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Whole genome analysis of cells permissive for late gene expression of HPV-16

ABSTRACT: Aim was to identify cellular factors that regulate HPV-16 late gene expression at the level of RNA processing Cervical cancer cells permissive for HPV16 late gene expression were identified and characterized. These cells either contained a novel spliced variant of the L1 mRNAs that bypassed the suppressed HPV16 late, 5’-splice site SD3632, produced elevated levels of RNA-binding proteins SRSF1 (ASF/SF2), SRSF9 (SRp30c) and HuR that are known to regulate HPV16 late gene expression, or were shown by a gene expression array analysis to overexpress the RALYL RNA-binding protein of the hnRNP C-family. Overexpression of RALYL, or RALY and hnRNP C1 that are two other members of the hnRNP C-family, induced HPV16 late gene expression from HPV16 subgenomic plasmids and from episomal forms of the full-length HPV16 genome. Induction of HPV16 late gene expression by the hnRNP C-proteins was dependent on the HPV16 early untranslated region to which these proteins also were shown to bind in vitro, and in living cells. Our experiments revealed that hnRNP C proteins that interacted with the HPV16 early untranslated region reached out to the splicing silencer complex at HPV16 SD3632 and derepressed this splice site, thereby activating production of HPV16 spliced late L1 mRNAs. In conclusion, hnRNP C- proteins bind to the HPV16 early untranslated region and control of HPV16 late L1 mRNA splicing.

ORGANISM(S): Homo sapiens

PROVIDER: GSE65166 | GEO | 2015/06/12

SECONDARY ACCESSION(S): PRJNA273314

REPOSITORIES: GEO

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Whole genome analysis of cells permissive for late gene expression of HPV-16

Project description:Aim was to identify cellular factors that regulate HPV-16 late gene expression at the level of RNA processing Cervical cancer cells permissive for HPV16 late gene expression were identified and characterized. These cells either contained a novel spliced variant of the L1 mRNAs that bypassed the suppressed HPV16 late, 5‚Äô-splice site SD3632, produced elevated levels of RNA-binding proteins SRSF1 (ASF/SF2), SRSF9 (SRp30c) and HuR that are known to regulate HPV16 late gene expression, or were shown by a gene expression array analysis to overexpress the RALYL RNA-binding protein of the hnRNP C-family. Overexpression of RALYL, or RALY and hnRNP C1 that are two other members of the hnRNP C-family, induced HPV16 late gene expression from HPV16 subgenomic plasmids and from episomal forms of the full-length HPV16 genome. Induction of HPV16 late gene expression by the hnRNP C-proteins was dependent on the HPV16 early untranslated region to which these proteins also were shown to bind in vitro, and in living cells. Our experiments revealed that hnRNP C proteins that interacted with the HPV16 early untranslated region reached out to the splicing silencer complex at HPV16 SD3632 and derepressed this splice site, thereby activating production of HPV16 spliced late L1 mRNAs. In conclusion, hnRNP C- proteins bind to the HPV16 early untranslated region and control of HPV16 late L1 mRNA splicing. Total cellular RNA was extracted from stable cell lines. Samples were prepared in triplicates. C33ARSVNeo served as control cell line.

2015-06-12 | E-GEOD-65166 | biostudies-arrayexpress

ChIP-Seq hnRNP E1, Cervical cancer SiHa cells

Project description:Based on the specificity with which the unique KH structural domains of hnRNP E1 bind with RNA/DNA, considering that HPV16 provides RNA/DNA binding sites, we hypothesized that hnRNP E1 may be crucial to HPV16 oncogenes expression and cervical carcinogenesis. Based on the main purpose of this study was to explore the role of hnRNP E1 on the regulation of HPV16 oncogene expression in cervical cancerization, we conducted ChIP-seq in the untreated SiHa cell line.

2022-06-16 | GSE203023 | GEO

Integrative genome-wide analysis reveals cooperative regulation of alternative splicing by hnRNP proteins

Project description:This SuperSeries is composed of the following subset Series: GSE34992: Integrative genome-wide analysis reveals cooperative regulation of alternative splicing by hnRNP proteins (splice array) GSE34993: Integrative genome-wide analysis reveals cooperative regulation of alternative splicing by hnRNP proteins (CLIP-Seq) GSE34995: Integrative genome-wide analysis reveals cooperative regulation of alternative splicing by hnRNP proteins (RNA-Seq) Refer to individual Series

2012-02-20 | E-GEOD-34996 | biostudies-arrayexpress

Integrative genome-wide analysis reveals cooperative regulation of alternative splicing by hnRNP proteins (splicing arrays)

Project description:Understanding how RNA binding proteins control the splicing code is fundamental to human biology and disease. Here we present a comprehensive study to elucidate how heterogeneous nuclear ribonucleoparticle (hnRNP) proteins, among the most abundant RNA binding proteins, coordinate to regulate alternative pre-mRNA splicing (AS) in human cells. Using splicing-sensitive microarrays, cross-linking and immunoprecipitation coupled with high-throughput sequencing, and cDNA sequencing, we find that more than half of all AS events are regulated by multiple hnRNP proteins, and that some combinations of hnRNP proteins exhibit significant synergy, whereas others act antagonistically. Our analyses reveal position-dependent RNA splicing maps, in vivo consensus binding sites, a surprising level of cross- and auto-regulation among hnRNP proteins, and the coordinated regulation by hnRNP proteins of dozens of other RNA binding proteins and genes associated with cancer. Our findings define an unprecedented degree of complexity and compensatory relationships among hnRNP proteins and their splicing targets that likely confer robustness to cells. In triplicate, polyA-selected RNA was extracted from control, hnRNP A1, hnRNP A2/B1, hnRNP H1, hnRNP F, hnRNP M, and hnRNP U siRNA treated human 293T cells, and hybridized to custom splice-junction arrays

2012-02-20 | E-GEOD-34992 | biostudies-arrayexpress

Frequent mutation of the FOXA1 untranslated region in prostate cancer

Project description:We sequenced the coding and untranslated regions of 72 prostate cancer driver genes in 712 plasma cell free DNA samples from 428 men with metastatic prostate cancer, in an effort to understand the role of untranslated region mutations in late stage prostate cancer.

| EGAS00001003113 | EGA

circularRNA Sequencing of HPV16 positive cervical cancer tissues, HSIL tissues and normal cervical epithelial tissues

Project description:To explore the circRNA expression profiles during the development and progression of cervical cancer, we performed RNA sequencing analysis with ribosomal RNA-depleted in HPV negative normal cervical epithelium, HPV16 positive normal cervical epithelium, HPV16 positive high-grade squamous intraepithelial lesion (HSIL), and HPV16 positive cervical squamous cell carcinoma tissues,6 cases in each group.Totally 66868 circRNAs were identified (Back-spliced junctions reads≥1)

2020-12-21 | GSE147009 | GEO

Analysis of HPV16 E2 host gene expression using TERT immortalized keratinocytes (NOKs) cell lines and RNA-sequencing

Project description:HPV must reprogram host gene expression to promote infection, and HPV proteins E6 and E7 contribute to this via targeting of cellular transcription factors including p53 and pRb respectively. The HPV16 E2 protein regulated host gene expression in U2OS cells and in this study we extend these observations into NOKs that are capable of suporting late stages of the HPV16 life cycle. We observed repression of innate immune genes by E2 that are also repressed by the intact HPV16 genome in NOKs. There was a highly significant overlap of the E2 regulated genes with those regulated by the intact HPV16 genome in the same cell type. siRNA targeting of E2 reversed repression of E2 targed genes. The ability of E2 to repress innate immune genes was confirmed in an ano-genital immortalized keratinocyte cell line, N/Tert-1.

