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Cell Apr 2016The question of how genomic information is expressed to determine phenotypes is of central importance for basic and translational life science research and has been... (Review)
Review
The question of how genomic information is expressed to determine phenotypes is of central importance for basic and translational life science research and has been studied by transcriptomic and proteomic profiling. Here, we review the relationship between protein and mRNA levels under various scenarios, such as steady state, long-term state changes, and short-term adaptation, demonstrating the complexity of gene expression regulation, especially during dynamic transitions. The spatial and temporal variations of mRNAs, as well as the local availability of resources for protein biosynthesis, strongly influence the relationship between protein levels and their coding transcripts. We further discuss the buffering of mRNA fluctuations at the level of protein concentrations. We conclude that transcript levels by themselves are not sufficient to predict protein levels in many scenarios and to thus explain genotype-phenotype relationships and that high-quality data quantifying different levels of gene expression are indispensable for the complete understanding of biological processes.
Topics: Animals; Gene Expression Regulation; Humans; Protein Biosynthesis; Protein Processing, Post-Translational; Proteins; Proteomics; RNA, Messenger; Transcription, Genetic
PubMed: 27104977
DOI: 10.1016/j.cell.2016.03.014 -
Cell Apr 2019G protein-coupled receptor (GPCR) signaling is the primary method eukaryotes use to respond to specific cues in their environment. However, the relationship between...
G protein-coupled receptor (GPCR) signaling is the primary method eukaryotes use to respond to specific cues in their environment. However, the relationship between stimulus and response for each GPCR is difficult to predict due to diversity in natural signal transduction architecture and expression. Using genome engineering in yeast, we constructed an insulated, modular GPCR signal transduction system to study how the response to stimuli can be predictably tuned using synthetic tools. We delineated the contributions of a minimal set of key components via computational and experimental refactoring, identifying simple design principles for rationally tuning the dose response. Using five different GPCRs, we demonstrate how this enables cells and consortia to be engineered to respond to desired concentrations of peptides, metabolites, and hormones relevant to human health. This work enables rational tuning of cell sensing while providing a framework to guide reprogramming of GPCR-based signaling in other systems.
Topics: Gene Expression; Genetic Engineering; Humans; Pheromones; Receptors, G-Protein-Coupled; Saccharomyces cerevisiae; Saccharomyces cerevisiae Proteins; Signal Transduction; Transcription Factors
PubMed: 30955892
DOI: 10.1016/j.cell.2019.02.023 -
STAR Protocols Dec 2023This overview guides both novices and experienced researchers facing challenging targets to select the most appropriate gene expression system for producing a particular... (Review)
Review
This overview guides both novices and experienced researchers facing challenging targets to select the most appropriate gene expression system for producing a particular protein. By answering four key questions, readers can determine the most suitable gene expression system following a decision scheme. This guide addresses the most commonly used and accessible systems and provides brief descriptions of the main gene expression systems' key characteristics to assist decision making. Additionally, information has been included for selected less frequently used "exotic" gene expression systems.
Topics: Ligands; Databases, Pharmaceutical; Recombinant Proteins; Gene Expression
PubMed: 37917580
DOI: 10.1016/j.xpro.2023.102572 -
Nucleic Acids Research May 2023In situ capturing technologies add tissue context to gene expression data, with the potential of providing a greater understanding of complex biological systems....
In situ capturing technologies add tissue context to gene expression data, with the potential of providing a greater understanding of complex biological systems. However, splicing variants and full-length sequence heterogeneity cannot be characterized at spatial resolution with current transcriptome profiling methods. To that end, we introduce spatial isoform transcriptomics (SiT), an explorative method for characterizing spatial isoform variation and sequence heterogeneity using long-read sequencing. We show in mouse brain how SiT can be used to profile isoform expression and sequence heterogeneity in different areas of the tissue. SiT reveals regional isoform switching of Plp1 gene between different layers of the olfactory bulb, and the use of external single-cell data allows the nomination of cell types expressing each isoform. Furthermore, SiT identifies differential isoform usage for several major genes implicated in brain function (Snap25, Bin1, Gnas) that are independently validated by in situ sequencing. SiT also provides for the first time an in-depth A-to-I RNA editing map of the adult mouse brain. Data exploration can be performed through an online resource (https://www.isomics.eu), where isoform expression and RNA editing can be visualized in a spatial context.
Topics: Animals; Mice; Alternative Splicing; Sequence Analysis, RNA; Protein Isoforms; Gene Expression Profiling; Gene Expression; Transcriptome
PubMed: 36928528
DOI: 10.1093/nar/gkad169 -
Proceedings of the National Academy of... Jan 2007In vivo electroporation is a powerful technique for the introduction of genes into organisms. Temporal and spatial regulation of expression of introduced genes, or of...
