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Bidirectional Gene Promoters
Transcription system and chromosomal structure
- 1st Edition - November 23, 2022
- Author: Fumiaki Uchiumi
- Language: English
- Paperback ISBN:9 7 8 - 0 - 1 2 - 8 1 8 7 8 7 - 6
- eBook ISBN:9 7 8 - 0 - 1 2 - 8 1 9 0 6 8 - 5
- eBook ISBN:9 7 8 - 0 - 1 2 - 8 1 9 4 6 1 - 4
Recent studies in human genetics and in silico analyses have revealed that a number of genes are head-head orientated with other genes or non-coding RNAs. The expression of regula… Read more
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Request a sales quoteRecent studies in human genetics and in silico analyses have revealed that a number of genes are head-head orientated with other genes or non-coding RNAs. The expression of regulatory element-containing 5’-upstream regions of gene pairs are referred to as bi-directional promoters and are thought to have a key role in biological regulatory mechanisms.
For example, tumor suppressor protein-encoding TP53 and BRCA1 genes are head-head bound with WRAP53 and NBR2, respectively. DNA-repair factor-encoding ATM and PRKDC (DNA-PKcs) genes have bidirectional partner NPAT and MCM4, respectively. Surveillance of the human DNA database has revealed that the numbers of DNA repair/mitochondrial function/immune response-associated genes are bound with other genes that are transcribed to opposite direction. The observations may encourage us to investigate in the molecular mechanisms how DNA repair/mitochondrial function/immune response-associated genes are regulated by bidirectional promoters. Not only protein-coding genes, but also quite a few ncRNAs, which play important roles in various cellular events, are transcribed under the regulation of the bidirectional promoters. More importantly, we know that dysregulation in the promoter activity and transcription initiation of genes might cause human diseases.
- Provides an overview of the process of transcription
- Explains why there so many bidirectional promoters present in human genomes
- Covers how the diverse biological functions of (non-coding RNAs) ncRNAs are controlled
Basic scientists and clinical or medicinal scientists who are investigating transcriptional regulation in mammalian cells
- Cover image
- Title page
- Table of Contents
- Copyright
- Preface
- Chapter 1: Introductory Chapter: DNA Replication and Transcription
- Abstract
- DNA replication origin in eukaryotic cells
- Helicases that regulate transcription and DNA replication
- From the RNA world to the DNA/RNA/protein world
- Viruses and transposable elements
- Alterations in transcriptional state during the aging process
- Conclusion
- References
- Section I: Biological significances of the bidirectional transcription in eukaryotic cells
- Chapter 2: Mitochondrial function and immune response-regulating factor-encoding gene promoters
- Abstract
- Origin of mitochondria and endosymbiosis
- Known functions of mitochondria
- Mitochondrial dysfunction and human diseases
- Bidirectional promoters of human mitochondrial function-associated genes
- Immune responses and mitochondrial functions are dependent on each other
- Bidirectional promoters of human interferon-stimulated gene (ISG) promoters
- Glycolysis enzyme-encoding gene promoters
- Conclusion
- References
- Chapter 3: DNA repair factor-encoding gene promoters
- Abstract
- Slight but appropriate low levels of mutation are essential for evolution
- Classification of the DNA repair systems in mammalian cells
- Dysfunctions in the DNA repair system that cause human diseases
- Bidirectional promoters of human DNA repair factor-encoding genes
- Mitonuclear communication, telomere maintenance, and nicotinamide adenine dinucleotide (NAD+)
- DNA repair factors that localize in mitochondria
- Cross-talk between DNA repair and immunological responses
- Conclusion
- References
- Chapter 4: Regulation of non-coding RNA promoters
- Abstract
- From the RNA world: re-evaluation of non-coding RNAs (ncRNAs)
- Classification of ncRNAs and relationships with DNA repair, mitochondrial function, and the immune system
- The ncRNAs that may play roles in pathogenesis of age-related human diseases
- Bidirectional promoters of lncRNAs and the head-head linked genes
- Bidirectional promoters of the miRNA host and the oppositely transcribed partner genes
- Conclusion
- References
- Chapter 5: Parameters that determine the direction of transcription
- Abstract
- Transcription that plays an essential role in the Central Dogma
- Transcription systems in mammalian cells
- Classification of site-specific transcription factors in mammalian cells
- The transcriptional regulators: stresses, hormones, and nutrients
- cis-elements that are present near transcription start sites (TSSs) of human bidirectional promoters
- Epigenetic regulation of bidirectional transcription
- Factors or parameters that determine unidirectional or bidirectional transcription
