scholarly journals Mechanisms of miRNA-Mediated Gene Regulation from Common Downregulation to mRNA-Specific Upregulation

2014 ◽  
Vol 2014 ◽  
pp. 1-15 ◽  
Author(s):  
Ayla Valinezhad Orang ◽  
Reza Safaralizadeh ◽  
Mina Kazemzadeh-Bavili
Keyword(s):  
Gene Expression ◽  
Gene Regulation ◽  
Regulatory Gene ◽  
Gene Families ◽  
Protein Translation ◽  
Cell Types ◽  
Posttranscriptional Gene Regulation ◽  
Gene Regulatory ◽  
To Come ◽  
Different Cell Types

Discovered in 1993, micoRNAs (miRNAs) are now recognized as one of the major regulatory gene families in eukaryotes. To date, 24521 microRNAs have been discovered and there are certainly more to come. It was primarily acknowledged that miRNAs result in gene expression repression at both the level of mRNA stability by conducting mRNA degradation and the level of translation (at initiation and after initiation) by inhibiting protein translation or degrading the polypeptides through binding complementarily to 3′UTR of the target mRNAs. Nevertheless, some studies revealed that miRNAs have the capability of activating gene expression directly or indirectly in respond to different cell types and conditions and in the presence of distinct cofactors. This reversibility in their posttranslational gene regulatory natures enables the bearing cells to rapidly response to different cell conditions and consequently block unnecessary energy wastage or maintain the cell state. This paper provides an overview of the current understandings of the miRNA characteristics including their genes and biogenesis, as well as their mediated downregulation. We also review up-to-date knowledge of miRNA-mediated gene upregulation through highlighting some notable examples and discuss the emerging concepts of their associations with other posttranscriptional gene regulation processes.

scholarly journals Robust enhancer-gene regulation identified by single-cell transcriptomes and epigenomes

2021 ◽  
Author(s):  
Fangming Xie ◽  
Ethan J. Armand ◽  
Zizhen Yao ◽  
Hanqing Liu ◽  
Anna Bartlett ◽  
...  
Keyword(s):  
Gene Expression ◽  
Gene Regulation ◽  
Single Cell ◽  
Mouse Brain ◽  
Cell Types ◽  
Regulatory Elements ◽  
Simple Correlation ◽  
False Prediction ◽  
Different Cell Types

Integrating single-cell transcriptomes and epigenomes across diverse cell types can link genes with the cis-regulatory elements (CREs) that control expression. Gene co-expression across cell types confounds simple correlation-based analysis and results in high false prediction rates. We developed a procedure that controls for co-expression between genes and integrates multiple molecular modalities, and used it to identify >10,000 gene-CRE pairs that contribute to gene expression programs in different cell types in the mouse brain.

Dpp signaling thresholds in the dorsal ectoderm of the Drosophila embryo

Development ◽  
2000 ◽  
Vol 127 (15) ◽  
pp. 3305-3312 ◽  
Author(s):  
H.L. Ashe ◽  
M. Mannervik ◽  
M. Levine
Keyword(s):  
Gene Expression ◽  
Target Genes ◽  
Histone Acetyltransferase ◽  
Cell Types ◽  
Drosophila Embryo ◽  
Present Evidence ◽  
Drosophila Homolog ◽  
Dorsal Ectoderm ◽  
Transgenic Embryos ◽  
Different Cell Types

The dorsal ectoderm of the Drosophila embryo is subdivided into different cell types by an activity gradient of two TGF(β) signaling molecules, Decapentaplegic (Dpp) and Screw (Scw). Patterning responses to this gradient depend on a secreted inhibitor, Short gastrulation (Sog) and a newly identified transcriptional repressor, Brinker (Brk), which are expressed in neurogenic regions that abut the dorsal ectoderm. Here we examine the expression of a number of Dpp target genes in transgenic embryos that contain ectopic stripes of Dpp, Sog and Brk expression. These studies suggest that the Dpp/Scw activity gradient directly specifies at least three distinct thresholds of gene expression in the dorsal ectoderm of gastrulating embryos. Brk was found to repress two target genes, tailup and pannier, that exhibit different limits of expression within the dorsal ectoderm. These results suggest that the Sog inhibitor and Brk repressor work in concert to establish sharp dorsolateral limits of gene expression. We also present evidence that the activation of Dpp/Scw target genes depends on the Drosophila homolog of the CBP histone acetyltransferase.

