Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1008694 | ENA |
REPOSITORIES: ENA
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Project description:Alu element is a major contributor to lineage-specific new exons in the primate and human genomes. Recent studies indicate that some Alu exons have high transcript inclusion levels or tissue-specific splicing profiles, and may play important regulatory roles in modulating mRNA degradation or translational efficiency. However, the contribution of Alu exons to the human proteome remains unclear and controversial. The prevailing view is that exons derived from young repetitive elements (such as Alu) are restricted to regulatory functions but do not have adequate evolutionary time to be incorporated into stable, functional proteins. In this work, we adopt a proteotranscriptomics approach to systematically assess the contribution of Alu exons to the human proteome. Using RNA sequencing, ribosome profiling, and mass spectrometry data of diverse human tissues and cell lines, we provide evidence for the translational activities of Alu exons and the presence of Alu exon derived peptides in human proteins. These Alu exon peptides represent species-specific protein differences between primates and other mammals, and in certain instances even between humans and closely related nonhuman primates. In the RNA editing enzyme ADARB1, which contains an Alu exon peptide in its catalytic domain, RNA editing analyses of RNA-sequencing data demonstrate that both the Alu exon skipping and inclusion isoforms encode active RNA editing enzymes, while the Alu exon peptide may fine tune the editing activities of the ADARB1 protein products . Together, our data indicate that Alu elements have contributed to the acquisition of novel protein sequences during primate and human evolution. Comparing the A-I RNA editing levels during HEK293 (control), ADARB1 long isoform (with Alu exon) transfected, and short isoform (without Alu exon) transfected cells, each group has 3 replicates.
2015-12-10 | E-GEOD-65999 | biostudies-arrayexpress
Project description:Alu elements are major contributors to lineage-specific new exons in primate and human genomes. Recent studies indicate that some Alu exons have high transcript inclusion levels or tissue-specific splicing profiles, and may play important regulatory roles in modulating mRNA degradation or translational efficiency. However, the contribution of Alu exons to the human proteome remains unclear and controversial. The prevailing view is that exons derived from young repetitive elements, such as Alu elements, are restricted to regulatory functions and have not had adequate evolutionary time to be incorporated into stable, functional proteins. We adopt a proteotranscriptomics approach to systematically assess the contribution of Alu exons to the human proteome. Using RNA sequencing, ribosome profiling and proteomics data from human tissues and cell lines, we provide evidence for the translational activities of Alu exons and the presence of Alu exon derived peptides in human proteins. These Alu exon peptides represent species-specific protein differences between primates and other mammals, and in certain instances between humans and closely related primates. In the case of the RNA editing enzyme ADARB1, which contains an Alu exon peptide in its catalytic domain, RNA sequencing analyses of A-to-I editing demonstrate that both the Alu exon skipping and inclusion isoforms encode active enzymes. The Alu exon derived peptide may fine tune the overall editing activity and, in limited cases, the site selectivity of ADARB1 protein products. Our data indicate that Alu elements have contributed to the acquisition of novel protein sequences during primate and human evolution.
2015-12-10 | GSE65999 | GEO
Project description:The contribution of Alu exons to the human proteome
| PRJNA275667 | ENA
Project description:Secretome-mediated signaling from human iPSC-derived cardiomyocytes (TGF-beta induced dysfunction) to primary human cardiac fibroblasts was investigated to identify downstream regulators of fibrosis. Quantitative proteomic profiling revealed a dynamic reprogramming of fibroblast global proteome, with dysregulation of proteins implicated in extracellular matrix (ECM) remodelling, cytoskeleton organization, lysosome function, and oxidoreductase- and kinase activity. Protein modification-focused processing analyses of mass spectrometry proteome data further highlight phospho-proteome alterations in pro-fibrotic pathways regulated by kinases (CK2, CDK1, CDK2, MAPK1, PRKACA, PRKG1). We verified upregulated casein kinase 2 (CK2) substrate levels in secretome-treated fibroblasts, and pharmacological inhibition of CK2 using Tetrabromobenzotriazole significantly abrogated reactive oxygen species levels and activation state
2023-06-27 | MSV000092293 | MassIVE
Project description:Alu SINEs are the most numerous frequently occurring transcription units in our genome and possess sequence competence for transcription by RNA Pol III. However, through poorly understood mechanisms, the Alu RNA levels are maintained at very low levels in normal somatic cells with obvious benefits of low rates of Alu retrotransposition and energy-economical deployment of RNA Pol III to the tRNA genes which share promoter structure and polymerase requirements with Alu SINEs. Using comparative ChIP sequencing, we unveil that a repeat binding protein, CGGBP1, binds to the transcriptional regulatory regions of Alu SINEs thereby impeding Alu transcription by inhibiting RNA Pol III recruitment. We show that this Alu-silencing depends on growth factor stimulation of cells and subsequent tyrosine phosphorylation of CGGBP1. Importantly, CGGBP1 ensures a sequence-specific discriminative inhibition of RNA Pol III activity at Alu promoters, while sparing the structurally similar tRNA promoters. Our data suggest that CGGBP1 contributes to growth-related transcription by preventing the hijacking of RNA Pol III by Alu SINEs. This study was used to find out the effect of CGGBP1 on serum-induced changes in gene expression and effect of serum on gene expression regulation by CGGBP1. Gene expression profiling of normal human fibroblasts under 4 different experimental perturbations: serum starvation or serum stimulation and CGGBP1 depletion or normal CGGBP1 levels.