In vivo electroporation is a powerful technique for the introduction of genes into organisms. Temporal and spatial regulation of expression of introduced genes, or of RNAi, would further enhance the utility of this method. Here we demonstrate conditional regulation of gene expression from electroporated plasmids in the postnatal rat retina and the embryonic mouse brain. For temporal regulation, Cre/loxP-mediated inducible expression vectors were used in combination with a vector expressing a conditionally active form of Cre recombinase, which is activated by 4-hydroxytamoxifen. Onset of gene expression was regulated by the timing of 4-hydroxytamoxifen administration. For spatial regulation, transgenes were expressed by using promoters specific for rod photoreceptors, bipolar cells, amacrine cells, Müller glia or progenitor cells. Combinations of these constructs will facilitate a variety of experiments, including cell-type-specific gene misexpression, conditional RNAi, and fate mapping of progenitor and precursor cells.
Topics: Animals; Basic Helix-Loop-Helix Transcription Factors; Cell Line; Cell Lineage; Electroporation; Gene Expression; Gene Expression Regulation; Homeodomain Proteins; Humans; Integrases; Promoter Regions, Genetic; RNA Interference; Rats; Retina; Transcription Factor HES-1; Transfection
PubMed: 17209010
DOI: 10.1073/pnas.0610155104 -
BMB Reports Aug 2021In the tumor microenvironment, immune checkpoint ligands (ICLs) must be expressed in order to trigger the inhibitory signal via immune checkpoint receptors (ICRs).... (Review)
Review
In the tumor microenvironment, immune checkpoint ligands (ICLs) must be expressed in order to trigger the inhibitory signal via immune checkpoint receptors (ICRs). Although ICL expression frequently occurs in a manner intrinsic to tumor cells, extrinsic factors derived from the tumor microenvironment can fine-tune ICL expression by tumor cells or prompt non-tumor cells, including immune cells. Considering the extensive interaction between T cells and other immune cells within the tumor microenvironment, ICL expression on immune cells can be as significant as that of ICLs on tumor cells in promoting antitumor immune responses. Here, we introduce various regulators known to induce or suppress ICL expression in either tumor cells or immune cells, and concise mechanisms relevant to their induction. Finally, we focus on the clinical significance of understanding the mechanisms of ICLs for an optimized immunotherapy for individual cancer patients. [BMB Reports 2021; 54(8): 403-412].
Topics: Gene Expression; Gene Expression Regulation, Neoplastic; Humans; Immune Checkpoint Proteins; Immunotherapy; Ligands; Neoplasms; Receptors, Immunologic; Tumor Microenvironment
PubMed: 34078531
DOI: 10.5483/BMBRep.2021.54.8.054 -
The International Journal of... Mar 2001Assessing human cerebrospinal fluid (CSF) provides a practical way to conduct longitudinal molecular analyses of changes during the course of neurological disease.... (Review)
Review
Assessing human cerebrospinal fluid (CSF) provides a practical way to conduct longitudinal molecular analyses of changes during the course of neurological disease. Integrated and parallel analyses of neurotransmitters, neuropeptides and proteins in CSF may reveal better insights into complex interaction of numerous cell types in the central nervous system (CNS) at an unprecedented level of complexity and detail. Intricate molecular fingerprints of CSF proteins may pinpoint multiple underlying pathogenic mechanisms as well as an acute and a chronic CNS disease component. Some of these changes may be mapped to altered protein expression patterns in clinically relevant cell populations with a causative or diagnostic disease link. A CNS proteome database of primary human CNS tissues may avoid ambiguities of experimental models and accelerate pre- and clinical development of more specific diagnostic and prognostic disease markers and new selective therapeutics.
Topics: Biomarkers; Brain; Gene Expression; Humans; Mental Disorders; Neuropeptides; Neurotransmitter Agents; Proteins; Proteome
PubMed: 11343634
DOI: 10.1017/S1461145701002267 -
Scientific Reports Jul 2023Aberrant formation of biomolecular condensates has been proposed to play a role in several cancers. The oncogenic fusion protein BRD4-NUT forms condensates and drives...