scholarly journals Hypercapnia Regulates Gene Expression and Tissue Function

2020 ◽  
Vol 11 ◽  
Author(s):  
Masahiko Shigemura ◽  
Lynn C. Welch ◽  
Jacob I. Sznajder
Keyword(s):  
Gene Expression ◽  
Lung Diseases ◽  
Transcriptional Response ◽  
Cell Types ◽  
Chronic Lung Diseases ◽  
Tissue Responses ◽  
Mammalian Tissues ◽  
Specific Tissue ◽  
Different Cell Types ◽  
Alveolar Gas Exchange

Carbon dioxide (CO2) is produced in eukaryotic cells primarily during aerobic respiration, resulting in higher CO2 levels in mammalian tissues than those in the atmosphere. CO2 like other gaseous molecules such as oxygen and nitric oxide, is sensed by cells and contributes to cellular and organismal physiology. In humans, elevation of CO2 levels in tissues and the bloodstream (hypercapnia) occurs during impaired alveolar gas exchange in patients with severe acute and chronic lung diseases. Advances in understanding of the biology of high CO2 effects reveal that the changes in CO2 levels are sensed in cells resulting in specific tissue responses. There is accumulating evidence on the transcriptional response to elevated CO2 levels that alters gene expression and activates signaling pathways with consequences for cellular and tissue functions. The nature of hypercapnia-responsive transcriptional regulation is an emerging area of research, as the responses to hypercapnia in different cell types, tissues, and species are not fully understood. Here, we review the current understanding of hypercapnia effects on gene transcription and consequent cellular and tissue functions.

scholarly journals Cell-type-specific analysis of alternative polyadenylation using single-cell transcriptomics data

2019 ◽  
Vol 47 (19) ◽  
pp. 10027-10039 ◽  
Author(s):  
Eldad David Shulman ◽  
Ran Elkon
Keyword(s):  
Gene Regulation ◽  
Single Cell ◽  
Alternative Polyadenylation ◽  
Cell Types ◽  
Protein Coding ◽  
Multiple Datasets ◽  
Transcriptomics Data ◽  
Cell Type Specific ◽  
Transcriptional Gene Regulation ◽  
Different Cell Types

AbstractAlternative polyadenylation (APA) is emerging as an important layer of gene regulation because the majority of mammalian protein-coding genes contain multiple polyadenylation (pA) sites in their 3′ UTR. By alteration of 3′ UTR length, APA can considerably affect post-transcriptional gene regulation. Yet, our understanding of APA remains rudimentary. Novel single-cell RNA sequencing (scRNA-seq) techniques allow molecular characterization of different cell types to an unprecedented degree. Notably, the most popular scRNA-seq protocols specifically sequence the 3′ end of transcripts. Building on this property, we implemented a method for analysing patterns of APA regulation from such data. Analyzing multiple datasets from diverse tissues, we identified widespread modulation of APA in different cell types resulting in global 3′ UTR shortening/lengthening and enhanced cleavage at intronic pA sites. Our results provide a proof-of-concept demonstration that the huge volume of scRNA-seq data that accumulates in the public domain offers a unique resource for the exploration of APA based on a very broad collection of cell types and biological conditions.

scholarly journals Differential Regulation of Human Interferon A Gene Expression by Interferon Regulatory Factors 3 and 7

2009 ◽  
Vol 29 (12) ◽  
pp. 3435-3450 ◽  
Author(s):  
Pierre Génin ◽  
Rongtuan Lin ◽  
John Hiscott ◽  
Ahmet Civas
Keyword(s):  
Gene Expression ◽  
Differential Expression ◽  
Transcriptional Activation ◽  
Cell Types ◽  
Inhibitory Effect ◽  
Human Interferon ◽  
Gene Promoters ◽  
Nucleotide Substitutions ◽  
D Modules ◽  
Different Cell Types