2018-10-23 | GSE121627 | GEO

Global Profiling of hnRNP A2/B1-RNA Interactions on Chromatin Suggests Additional Roles Outside of Splicing

Project description:Long noncoding RNAs (lncRNAs) often carry out their functions through associations with adaptor proteins. We recently identified heterogeneous ribonucleoprotein (hnRNP) A2/B1 as an adaptor of the human HOTAIR lncRNA. hnRNP A2 and B1 are splice isoforms of the same gene. Spliced HOTAIR preferentially associates with the B1 isoform, which may contribute to a mechanism matching lncRNAs with RNA transcripts of target genes. In this study we used enhanced cross-linking immunoprecipitation (eCLIP) to map the complete set of direct interactions between A2/B1 and RNA in breast cancer cells. We identified multiple additional sites of isoform specificity that correlate with differences in binding motif enrichment. Surprisingly, a strong A2/B1 binding site occurs in the third intron of HOTAIR, which interrupts a known RNA-RNA interaction hotspot and is retained at a higher frequency than other HOTAIR introns. In vitro eCLIP experiments suggest that A2/B1 may redistribute to exonic binding sites once this intron is spliced. A2/B1 associates with multiple lncRNAs at regions that may contribute to downstream regulation and function of the lncRNA. Finally, we performed cellular fractionation experiments to characterize the pattern of RNA association of A2/B1 in chromatin, nucleoplasm, and cytoplasm and find that a majority of interactions occur on chromatin, even those that do not contribute to co-transcriptional splicing. Our data characterize the multiple functions of a repurposed splicing factor, including isoform-biased interactions, and highlight that the vast majority of these functions occur on chromatin-associated RNA.

2018-08-20 | GSE103165 | GEO

Co-regulation of splicing by Rbfox1 and hnRNP M [hnRNPM k-d+Rbfox1 RNA-Seq]

Project description:hnRNP M and Rbfox proteins are subunits of the Large Assembly of Splicing Regulators (LASR). The purpose of this study is to investigate how these two splicing factors affect each others' role in regulating splice site choices in pre-mRNA. hnRNP M is knocked down by RNAi in Flp-In T-REx 293 cells (Invitrogen), whereas Rbfox1 is expressed inducibly under tetracycline control from construct integrated into the genome at the FRT site. Using this system, splicing and expression profiles of cells expressing and/or lacking these proteins are compared on a whole genome level by RNA-seq technology.

2016-04-21 | GSE76476 | GEO

Rip-Chip profiling of HnRNP A1 nuclear complexes in HuR WT and HuR KO cells

Project description:Post-transcriptional regulatory networks are dependent on the interplay of many RNA-binding proteins having a major role in mRNA processing events in mammals. We have been interested in the concerted action of the two RNA-binding proteins hnRNP A1 and HuR, both stable components of immunoselected hnRNP complexes and having a major nuclear localization. Specifically, we present here the application of the RNA-immunoprecipitation (RIP)-Chip technology to identify a population of nuclear transcripts associated with hnRNP A1-RNPs as isolated from the nuclear extract of either HuR WT or HuR-depleted (KO) mouse embryonic fibroblast (MEF) cells. The outcome of this analysis was a list of target genes regulated via HuR for their association (either increased or reduced) with the nuclear hnRNP A1-RNP complexes. Real time PCR analysis was applied to validate a selected number of nuclear mRNA transcripts, as well as to identify pre-spliced transcripts (in addition to their mature mRNA counterpart) within the isolated nuclear hnRNP A1-RNPs. The differentially enriched mRNAs were found to belong to GO categories relevant to biological processes anticipated for hnRNP A1 and HuR (such as transport, transcription, translation, apoptosis and cell cycle) indicative of their concerted function in mRNA metabolism. Ribonucleoprotein Immunoprecipitation (RIP) using hnRNP A1 specific antibody was performed in nuclear extracts from HuR WT and HuR KO Mouse Embryonic Fibroblasts (MEFs). RNA isolated from these IPs together with nuclear RNA from the two cell types, was subjected to microarray analysis. Three biological replicates, representing three independent experiments, are available for each condition except in the case of nuclear RNA isolated from HuR WT MEFs that one replicate didn’t pass the quality control.

2013-11-01 | E-GEOD-49225 | biostudies-arrayexpress

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