scholarly journals HIV Modifies the m6A and m5C Epitranscriptomic Landscape of the Host Cell

2021 ◽  
Vol 1 ◽  
Author(s):  
Sara Cristinelli ◽  
Paolo Angelino ◽  
Andrew Janowczyk ◽  
Mauro Delorenzi ◽  
Angela Ciuffi
Keyword(s):  
Hiv Infection ◽  
High Throughput ◽  
Rna Splicing ◽  
High Throughput Sequencing ◽  
Infection Model ◽  
Rna Modifications ◽  
Hiv Replication ◽  
Web Resource ◽  
Mrna Extraction ◽  
The Impact

The study of RNA modifications, today known as epitranscriptomics, is of growing interest. The N6-methyladenosine (m6A) and 5-methylcytosine (m5C) RNA modifications are abundantly present on mRNA molecules, and impact RNA interactions with other proteins or molecules, thereby affecting cellular processes, such as RNA splicing, export, stability, and translation. Recently m6A and m5C marks were found to be present on human immunodeficiency (HIV) transcripts as well and affect viral replication. Therefore, the discovery of RNA methylation provides a new layer of regulation of HIV expression and replication, and thus offers novel array of opportunities to inhibit replication. However, no study has been performed to date to investigate the impact of HIV replication on the transcript methylation level in the infected cell. We used a productive HIV infection model, consisting of the CD4+ SupT1 T cell line infected with a VSV-G pseudotyped HIVeGFP-based vector, to explore the temporal landscape of m6A and m5C epitranscriptomic marks upon HIV infection, and to compare it to mock-treated cells. Cells were collected at 12, 24, and 36 h post-infection for mRNA extraction and FACS analysis. M6A RNA modifications were investigated by methylated RNA immunoprecipitation followed by high-throughput sequencing (MeRIP-Seq). M5C RNA modifications were investigated using a bisulfite conversion approach followed by high-throughput sequencing (BS-Seq). Our data suggest that HIV infection impacted the methylation landscape of HIV-infected cells, inducing mostly increased methylation of cellular transcripts upon infection. Indeed, differential methylation (DM) analysis identified 59 m6A hypermethylated and only 2 hypomethylated transcripts and 14 m5C hypermethylated transcripts and 7 hypomethylated ones. All data and analyses are also freely accessible on an interactive web resource (http://sib-pc17.unil.ch/HIVmain.html). Furthermore, both m6A and m5C methylations were detected on viral transcripts and viral particle RNA genomes, as previously described, but additional patterns were identified. This work used differential epitranscriptomic analysis to identify novel players involved in HIV life cycle, thereby providing innovative opportunities for HIV regulation.

scholarly journals HIV modifies the m6A and m5C epitranscriptomic landscape of the host cell

2021 ◽  
Author(s):  
Sara Cristinelli ◽  
Paolo Angelino ◽  
Andrew Janowczyk ◽  
Mauro Delorenzi ◽  
Angela Ciuffi
Keyword(s):  
Hiv Infection ◽  
High Throughput ◽  
Rna Splicing ◽  
High Throughput Sequencing ◽  
Infection Model ◽  
Rna Modifications ◽  
Hiv Replication ◽  
Web Resource ◽  
Mrna Extraction ◽  
The Impact

AbstractThe study of RNA modifications, today known as epitranscriptomics, is of growing interest. The N6-methyladenosine (m6A) and 5-methylcytosine (m5C) RNA modifications are abundantly present on mRNA molecules, and impact RNA interactions with other proteins or molecules, thereby affecting cellular processes, such as RNA splicing, export, stability and translation. Recently m6A and m5C marks were found to be present on human immunodeficiency (HIV) transcripts as well and affect viral replication. Therefore, the discovery of RNA methylation provides a new layer of regulation of HIV expression and replication, and thus offers novel array of opportunities to inhibit replication. However, no study has been performed to date to investigate the impact of HIV replication on the transcript methylation level in the infected cell. We used a productive HIV infection model, consisting of the CD4+ SupT1 T cell line infected with a VSV-G pseudotyped HIVeGFP-based vector, to explore the temporal landscape of m6A and m5C epitranscriptomic marks upon HIV infection, and compare it to mock-treated cells. Cells were collected at 12, 24 and 36h post-infection for mRNA extraction and FACS analysis. M6A RNA modifications were investigated by methylated RNA immunoprecipitation followed by high-throughput sequencing (MeRIP-Seq). M5C RNA modifications were investigated using a bisulfite conversion approach followed by high-throughput sequencing (BS-Seq).Our data suggest that HIV Infection impacted the methylation landscape of HIV-infected cells, inducing mostly increased methylation of cellular transcripts upon infection. Indeed, differential methylation (DM) analysis identified 59 m6A hypermethylated and only 2 hypomethylated transcripts and 14 m5C hypermethylated transcripts and 7 hypomethylated ones. All data and analyses are also freely accessible on an interactive web resource (http://sib-pc17.unil.ch/HIVmain.html). Furthermore, both m6A and m5C methylations were detected on viral transcripts and viral particle RNA genomes, as previously described, but additional patterns were identified.This work used differential epitranscriptomic analysis to identify novel players involved in HIV life cycle, thereby providing innovative opportunities for HIV regulation.