- Conclusion
- References
- Section II: Control of bidirectional promoters and the relevance to human diseases
- Chapter 6: Dysregulation of transcription and human diseases
- Abstract
- Mutations on transcription regulatory regions and human diseases
- Transcription in cancer cells
- Classification of human epigenetic factors
- Epigenetic factor-encoding gene promoters
- Histone protein-encoding gene promoters
- Epigenetic alterations during aging that might increase cancer risk
- Oxidative stress factor-encoding gene promoters
- Epigenetic dysregulation in neurodegenerative diseases and immune disorders
- Conclusion
- References
- Chapter 7: Human proto-oncogene promoters
- Abstract
- Classification of protein factors that are encoded on human proto-oncogenes
- The 5’-flanking regions of the human proto-oncogenes
- Amplification of proto-oncogenes
- Proto-oncogene expression can be epigenetically regulated
- Conclusion
- References
- Section III: In silico and bioinformatic studies in gene expression system
- Chapter 8: Distal transcriptional enhancers and repressors of bidirectional promoters
- Abstract
- Initiation, elongation, enhancement, and termination of transcription
- Enhancers that determine uni/bidirectional transcription
- Molecular mechanism of transcription termination
- Tail-to-head configurated gene pairs
- Silencers
- Insulators
- Biological meaning of the looping structure of chromosomes: lessons from retroviruses
- Conclusion
- References
- Chapter 9: The landscape of the repeated sequences in the human genome
- Abstract
- Repeated sequences contribute to form-specific structures of the human chromosomes
- Telomeres and subtelomeres
- Centromeres
- Identical repeated sequence (IRS) and variable number of tandem repeat (VNTR)
- CpG islands
- Euchromatin and heterochromatin
- Common fragile sites (CFSs) in the chromosomes
- Conclusion
- References
- Chapter 10: Biological roles of loop structures
- Abstract
- Loop structures of oligopeptides and polypeptides
- Loop structures of RNAs
- RNAs have evolved to form hairpin- or stem-loop structures to gain biological functions
- Loop structures of the chromosomal DNAs
- Loop structures that play essential roles in DNA replication, repair, and recombination
- Sequence motifs that give driving forces to initiate DNA replication
- Conclusion
- References
- Section IV: Evolution of the transcription system in eukaryotic cells
- Chapter 11: Are transposable elements enemies within?
- Abstract
- Gene expression systems of eukaryotes, prokaryotes, and viruses
- Genomic structures that correspond to rRNAs and tRNAs
- Extra chromosomal circular DNAs (eccDNAs) and loop structure formation by RNAs
- Mitochondrial DNA (mtDNA) is a double-stranded circular DNA
- Evolution with linear or circular DNA
- Transposable elements might have regulated the evolution rate to protect the genome
- Transposable elements and their structures in the human genome
- Comparison of genomic structures of retrotransposons with that of functional genes
- Transpositions that cause human diseases
- Conclusion
- References
- Chapter 12: Molecular mechanisms that have made bidirectional gene promoters
- Abstract
- Hypothesis: endosymbiosis might have generated organelles and it enabled evolution
- Horizontal gene transfer (HGT) that might have contributed to the evolution of organisms
- How have DNAs been transferred to the nucleus and integrated into the genome?
- Ribonucleotides (NTPs) or deoxyribonucleotides (dNTPs)
- Dynamism of chromosomes during meiosis and immunological V(D)J recombination
- Failure in recombination and integration of DNAs
- Why are varieties of transcription factors encoded on the genome?
- An unanswered question remains: How were bidirectional promoters made?
- References
- Index
- No. of pages: 234
- Language: English
- Edition: 1
- Published: November 23, 2022
- Imprint: Elsevier
- Paperback ISBN: 9780128187876
- eBook ISBN: 9780128190685
- eBook ISBN: 9780128194614
FU
Fumiaki Uchiumi
Professor Uchiumi received his Bachelor's degree (Chemistry) from Tokyo University of Science in 1987. In 1993, after obtaining his Ph.D. degree (Molecular Biology) from Tokyo University, he joined Professor S. Tanuma's Laboratory at Tokyo University of Science as an Assistant Professor. He obtained his second Ph.D. (Pharmaceutical Science) from Tokyo University of Science in 1999 and in 2000 was promoted to the position of Lecturer at Tokyo University of Science. Professor Uchiumi then went abroad as a post-doctoral researcher for the United States-Japan Cooperative Cancer Research Program in Professor E. Fanning’s Laboratory at Vanderbilt University, 2000-2001. Professor Uchiumi was promoted to Associate Professor and then Full Professor at Tokyo University of Science in 2010 and 2016, respectively.
Affiliations and expertise
Professor of Pharmaceutical Sciences, Tokyo University of Science, JapanRead Bidirectional Gene Promoters on ScienceDirect