ABSTRACT Differential expression of the human interferon A (IFN-A) gene cluster is modulated following paramyxovirus infection by the relative amounts of active interferon regulatory factor 3 (IRF-3) and IRF-7. IRF-3 expression activates predominantly IFN-A1 and IFN-B, while IRF-7 expression induces multiple IFN-A genes. IFN-A1 gene expression is dependent on three promoter proximal IRF elements (B, C, and D modules, located at positions −98 to −45 relative to the mRNA start site). IRF-3 binds the C module of IFN-A1, while other IFN-A gene promoters are responsive to the binding of IRF-7 to the B and D modules. Maximal expression of IFN-A1 is observed with complete occupancy of the three modules in the presence of IRF-7. Nucleotide substitutions in the C modules of other IFN-A genes disrupt IRF-3-mediated transcription, whereas a G/A substitution in the D modules enhances IRF7-mediated expression. IRF-3 exerts dual effects on IFN-A gene expression, as follows: a synergistic effect with IRF-7 on IFN-A1 expression and an inhibitory effect on other IFN-A gene promoters. Chromatin immunoprecipitation experiments reveal that transient binding of both IRF-3 and IRF-7, accompanied by CBP/p300 recruitment to the endogenous IFN-A gene promoters, is associated with transcriptional activation, whereas a biphasic recruitment of IRF-3 and CBP/p300 represses IFN-A gene expression. This regulatory mechanism contributes to differential expression of IFN-A genes and may be critical for alpha interferon production in different cell types by RIG-I-dependent signals, leading to innate antiviral immune responses.

scholarly journals Global Analysis of Cell Type-Specific Gene Expression

2003 ◽  
Vol 4 (2) ◽  
pp. 208-215 ◽  
Author(s):  
David W. Galbraith
Keyword(s):  
Gene Expression ◽  
Fluorescent Protein ◽  
Global Analysis ◽  
Expression Patterns ◽  
Three Dimensional ◽  
Global Gene Expression ◽  
Cell Types ◽  
Reasonable Assumption ◽  
Specific Gene ◽  
Different Cell Types

The tissues and organs of multicellular eukaryotes are frequently observed to comprise complex three-dimensional interspersions of different cell types. It is a reasonable assumption that different global patterns of gene expression are found within these different cell types. This review outlines general experimental strategies designed to characterize these global gene expression patterns, based on a combination of methods of transgenic fluorescent protein (FP) expression and targeting, of flow cytometry and sorting and of high-throughput gene expression analysis.

Gene Expression in Different Cell Types of Aging Rat Brain

1991 ◽  
Vol 56 (3) ◽  
pp. 812-817 ◽  
Author(s):  
J. Venugopal ◽  
Kalluri Subba Rao
Keyword(s):  
Gene Expression ◽  
Rat Brain ◽  
Cell Types ◽  
Aging Rat ◽  
Different Cell Types

scholarly journals After the Fact(or): Posttranscriptional Gene Regulation in EnterohemorrhagicEscherichia coliO157:H7

2018 ◽  
Vol 200 (19) ◽  
Author(s):  
Amber B. Sauder ◽  
Melissa M. Kendall
Keyword(s):  
Gene Expression ◽  
Gene Regulation ◽  
Posttranscriptional Regulation ◽  
Posttranslational Regulation ◽  
Content Type ◽  
Infectious Dose ◽  
Posttranscriptional Gene Regulation ◽  
Niche Adaptation ◽  
Intestinal Pathogen ◽  
The Stability

ABSTRACTTo adapt to ever-changing environments, pathogens quickly alter gene expression. This can occur through transcriptional, posttranscriptional, or posttranslational regulation. Historically, transcriptional regulation has been thoroughly studied to understand pathogen niche adaptation, whereas posttranscriptional and posttranslational gene regulation has only relatively recently been appreciated to play a central role in bacterial pathogenesis. Posttranscriptional regulation may involve chaperones, nucleases, and/or noncoding small RNAs (sRNAs) and typically controls gene expression by altering the stability and/or translation of the target mRNA. In this review, we highlight the global importance of posttranscriptional regulation to enterohemorrhagicEscherichia coli(EHEC) gene expression and discuss specific mechanisms of how EHEC regulates expression of virulence factors critical to host colonization and disease progression. The low infectious dose of this intestinal pathogen suggests that EHEC is particularly well adapted to respond to the host environment.

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