scholarly journals High-Throughput Sequencing is a Crucial Tool to Investigate the Contribution of Human Endogenous Retroviruses (HERVs) to Human Biology and Development

Viruses ◽  
2020 ◽  
Vol 12 (6) ◽  
pp. 633 ◽  
Author(s):  
Maria Paola Pisano ◽  
Nicole Grandi ◽  
Enzo Tramontano
Keyword(s):  
High Throughput ◽  
High Throughput Sequencing ◽  
Developmental Stages ◽  
Large Fraction ◽  
Expression Patterns ◽  
Cell Types ◽  
Endogenous Retroviruses ◽  
Human Endogenous Retroviruses ◽  
Retroviral Infections ◽  
The Impact

Human Endogenous retroviruses (HERVs) are remnants of ancient retroviral infections that represent a large fraction of our genome. Their transcriptional activity is finely regulated in early developmental stages and their expression is modulated in different cell types and tissues. Such activity has an impact on human physiology and pathology that is only partially understood up to date. Novel high-throughput sequencing tools have recently allowed for a great advancement in elucidating the various HERV expression patterns in different tissues as well as the mechanisms controlling their transcription, and overall, have helped in gaining better insights in an all-inclusive understanding of the impact of HERVs in biology of the host.

scholarly journals Multi-Body-Site Microbiome and Culture Profiling of Military Trainees Suffering from Skin and Soft Tissue Infections at Fort Benning, Georgia

mSphere ◽  
2016 ◽  
Vol 1 (5) ◽  
Author(s):  
Jatinder Singh ◽  
Ryan C. Johnson ◽  
Carey D. Schlett ◽  
Emad M. Elassal ◽  
Katrina B. Crawford ◽  
...  
Keyword(s):  
High Throughput ◽  
High Throughput Sequencing ◽  
Bacterial Community Composition ◽  
Soft Tissue Infections ◽  
Microbial Composition ◽  
Content Type ◽  
Microbial Dysbiosis ◽  
Lack Of Information ◽  
The Impact ◽  
Nasal Microbiota

ABSTRACT While it is evident that nasal colonization with S. aureus increases the likelihood of SSTI, there is a significant lack of information regarding the contribution of extranasal colonization to the overall risk of a subsequent SSTI. Furthermore, the impact of S. aureus colonization on bacterial community composition outside the nasal microbiota is unclear. Thus, this report represents the first investigation that utilized both culture and high-throughput sequencing techniques to analyze microbial dysbiosis at multiple body sites of healthy and diseased/colonized individuals. The results described here may be useful in the design of future methodologies to treat and prevent SSTIs. Skin and soft tissue infections (SSTIs) are common in the general population, with increased prevalence among military trainees. Previous research has revealed numerous nasal microbial signatures that correlate with SSTI development and Staphylococcus aureus colonization. Thus, we hypothesized that the ecology of the inguinal, oropharynx, and perianal regions may also be altered in response to SSTI and/or S. aureus colonization. We collected body site samples from 46 military trainees with purulent abscess (SSTI group) as well as from 66 asymptomatic controls (non-SSTI group). We also collected abscess cavity samples to assess the microbial composition of these infections. Samples were analyzed by culture, and the microbial communities were characterized by high-throughput sequencing. We found that the nasal, inguinal, and perianal regions were similar in microbial composition and significantly differed from the oropharynx. We also observed differences in Anaerococcus and Streptococcus abundance between the SSTI and non-SSTI groups for the nasal and oropharyngeal regions, respectively. Furthermore, we detected community membership differences between the SSTI and non-SSTI groups for the nasal and inguinal sites. Compared to that of the other regions, the microbial compositions of the nares of S. aureus carriers and noncarriers were dramatically different; we noted an inverse correlation between the presence of Corynebacterium and the presence of Staphylococcus in the nares. This correlation was also observed for the inguinal region. Culture analysis revealed elevated methicillin-resistant S. aureus (MRSA) colonization levels for the SSTI group in the nasal and inguinal body sites. Together, these data suggest significant microbial variability in patients with SSTI as well as between S. aureus carriers and noncarriers. IMPORTANCE While it is evident that nasal colonization with S. aureus increases the likelihood of SSTI, there is a significant lack of information regarding the contribution of extranasal colonization to the overall risk of a subsequent SSTI. Furthermore, the impact of S. aureus colonization on bacterial community composition outside the nasal microbiota is unclear. Thus, this report represents the first investigation that utilized both culture and high-throughput sequencing techniques to analyze microbial dysbiosis at multiple body sites of healthy and diseased/colonized individuals. The results described here may be useful in the design of future methodologies to treat and prevent SSTIs.

