Transkripsiyon
Özet
Moleküler biyolojide, transkripsiyon süreci, hücrenin genetik bilgisinin ifade edilmesi için merkezi bir role sahiptir. Bu bölümde, bu kritik sürecin detaylı bir incelemesi gerçekleştirilmektedir. DNA'dan RNA'ya olan bilgi transferi, yaşamın temel dinamiklerinden biridir. RNA polimerazın katalitik işleyişi, bu bilgi akışını yönlendiren ana mekanizmalardan biridir. Ayrıca, promoter bölgelerinin tanımlanması ve işlevi, genlerin ne zaman ve nasıl ifade edileceğini belirler. Transkripsiyon faktörlerinin etkileşimleri, bu ifadenin regüle edilmesinde kritik bir rol oynar. Bölüm, ayrıca, transkripsiyon sonrası modifikasyonları ve hücre içi sinyal yollarının transkripsiyon üzerindeki etkilerini inceler. Bu faktörler bir araya geldiğinde, gen ekspresyonunun ne kadar karmaşık ve koordineli bir süreç olduğu açığa çıkar.
Referanslar
Burnside K, Rajagopal L. Regulation of prokaryotic gene expression by eukaryotic-like enzymes. Curr Opin Microbiol. 2012 Apr;15(2):125–31.
Kreuzer KN. DNA Damage Responses in Prokaryotes: Regulating Gene Expression, Modulating Growth Patterns, and Manipulating Replication Forks. Cold Spring Harb Perspect Biol. 2013 Nov 1;5(11):a012674–a012674.
Ruff E, Record M, Artsimovitch I. Initial Events in Bacterial Transcription Initiation. Biomolecules. 2015 May 27;5(2):1035–62.
Feklístov A, Sharon BD, Darst SA, Gross CA. Bacterial Sigma Factors: A Historical, Structural, and Genomic Perspective. Annu Rev Microbiol. 2014 Sep 8;68(1):357–76.
Bae B, Feklistov A, Lass-Napiorkowska A, Landick R, Darst SA. Structure of a bacterial RNA polymerase holoenzyme open promoter complex. Elife. 2015 Sep 8;4.
Marbach A, Bettenbrock K. lac operon induction in Escherichia coli: Systematic comparison of IPTG and TMG induction and influence of the transacetylase LacA. J Biotechnol. 2012 Jan;157(1):82–8.
Lewis M. Allostery and the lac Operon. J Mol Biol. 2013 Jul;425(13):2309–16.
Howe JA, Wang H, Fischmann TO, Balibar CJ, Xiao L, Galgoci AM, et al. Selective small-molecule inhibition of an RNA structural element. Nature. 2015 Oct 30;526(7575):672–7.
Wang B, Barahona M, Buck M. Amplification of small molecule-inducible gene expression via tuning of intracellular receptor densities. Nucleic Acids Res. 2015 Feb 18;43(3):1955–64.
Worthington RJ, Richards JJ, Melander C. Small molecule control of bacterial biofilms. Org Biomol Chem. 2012;10(37):7457.
Paget M. Bacterial Sigma Factors and Anti-Sigma Factors: Structure, Function and Distribution. Biomolecules. 2015 Jun 26;5(3):1245–65.
Yang Y, Darbari VC, Zhang N, Lu D, Glyde R, Wang Y-P, et al. Structures of the RNA polymerase-σ 54 reveal new and conserved regulatory strategies. