP-seq) and tracked phosphorylation of Pol II C-terminal domain (CTD) at nucleotide-resolution. We uncovered precise positional control of Pol II CTD phosphorylation as transcription proceeds from the initiating nucleotide, through early and late promoter-proximal pause, and into productive elongation. Pol II CTD was predominantly unphosphorylated in the early pause-region, whereas serine-2- and serine-5-phosphorylations occurred preferentially in the later pause-region. Serine-7-phosphorylation dominated after the pause-release in a region where Pol II accelerates to its full elongational speed. Interestingly, tracking transcription upon heat-induced reprogramming demonstrated that Pol II with phosphorylated CTD remains paused on heat-repressed genes.
PubMed: 36778434
DOI: 10.1101/2023.02.04.527107 -
Frontiers in Cell and Developmental... 2021Polydatin (POL) is a natural active compound found in with reported anti-oxidant and antiviral effects. With the aging population there has been a stark increase in...
Polydatin (POL) is a natural active compound found in with reported anti-oxidant and antiviral effects. With the aging population there has been a stark increase in the prevalence of osteoporosis (OP), rendering it an imposing public health issue. The potential effect of POL as a therapy for OP remains unclear. Therefore, we sought to investigate the therapeutic effect of POL in OP and to elucidate the underlying signaling mechanisms in its regulatory process. The POL-targeted genes interaction network was constructed using the Search Tool for Interacting Chemicals (STITCH) database, and the shared Kyoto Encyclopedia of Genes and Genomes (KEGG). Pathways involved in OP and POL-targeted genes were identified. Quantitative real-time PCR (qRT-PCR) and enzyme-linked immunosorbent assay (ELISA) were performed to evaluate the osteogenic genes and the phosphorylation level in pre-osteoblastic cells. In addition, ALP and alizarin red staining was used to test the effect of POL on extracellular matrix mineralization. Twenty-seven KEGG pathways shared between POL-related genes and OP were identified. signaling was identified as a potential key mechanism. results highlighted a definitive anti-OP effect of POL. The phosphorylation levels of signaling, including α, , and , were significantly decreased in this regulatory process. Our results suggest that POL has a promising therapeutic effect in OP. signaling may be the underlying mechanism in this effect, providing a novel sight in discovering new drugs for OP.
PubMed: 34660587
DOI: 10.3389/fcell.2021.730362 -
PloS One 2023Antiretroviral therapy (ART) effectiveness is compromised by the emergence of HIV drug resistance mutations (DRM) and can lead to the failure of ART. Apart from...
BACKGROUND
Antiretroviral therapy (ART) effectiveness is compromised by the emergence of HIV drug resistance mutations (DRM) and can lead to the failure of ART. Apart from intrinsic viral factors, non-compliance with drugs and/or the use of sub-optimum therapy can lead to the emergence of DRMs. In Pakistan HIV currently exists as a concentrated epidemic, however, ART coverage is very low, and drug adherence is poor. ART is selected assuming without baseline genotyping. Pakistan has recently seen a rise in treatment failures, but the country's actual burden of DRM is still unknown. In this study, we perform the genetic and drug resistance analysis of the pol gene from Pakistani HIV-positive ART-naïve and ART-experienced individuals.
METHODS
In this study, HIV-1 pol was sequenced from 146 HIV-1 positive individuals, divided into ART-naïve (n = 37) and ART-experienced (n = 109). The sequences were also used to determine HIV-1 subtypes, the prevalence of DRM, and pol genetic variability.
RESULTS
DRM analysis identified numerous DRMs against reverse transcriptase inhibitors in both ART-naïve and ART-experienced groups, including a few that are classified as rare. Additionally, the ART-experienced group showed mutations associated with resistance to protease inhibitors. Genetic analysis showed negative selection pressure in both groups, but a higher rate of evolution in the ART-naïve group.
CONCLUSION
High prevalence of DRMs, especially against previous first-line treatment in ART- naïve and the accumulation of DRMs in ART-experienced groups is concerning and warrants that a more extensive DRM survey be carried out to inform first-line and second-line ART regimen recommendations.
Topics: Humans; Anti-Retroviral Agents; Drug Resistance, Multiple, Viral; Genes, pol; HIV Infections; HIV Seropositivity; HIV-1; Peptide Hydrolases; RNA-Directed DNA Polymerase
PubMed: 37616294
DOI: 10.1371/journal.pone.0290425 -
BioRxiv : the Preprint Server For... Dec 2023RNA polymerase II (pol II) can backtrack during transcription elongation, exposing the 3' end of nascent RNA. Nascent RNA sequencing can approximate the location of...
RNA polymerase II (pol II) can backtrack during transcription elongation, exposing the 3' end of nascent RNA. Nascent RNA sequencing can approximate the location of backtracking events that are quickly resolved; however, the extent and genome wide distribution of more persistent backtracking is unknown. Consequently, we developed a novel method to directly sequence the extruded, "backtracked" 3' RNA. Our data shows that pol II slides backwards more than 20 nucleotides in human cells and can persist in this backtracked state. Persistent backtracking mainly occurs where pol II pauses near promoters and intron-exon junctions, and is enriched in genes involved in translation, replication, and development, where gene expression is decreased if these events are unresolved. Histone genes are highly prone to persistent backtracking, and the resolution of such events is likely required for timely expression during cell division. These results demonstrate that persistent backtracking has the potential to affect diverse gene expression programs.
PubMed: 38168453
DOI: 10.1101/2023.12.13.571520