scholarly journals Potential use of human stem cell factor as adjunctive therapy for human immunodeficiency virus-related cytopenias

Blood ◽  
1991 ◽  
Vol 78 (12) ◽  
pp. 3200-3208
Author(s):  
SA Miles ◽  
K Lee ◽  
L Hutlin ◽  
KM Zsebo ◽  
RT Mitsuyasu
Keyword(s):  
Human Immunodeficiency Virus ◽  
Stem Cell ◽  
Hiv Infection ◽  
Stem Cell Factor ◽  
Clinical Utility ◽  
Human Stem Cell ◽  
Hiv Replication ◽  
Immunodeficiency Virus ◽  
The Impact ◽  
Human Stem Cell Factor

Hematopoietic dysfunction with peripheral cytopenias is a common complication of human immunodeficiency virus (HIV) infection. Symptomatic anemia is the most common cytopenia and occurs in the presence and absence of myelosuppressive drug therapy such as zidovudine. Drug-induced neutropenia and immune thrombocytopenia are also frequent and occur in up to 50% of acquired immunodeficiency syndrome (AIDS) patients. Attempts to reduce the impact of bone marrow failure have focused on dose reduction of zidovudine, ganciclovir, and chemotherapy, and the use of recombinant hematopoietic hormones such as erythropoietin (EPO) and granulocyte colony-stimulating factor (G-CSF). Despite these maneuvers, approximately 30% of patients with AIDS receiving zidovudine will become transfusion-dependent. This has led to investigations of other cytokines that may increase blood cell formation. The recent identification of decreased number and proliferation of hematopoietic progenitors in patients with HIV infection suggests that agents which have activity on progenitor cell pools may have clinical utility. We demonstrate that human stem cell factor (HuSCF) increases burst-forming unit-erythroid (BFU-E), colony- forming unit-granulocyte-monocyte (CFU-GM), and CFU-Mix formation in vitro in normal and HIV-infected individuals. HuSCF also decreases the sensitivity of BFU-E to inhibition by zidovudine without altering HIV replication in lymphocytes or monocytes, altering peripheral blood mononuclear cell proliferation to phytohemagglutinin (PHA) and interleukin-2 (IL-2) or altering the effectiveness of zidovudine or dideoxyinosine in inhibiting HIV replication in lymphocytes or monocytes. These studies suggest that HuSCF may have clinical utility in HIV infection as an adjunctive treatment for HIV-related cytopenias.

scholarly journals Impact of human gene annotations on RNA-seq differential expression analysis

2021 ◽  
Author(s):  
Yu Hamaguchi ◽  
Chao Zeng ◽  
Michiaki Hamada
Keyword(s):  
Differential Expression ◽  
High Throughput ◽  
High Throughput Sequencing ◽  
Human Gene ◽  
Gene Annotation ◽  
Differential Expression Analysis ◽  
Rna Seq ◽  
Gene Annotations ◽  
Sequencing Technologies ◽  
The Impact

Abstract Background: Differential expression (DE) analysis of RNA-seq data typically depends on gene annotations. Different sets of gene annotations are available for the human genome and are continually updated–a process complicated with the development and application of high-throughput sequencing technologies. However, the impact of the complexity of gene annotations on DE analysis remains unclear.Results: Using “mappability”, a metric of the complexity of gene annotation, we compared three distinct human gene annotations, GENCODE, RefSeq, and NONCODE, and evaluated how mappability affected DE analysis. We found that mappability was significantly different among the human gene annotations. We also found that increasing mappability improved the performance of DE analysis, and the impact of mappability mainly evident in the quantification step and propagated downstream of DE analysis systematically.Conclusions: We assessed how the complexity of gene annotations affects DE analysis using mappability. Our findings indicate that the growth and complexity of gene annotations negatively impact the performance of DE analysis, suggesting that an approach that excludes unnecessary gene models from gene annotations improves the performance of DE analysis.

scholarly journals Taxon appearance from extraction and amplification steps demonstrates the value of multiple controls in tick microbiota analysis

2019 ◽  
Author(s):  
Emilie Lejal ◽  
Agustín Estrada-Peña ◽  
Maud Marsot ◽  
Jean-François Cosson ◽  
Olivier Rué ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Dna Extraction ◽  
High Throughput ◽  
High Throughput Sequencing ◽  
Dna Amplification ◽  
Community Diversity ◽  
Analytical Process ◽  
Sequencing Technologies ◽  
And Gender ◽  
The Impact