Aberrant formation of biomolecular condensates has been proposed to play a role in several cancers. The oncogenic fusion protein BRD4-NUT forms condensates and drives changes in gene expression in Nut Carcinoma. Here we sought to understand the molecular elements of BRD4-NUT and its associated histone acetyltransferase (HAT), p300, that promote these activities. We determined that a minimal fragment of NUT (MIN) in fusion with BRD4 is necessary and sufficient to bind p300 and form condensates. Furthermore, a BRD4-p300 fusion protein also forms condensates and drives gene expression similarly to BRD4-NUT(MIN), suggesting the p300 fusion may mimic certain features of BRD4-NUT. The intrinsically disordered regions, transcription factor-binding domains, and HAT activity of p300 all collectively contribute to condensate formation by BRD4-p300, suggesting that these elements might contribute to condensate formation by BRD4-NUT. Conversely, only the HAT activity of BRD4-p300 appears necessary to mimic the transcriptional profile of cells expressing BRD4-NUT. Our results suggest a model for condensate formation by the BRD4-NUT:p300 complex involving a combination of positive feedback and phase separation, and show that multiple overlapping, yet distinct, regions of p300 contribute to condensate formation and transcriptional regulation.
Topics: Nuclear Proteins; Transcription Factors; Biomolecular Condensates; Oncogene Proteins, Fusion; Gene Expression
PubMed: 37488172
DOI: 10.1038/s41598-023-39102-9 -
Molecular Biology and Evolution Aug 2023Variation in gene expression across lineages is thought to explain much of the observed phenotypic variation and adaptation. The protein is closer to the target of...
Variation in gene expression across lineages is thought to explain much of the observed phenotypic variation and adaptation. The protein is closer to the target of natural selection but gene expression is typically measured as the amount of mRNA. The broad assumption that mRNA levels are good proxies for protein levels has been undermined by a number of studies reporting moderate or weak correlations between the two measures across species. One biological explanation for this discrepancy is that there has been compensatory evolution between the mRNA level and regulation of translation. However, we do not understand the evolutionary conditions necessary for this to occur nor the expected strength of the correlation between mRNA and protein levels. Here, we develop a theoretical model for the coevolution of mRNA and protein levels and investigate the dynamics of the model over time. We find that compensatory evolution is widespread when there is stabilizing selection on the protein level; this observation held true across a variety of regulatory pathways. When the protein level is under directional selection, the mRNA level of a gene and the translation rate of the same gene were negatively correlated across lineages but positively correlated across genes. These findings help explain results from comparative studies of gene expression and potentially enable researchers to disentangle biological and statistical hypotheses for the mismatch between transcriptomic and proteomic data.
Topics: Evolution, Molecular; RNA, Messenger; Proteins; Transcription, Genetic; Protein Biosynthesis; Genes; Selection, Genetic; Proteomics; Gene Expression Profiling
PubMed: 37498582
DOI: 10.1093/molbev/msad169 -
Medical Science Monitor : International... Feb 2021BACKGROUND Hepatocellular carcinoma (HCC) causes a heavy disease burden worldwide. Cell division cycle 45 (Cdc45) and its encoding gene (CDC45) have been studied for a...
BACKGROUND Hepatocellular carcinoma (HCC) causes a heavy disease burden worldwide. Cell division cycle 45 (Cdc45) and its encoding gene (CDC45) have been studied for a long time, but their expression patterns and roles in liver carcinogenesis and advanced HCC deterioration are still incompletely understood. This study integrated tissue microarray and bioinformatics analyses to explore the expression and clinical value of CDC45 and Cdc45 in HCC. MATERIAL AND METHODS In HCC, the expression and relationships with clinic-pathological parameters of CDC45 and Cdc45 were investigated by integrating the RNA-sequencing data, downloaded from The Cancer Genome Atlas and Oncomine databases, and tissue microarray with immunohistochemistry staining. Co-expressed genes and genetic alterations of CDC45 separately obtained from Oncomine and cBioPortal databases were identified to shed light on the potential mechanisms of CDC45 in HCC. RESULTS CDC45 and Cdc45 were both overexpressed in HCC tissues, and the CDC45 level progressively increased from stage I to III. The survival outcomes of the group with high CDC45 expression were significantly worse compared with the group with low expression. Amplification and deep deletion were 2 major significant alteration types in HCC patients, and the outcomes were worse in patients with altered versus unaltered CDC45. NUDT1, E2F1, CCNE2, MCM5, and CENPM were identified as the most significantly co-expressed genes. CONCLUSIONS CDC45 and Cdc45 were both upregulated in HCC, and increased expression levels and genetic alternations of CDC45 were correlated with worse prognosis in HCC patients. CDC45 may promote HCC by co-expressing with NUDT1, E2F1, CCNE2, MCM5, and CENPM.
Topics: Biomarkers, Tumor; Carcinoma, Hepatocellular; Cell Cycle Proteins; Computational Biology; Gene Expression; Gene Expression Profiling; Gene Expression Regulation, Neoplastic; Humans; Liver Neoplasms; Prognosis; Sequence Analysis, RNA; Transcriptome
PubMed: 33622998
DOI: 10.12659/MSM.928800