Components and mechanisms of regulation of gene expression.

@article{Yilmaz2010ComponentsAM,
  title={Components and mechanisms of regulation of gene expression.},
  author={Alper Yilmaz and Erich Grotewold},
  journal={Methods in molecular biology},
  year={2010},
  volume={674},
  pages={
          23-32
        }
}
The control of gene expression is a biological process essential to all organisms. This is accomplished through the interaction of regulatory proteins with specific DNA motifs in the control regions of the genes that they regulate. Upon binding to DNA, and through specific protein-protein interactions, these regulatory proteins convey signals to the basal transcriptional machinery, containing the respective RNA polymerases, resulting in particular rates of gene expression. In eukaryotes, in… 

Figures and Tables from this paper

Epigenetic control of gene regulation in plants.
Open Chromatin in Plant Genomes
TLDR
An overview of the historical perspective of DHS research in eukaryotes is provided and possible future directions of using DHS as a tool in plant genomics research are discussed.
Organization and Dynamics of Plant Chromatin
TLDR
An overview of the historical perspective of DHS research in eukaryotes is provided and possible future directions of using DHS as a tool in plant genomics research are discussed.
A statistical model to determine multiple binding sites of a transcription factor on DNA using ChIP-seq data
TLDR
A statistical model to identify multiple binding sites of a transcription factor within a short region of the genome using the ChlP-seq data is produced and the results were compared with existing peak-calling programs.
Systems biology based meth-miRNA–mRNA regulatory network identifies metabolic imbalance and hyperactive cell cycle signaling involved in hepatocellular carcinoma onset and progression
TLDR
It is suggested that simultaneous reversal ofhyper-methylation and/or oncogenic miRNA driven suppression of genes involved in metabolic pathways, and induction of hyper- methylation and or tumor suppressor miRNAs involved in cell cycle signaling have potential of inhibiting disease aggressiveness, and predicting good survival in HCC.
Statistical and Probabilistic Approaches to Predict Protein Abundance
The End of Snoring? Application of CRISPR/Cas9 Genome Editing for Sleep Disorders
TLDR
Since sleep disorders have been linked with specific genes, in this review, areas that require further investigation and experimental and/or clinical approaches to treat sleep disturbances using CRISPR/Cas9 are suggested.
Gene expression variation and parental allele inheritance in a Xiphophorus interspecies hybridization model
TLDR
Heterogeneity of genotype, introduced by inheritance of different alleles, accounts for the largest effects on global phenotypical variability.
CRNDE Expression Positively Correlates with EGFR Activation and Modulates Glioma Cell Growth
TLDR
Functional assays show that CRNDE depletion inhibits glioma cell growth both in vitro and in vivo, and is associated with induced cellular apoptosis with decreased Bcl2/Bax ratio.
...
1
2
...

References

SHOWING 1-10 OF 46 REFERENCES
Core promoters: active contributors to combinatorial gene regulation.
TLDR
The regulation of transcription was expected to rely exclusively on DNA-binding proteins that interact with distal promoters and enhancers, but today, this simplistic picture of the structure of core promoters for protein-coding genes has been replaced by a level of complexity that is not yet fully understood or appreciated.
Mediator – a universal complex in transcriptional regulation
TLDR
A model to account for the functional and evolutionary relationship between yeast and metazoan Mediators is discussed and an appendix is created, MEDB, in which information about all the S. cerevisiae Mediator subunits and their homologues in other eukaryotic cells are compiled.
The RNA polymerase II core promoter.
TLDR
Although core promoter structure was originally thought to be invariant, a remarkable degree of diversity has become apparent and this article reviews the structural and functional diversity of the RNA polymerase II core promoter.
Mechanisms of action of transcription activation and repression domains
  • S. Roberts
  • Biology
    Cellular and Molecular Life Sciences CMLS
  • 2000
TLDR
This review will focus on the current understanding of the nature of transcriptional regulatory domains and their targets in the transcription machinery.
Roles of RNA polymerase IV in gene silencing.
TFCONES: A database of vertebrate transcription factor-encoding genes and their associated conserved noncoding elements
TLDR
The conserved noncoding elements identified in TFCONES represent a catalog of highly prioritized putative cis-regulatory elements of TF-encoding genes and are candidates for functional assay.
PlnTFDB: an integrative plant transcription factor database
TLDR
An integrative plant transcription factor database that provides a web interface to access large (close to complete) sets of transcription factors of several plant species, currently encompassing Arabidopsis thaliana, Populus trichocarpa, Oryza sativa, Chlamydomonas reinhardtii and Ostreococcus tauri.
Alternative Sigma Factors and Their Roles in Bacterial Virulence
TLDR
This work presents several examples of alternative sigma factors that have been shown to contribute to virulence in at least one organism and describes how these proteins can contribute both directly and indirectly to bacterial virulence.
AGRIS and AtRegNet. A Platform to Link cis-Regulatory Elements and Transcription Factors into Regulatory Networks1[W][OA]
TLDR
The Arabidopsis Gene Regulatory Information Server (AGRIS) is developed, which provides the scientific community with a platform to establish regulatory networks at the genome level.
Targets of RNA-directed DNA methylation.
...
1
2
3
4
5
...