Transcriptionally Regulatory Sequences of Phylogenetic Significance
S. K. Dutta in DNA Systematics, 2019
The innate differences between organisms predict a varied complexity in transcriptional regulation for prokaryotes and eukaryotes. In bacteria and bacteriophages regulation is achieved largely by interaction between proteins, such as polymerase and repressors, with specific DNA sequences, such as promoters and operators. In eukaryotic cells transcriptional control involves many different regulatory sequences such as enhancers, long terminal repeats, internal as well as distal and proximal regulators, Z-DNA, etc., in addition to the classical promoters. While the plethora of macromolecular elements participating in the recognition of and interaction with these sequences are yet to be fully identified, it is clear that as in prokaryotes, eukaryotic chromatin requires interaction among and between proteins and nucleic acids. The presence of more complex transcriptional regulation in more highly evolved systems, such as methylation of specific sequences and temporal and tissue-specific expression of different members in a gene family during development, is only beginning to be understood at the phylogenetic level.
Genetics and genomics of exposure to high altitude
Andrew M. Luks, Philip N. Ainslie, Justin S. Lawley, Robert C. Roach, Tatum S. Simonson in Ward, Milledge and West's High Altitude Medicine and Physiology, 2021
The human genome, comprising more than 3.2 billion nucleotides of deoxyribonucleic acid (DNA) in the form of adenine (A), thymine (T), guanine (G), and cytosine (C), is organized in double-stranded bases within 23 pairs of chromosomes in the nucleus and ≈16,569 nucleotides in the circular mitochondrial genome. Only a small portion (∼2%) of the human genome encodes genes that are transcribed and translated into a sequence of amino acids that make up proteins to carry out various functions within the cell. The cellular roles of regulatory sequence outside coding portions of the genome (ENCODE Consortium 2012) and nonprotein-coding ribonucleic acids (RNAs) that are transcribed from DNA (Bartoszewski and Sikorski 2018) are active areas of research.
Framework
Peter W. Hochachka in Muscles as Molecular and Metabolic Machines, 2019
For isozyme systems like the LDHs, the issue of how many and what kinds of adaptations are required to move from slow to fast type muscles, or vice versa, can be addressed at two levels: (i) regulation of expression and (ii) regulation of function. With regard to the former, muscle-specific glycolytic isozymes are encoded by multiple unlinked genes, which seem to have common c/s-acting regions in their promoters to bind cellular transcription factors. These regulatory sequences are then thought to allow the unlinked genes to respond coordinately to physiological (or developmental) signals to orchestrate either up- or down-regulation of tissue-specific isozyme versions of the pathway (Webster and Murphy, 1988).
Advances, challenges and tools in characterizing bacterial serine, threonine and tyrosine kinases and phosphorylation target sites.
Published in Expert Review of Proteomics, 2019
Giovanni J. Pagano, Ryan J. Arsenault
The two-component system (TCS) involves a two-step phosphate transfer to carry a signal across a membrane. Generally, a histidine kinase senses an external stimulus through an extracellular sensing domain, then autophosphorylates on its catalytic domain inside the cell [2]. The histidine kinase donates the phosphate to a response regulator, which autophosphorylates on an aspartate residue. The response regulator then acts downstream, usually by binding DNA regulatory sequences to control gene expression. A variant of this system called the phosphorelay system includes an additional transfer step to a receiver domain on the histidine kinase or on a distinct protein, then to the response regulator [2]. While the two-component system is a linear sequence of transfers, recent studies have shown that auxiliary regulators and even eSTKs (see ‘1.3 Serine/threonine kinases’) can interact with the TCS.
The molecular mechanisms and targeting strategies of transcription factors in cholangiocarcinoma
Published in Expert Opinion on Therapeutic Targets, 2022
Jiao Wang, Fujing Ge, Tao Yuan, Meijia Qian, Fangjie Yan, Bo Yang, Qiaojun He, Hong Zhu
A transcription factor binds a DNA helices to specific regulatory sequences, subsequently activating or inhibiting gene transcription via a trans-activation or trans-repression domain, respectively [26]. TFs account for about 8% of the total human genes and 20% of all oncogenes discovered so far, and their mutations are the basis of many diseases, and about one-third of human developmental disorders are attributed to the dysfunction of TFs, which explains why the coding sites of TFs in the genome are so rich in ultra-conserved elements [27,28]. Considering that TFs are indispensable in CCA, we present an overview of the recent studies examining the various roles of TFs in regulating the progression and development of CCA. We also highlight possible therapeutic pathways and the latest treatment strategies for CCA by targeting TFs.
Allergen-induced asthma, chronic rhinosinusitis and transforming growth factor-β superfamily signaling: mechanisms and functional consequences
Published in Expert Review of Clinical Immunology, 2019
Harsha H. Kariyawasam, Simon B. Gane
The C-terminal of R-SMADs displays a characteristic -Ser-Ser-Xaa-Ser- motif of which the two latter serine residues are the target for phosphorylation (p) by activated type I receptors. The R-SMAD-Co-SMAD4 complex translocates into the nucleus. The complex can participate in the transcription of specific genes by acting directly as a transcription factor on the regulatory sequences as well as by activating other transcription factors. As such, by interacting with multiple transcription factors or co-activators and co-repressors, which in turn can interact with other multiple cellular signaling pathways, SMAD proteins provide a versatile system by which TGF-β superfamily ligands can achieve multiple context-dependent outcomes in a cell. Furthermore, the ligand activation of the type I receptor such as ALK-5 can also lead to activation of several alternative cell-signaling pathways. These pathways are SMAD independent and classified as non-canonical signaling that involves important pathways of the MAP kinase, phosphatidylinositol 3-kinase/AKT, and Rho-like GTPase as important examples [45]. Such parallel modulatory pathway ‘cross-talk’ allows further signaling versatility but also add breath-taking complexity to understanding the functional outcomes from such ligands. These non-canonical systems are not discussed in this review due to word constraints.
Related Knowledge Centers
- Activator
- DNA
- Gene Expression
- Nucleic Acid
- Repressor
- Rna Polymerase
- Regulation of Gene Expression
- Gene
- Transcription
- Transcription Factor