2015-12-21 | E-GEOD-54058 | biostudies-arrayexpress
Project description:Secretome-mediated signaling from human iPSC-derived cardiomyocytes (TGFβ induced dysfunction) to primary human cardiac fibroblasts was investigated to identify downstream regulators of fibrosis. Quantitative proteomic profiling revealed a dynamic reprogramming of fibroblast global proteome, with dysregulation of proteins implicated in extracellular matrix (ECM) remodelling, cytoskeleton organization, lysosome function, and oxidoreductase- and kinase activity. Protein modification-focused processing analyses of mass spectrometry proteome data further highlight phospho-proteome alterations in pro-fibrotic pathways regulated by various kinases (CK2, CDK1, CDK2, MAPK1, PRKACA, PRKG1). We verified upregulated casein kinase 2 (CK2) substrate levels in secretome-treated fibroblasts, and pharmacological inhibition of CK2 using TBB (4,5,6,7-Tetrabromobenzotriazole) significantly abrogated reactive oxygen species’ levels and activation state (SMA+).
2025-02-11 | PXD038854 | Pride
Project description:Cell-cell communication between keratinocytes and fibroblasts is essential for skin homeostasis, regulation and regeneration. How extracellular cytokine signaling, intra-cellular protein signaling and transcriptional regulation initiate and maintain this communication is still largely unknown. Here, we study in vitro the secretome and transcriptome dynamics that establish double paracrine cell-cell communication between primary human keratinocytes and fibroblasts. We find that keratinocyte-derived interleukin 1α initiates the cell communication, eliciting a constitutive NF-κB-mediated inflammation response in the fibroblasts. Their resulting transcriptome response over at least 12 hours induces a fibroblast secretome capable of enhancing keratinocyte migration. Applying partial least square regression to secretome perturbation experiments using recombinant proteins or antibodies demonstrates the synergistic interaction of early and late secreted inflammatory CC and CXC chemokines as well as IL6, whose relative composition directly controls keratinocyte migration. Conversely, inhibiting individual cytokines during cell-communication abrogates the keratinocyte phenotype. Hence, only the simultaneous activity of multiple inflammatory cytokines together with prolonged inflammatory response in the fibroblasts lead to increased keratinocyte migration after double paracrine cell communication, putatively serving as safeguard mechanisms for proper skin regeneration.
2019-10-22 | GSE53037 | GEO
Project description:The analysis of the secretome provides important information on cellular communication and on the recruitment and behavior of cells in specific tissues. Especially in the context of tumors, knowledge on the composition of the secretome plays an important role for diagnosis and therapy. Mass spectrometry-based analysis of cell-conditioned media is widely used for the unbiased characterization of cancer secretomes in vitro. Azide-containing amino acid labeling in combination with click chemistry now facilitates this type of analysis without serum starvation. The modified amino acids, however, are less efficiently incorporated into newly synthesized proteins. Utilizing transcriptome and proteome analysis, we describe here in detail the effects of labeling cells with the methionine analog azidohomoalanin (AHA) on the modulation of gene expression and protein composition. We observe that 11% – 34% of the proteins detected in the secretome were affected by AHA labeling regarding their expression levels in the transcriptome and/or proteome. Performing gene ontology analyses, our results provide a detailed view on the AHA-based induction of cellular stress and apoptosis-related pathways and provide first insights on how this might affect the composition of the secretome on a global scale.
2023-07-05 | GSE211231 | GEO
Project description:Alu retrotransposons, forming the largest family of mobile DNA elements in the human genome, have recently come to attention as a potential source of regulatory novelties, most notably by participating in enhancer function. Even though Alu transcription by RNA polymerase III is subjected to tight epigenetic silencing, their bulk expression has long been known to increase in response to various types of stress, including viral infection. Here we show that, in primary human fibroblasts, adenovirus small e1a triggered derepression of hundreds of individual Alus, by promoting TFIIIB recruitment by Alu-bound TFIIIC. Epigenome profiling revealed an e1a-induced decrease of H3K27 acetylation and increase of H3K4 monomethylation at derepressed Alus, making them resemble poised enhancers. The enhancer nature of e1a-targeted Alus was confirmed by the enrichment, in their upstream regions, of the EP300/CBP acetyltransferase and of the YAP1 and FOS transcription factors. The physical interaction of e1a with the chromatin remodeler EP400 turned out to be critical for Alu derepression, and upstream enrichment of EP400 was found to commonly demarcate expression-prone Alus. Our data suggest that e1a targets a subset of enhancer Alus whose transcriptional activation, mediated by e1a-EP400 interaction, may participate in the manipulation of enhancer activity by adenovirus.
2024-03-31 | GSE208685 | GEO
Project description:Through targeted CRISPR screening of the Toxoplasma gondii secretome, we identified GRA57 as a novel secreted effector required for survival in interferon-gamma (IFNg)-activated human foreskin fibroblasts (HFFs). In this experiment we aimed to determine if GRA57 affects the host cell transcriptional response to Toxoplasma, and also whether deletion of GRA57 affects the parasite transcriptome.
2023-05-27 | GSE230866 | GEO