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Proteins and Proteomics
Published in Firdos Alam Khan, Biotechnology Fundamentals, 2020
TBP is a general TF that binds specifically to a DNA sequence called the TATA box. This DNA sequence is found about 30 base pairs upstream of the transcription start site in some eukaryotic gene promoters. TBP, along with a variety of TBP-associated factors, make up the TFIID, a general TF that in turn makes up part of the RNA polymerase II preinitiation complex. As one of the few proteins in the preinitiation complex that binds DNA in a sequence-specific manner, it helps position RNA polymerase II over the transcription start site of the gene. However, it is estimated that only 10%–20% of human promoters have TATA boxes. Therefore, TBP is probably not the only protein involved in positioning RNA polymerase II. TBP is involved in DNA melting (double strand separation) by bending the DNA by 80° (the AT-rich sequence to which it binds facilitates easy melting). The TBP is an unusual protein in that it binds the minor groove using a β sheet.
Proteins and proteomics
Published in Firdos Alam Khan, Biotechnology Fundamentals, 2018
The TBP is a general transcription factor that binds specifically to a DNA sequence called the TATA box. This DNA sequence has found about 30 base pairs upstream of the transcription start site in some eukaryotic gene promoters. TBP, along with a variety of TBP-associated factors, make up the TFIID, a general transcription factor that in turn makes up part of the RNA polymerase II preinitiation complex. As one of the few proteins in the preinitiation complex that binds DNA in a sequence-specific manner, it helps position RNA polymerase II over the transcription start site of the gene. However, it is estimated that only 10%–20% of human promoters have TATA boxes. Therefore, TBP is probably not the only protein involved in positioning RNA polymerase II. TBP is involved in DNA melting (dou-ble strand separation) by bending the DNA by 80° (the AT-rich sequence to which it binds facilitates easy melting). The TBP is an unusual protein since it binds the minor groove using a β sheet.
Binding processes and transcription rates
Published in Christian Mazza, Michel Benaïm, Stochastic Dynamics for Systems Biology, 2016
Christian Mazza, Michel Benaïm
Signaling pathways are instumental for gene transcription, through their action on transcription-controlling proteins, the so-called transcription factors (TF); see, e.g., [120]. TF interact with regulatory DNA motifs called promoter, enhancer or silencer sequences. Transcription is divided into three main phases: initiation, elongation and termination; we will present models describing the first phase. In eukaryotic cells, multiprotein complexes are formed; they are composed of RNA polymerase II and six general transcription factors. These TF are not gene specific and can thus be used for various genes. The activity of RNA polymerase, and of the general and gene-specific TF are controlled by signaling cascades, which are themselves activated by external stimuli. The DNA sequences of promoters and enhancers are composed of several distinct binding sites where gene specific transcription factors can bind, and thus enhance (positive regulation) or prevent (inhibition) transcription.
Differentially expressed long-chain noncoding RNAs in human neuroblastoma cell line (SH-SY5Y): Alzheimer’s disease cell model
Published in Journal of Toxicology and Environmental Health, Part A, 2019
Ming Zhang, Yuan-Qing Zhang, Xie-Ze Wei, Charles Lee, Dong-Sheng Huo, He Wang, Zhi-Ying Zhao
To identify potential lncRNAs and the moieties that these constituents regulate, GO analysis was performed for the differentially expressed lncRNAs to determine which are enriched in GO terms of biological process, cellular component and molecular function as illustrated in Figure 5. The major GO enrichment terms focused on the biological process was categorized as follows: 1) regulation of transcription; 2) DNA-templated; 3) transcription; 4) signal transduction; 5) transport; 6) phosphorylation; 7) positive regulation of transcription from RNA polymerase II promoter; 8) cell cycle; 9) oxidation-reduction process; 10) and nervous system development. The major GO enrichment terms in the present study in the cellular component category were as follows: 1) membrane; 2) nucleus; 3) cytoplasm; 4) cytosol; 5) integral component of membrane; 6) extracellular exosome; 7) mitochondrion; 8) extracellular region; 9) cytoskeleton; 10) endoplasmic reticulum. The major GO enrichment terms in the molecular function category were as follows: 1) protein binding; 2) metal ion binding; 3) nucleotide binding; 4) DNA binding; 5) ATP binding; 6) transferase activity; 7) nucleic acid binding; 8) RNA binding; 9) zinc ion binding; and 10) hydrolase activity.