AbstractBackgroundThe development of high throughput sequencing technologies has substantially improved analysis of bacterial community diversity, composition, and functions. Over the last decade, high throughput sequencing has been used extensively to identify the diversity and composition of tick microbial communities. However, a growing number of studies are warning about the impact of contamination brought along the different steps of the analytical process, from DNA extraction to amplification. In low biomass samples, e.g. individual tick samples, these contaminants may represent a large part of the obtained sequences, and thus generate considerable errors in downstream analyses and in the interpretation of results. Most studies of tick microbiota either do not mention the inclusion of controls during the DNA extraction or amplification steps, or consider the lack of an electrophoresis signal as an absence of contamination. In this context, we aimed to assess the proportion of contaminant sequences resulting from these steps. We analyzed the microbiota of individual Ixodes ricinus ticks by including several categories of controls throughout the analytical process: crushing, DNA extraction, and DNA amplification.ResultsControls yielded a significant number of sequences (1,126 to 13,198 mean sequences, depending on the control category). Some operational taxonomic units (OTUs) detected in these controls belong to genera reported in previous tick microbiota studies. In this study, these OTUs accounted for 50.9% of the total number of sequences in our samples, and were considered contaminants. Contamination levels (i.e. the percentage of sequences belonging to OTUs identified as contaminants) varied with tick stage and gender: 76.3% of nymphs and 75% of males demonstrated contamination over 50%, while most females (65.7%) had rates lower than 20%. Contamination mainly corresponded to OTUs detected in crushing and DNA extraction controls, highlighting the importance of carefully controlling these steps.ConclusionHere, we showed that contaminant OTUs from extraction and amplification steps can represent more than half the total sequence yield in sequencing runs, and lead to unreliable results when characterizing tick microbial communities. We thus strongly advise the routine use of negative controls in tick microbiota studies, and more generally in studies involving low biomass samples.

High-throughput sequencing-based analysis of the composition and diversity of endophytic bacterial community in seeds of upland rice

2020 ◽  
Author(s):  
Zhishan Wang ◽  
Yongqiang Zhu ◽  
Ruixue Jing ◽  
Xianyu Wu ◽  
Ni Li ◽  
...  
Keyword(s):  
Community Structure ◽  
High Throughput ◽  
High Throughput Sequencing ◽  
Upland Rice ◽  
Functional Evaluation ◽  
Soil Environment ◽  
Soil Microbial Community Structure ◽  
The Core ◽  
Rice Seeds ◽  
The Impact

Abstract Upland rice is an ecotype crop formed by long-term domestication and evolution of rice in the dry land without water layer. Generally, its stem and leaf are thick and luxuriant, its leaf is wide and light, its root system is developed, its root hair is abundant, its osmotic pressure of root and cell juice concentration of leaf are high, and it is drought resistant, heat-resistant and water absorbing. The purpose of this study is to reveal the “core flora” of endophytes in upland rice seeds by studying the diversity and community structure of endophytes in upland rice seeds, and to reveal the impact of soil environment on the formation of endophyte community structure in upland rice seeds by comparing with soil environment microorganisms in upland rice habitats. In this study, the high-throughput sequencing technology based on the Illumina Hiseq 2500 platform was used to study the structure and diversity of endophytic bacterial communities using upland rice varieties collected in different places and soil samples from their unified planting sites as materials. There are 42 endophytic OTUs coexisted in the 14 samples. At the phylum level, the first dominant phyla was Proteobacteria (93.81–99.99%) in all 14 samples. At the genus level, Pantoea (8.77% -87.77%), Pseudomonas (1.15–61.58%), Methylobacterium (0.40–4.64%), Sphingomonas (0.26–3.85%), Microbacterium (0.01–4.67%) and Aurantimonas (0.04–4.34%), which are probably the core microflora in upland rice seeds, served as the dominant genera that coexisted in all upland rice seeds tested. Compared with the soil microbial community structure in the upland rice uniform planting site, it was found that it had little effect on the endophytic community structure in upland rice seeds. This study is of great significance for the isolation, screening, functional evaluation and re-action of some functional microorganisms in upland rice in order to improve its agronomic traits. It also provides a certain reference for the interaction between microorganisms and plants.

scholarly journals RMBase: a resource for decoding the landscape of RNA modifications from high-throughput sequencing data

2015 ◽  
Vol 44 (D1) ◽  
pp. D259-D265 ◽  
Author(s):  
Wen-Ju Sun ◽  
Jun-Hao Li ◽  
Shun Liu ◽  
Jie Wu ◽  
Hui Zhou ◽  
...  
Keyword(s):  
High Throughput ◽  
High Throughput Sequencing ◽  
Sequencing Data ◽  
Rna Modifications ◽  
High Throughput Sequencing Data
Sign in / Sign up

Export Citation Format

Share Document