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Signal transduction and exercise
Published in Adam P. Sharples, James P. Morton, Henning Wackerhage, Molecular Exercise Physiology, 2022
Brendan Egan, Adam P. Sharples
Additionally, estimates suggest that there are ~1,800 DNA-binding transcription factors in the human genome (55). Of these, the regulatory transcription factors have a DNA-binding domain that recognises a specific DNA motif. Some common types of DNA-binding domain include the C2H2 zinc-finger, homeodomain and basic helix-loop-helix (55). Often, it is necessary for transcription factors to form homo- or heterodimers (protein-protein interactions) in order to create a correct DNA-binding motif. These transcription factors are further regulated by the binding of co-factors, such as the abovementioned PGC-1α, and its interaction with the transcription factors NRF-1, NRF-2, MEF2, ERRα and TFAM in the regulation of skeletal muscle gene expression. Moreover, a single session of aerobic exercise alters the DNA-binding activity of a variety of transcription factors, including MEF2 (56), NF-κB (57), and NRF-1 and NRF-2 (58).
Muscle Disorders
Published in Philip B. Gorelick, Fernando D. Testai, Graeme J. Hankey, Joanna M. Wardlaw, Hankey's Clinical Neurology, 2020
Kourosh Rezania, Peter Pytel, Betty Soliven
Lamin A/C and emerin are part of the inner nuclear envelope. They are thought to have a role in maintaining nuclear shape and to be important for scaffolding DNA in the nucleus. Through DNA binding, these proteins may influence gene expression.
ChIP-seq analysis
Published in Altuna Akalin, Computational Genomics with R, 2020
In order to calculate the percentage of CTCF peaks which contain a known CTCF motif. We need to find the CTCF motif and have the computational tools to search for that motif. The DNA binding motifs can be extracted from the MotifDB Bioconductor database. The MotifDB is an agglomeration of multiple motif databases.
Epigenetic control of skin immunity
Published in Immunological Medicine, 2023
Human cells contain two meters of genomic DNA that is tightly folded and packed within the nucleus. Genomic DNA forms a secondary structure referred to as chromatin that fits into a limited space [7]. The basic unit of chromatin, the nucleosome, is consisted of 147 bp genomic DNA and a core histone octamer. DNA is negatively charged and histones are positively charged, and the opposing charges allow DNA to wrap itself tightly around the histone octamer to form a nucleosome. Initiation of transcription requires the binding of RNA polymerase II and several basic transcription factors, called TFIIA and TFIIB, bind to promoters located near the transcription start sites [8]. Sequence-specific DNA-binding transcription factors (TFs) are involved in the enhancement of transcription. TFs bind to enhancers and cause genomic DNA to form looped structures that shorten the distance between enhancers and promoters, thereby promoting the transcription of the target genes. Transcriptional activity is also closely related to the degree of DNA condensation associated with chromatin structure [6,8]. Tightly packed chromatin, called closed chromatin or heterochromatin, restricts the access of RNA polymerase II and the transcription factors to the regulatory sites, and consequently, suppresses the expression of target genes. Open chromatin or euchromatin that is less condensed allows easier access of the transcriptional machinery to DNA, thus setting target genes to be more actively transcribed.
1,3-dimethyl-6-nitroacridine derivatives induce apoptosis in human breast cancer cells by targeting DNA
Published in Drug Development and Industrial Pharmacy, 2019
Qian Zhou, Hongshuai Wu, Chaoqun You, Zhiguo Gao, Kai Sun, Mingxin Wang, Fanghui Chen, Baiwang Sun
First, we used spectroscopic techniques to study the DNA binding affinity of these compounds. The results showed that the compounds act as effective DNA binding agents, with calculated binding constants of Kb = 3.898–5.341 × 104 M−1. The replacements of nitro at position 6 and methyl at positions 1 and 3, which altered the planarity of acridine ring, thus affected the DNA binding mode of the compounds. The introduction of different substituents at position 9 also affected the DNA binding mode and affinity. The acridine moiety can partially insert into DNA and the flexible ligands bind with DNA in the mode of groove binding. The compounds containing aromatic amino substituents showed higher DNA binding affinity than the other compounds. Interestingly, the binding constants decreased for the substituent alkyl increased in benzene ring of the aromatic amines. Compounds 1 and 6 with highest binding constants may be due to ethyl ester, which helps to attain a better fit for the DNA grooves.
Promoter haplotypes of the corticotropin-releasing hormone encoding gene modulate the physiological stress response in vitro and in vivo
Published in Stress, 2019
Ting Li-Tempel, Tobias Suer, Tobias Tempel, Mauro F. Larra, Ulrike Winnikes, Hartmut Schächinger, Jobst Meyer, Andrea B. Schote
We focused on two SNPs that were previously shown to impact mainly cAMP-dependent transcription factor binding. Rs3176921 changes the consensus sequence of the binding box of nuclear transcription factor Y (NF-Y) from CCAAT to CCACT, and therewith disrupts NF-Y binding (Wagner et al., 2006) as well as significantly affects the expression of genes involved in complex pathways (Chassanidis et al., 2009; Chen, Mo, Li, Zeng, & Xu, 2007; Dolfini, Gatta, & Mantovani, 2012). Further evidence is accumulating that alteration of the NF-Y structure is not the direct cause of any specific disease. Rather the efficiency of DNA-binding might play a role on the development of several pathological conditions, resulting either in altered proteins, or altered gene expression patterns (Dolfini et al., 2012). Further, rs5030875 is in a high linkage disequilibrium with the SNP rs5030876, which results in the exchange of a nucleotide within the binding site of the transcription factor activating transcription factor 6 (ATF6). ATF6 is a member of the human ARF/CREB (cAMP response element binding protein) family. ATF6 participates in two independent signaling pathways, both leading to transcriptional activation in the nucleus (Yoshida, Haze, Yanagi, Yura, & Mori, 1998), interaction with cAMP responsive elements (Fawcett, Martindale, Guyton, Hai, & Holbrook, 1999), and finally differences in the CRH promoter activity (Wagner et al., 2006).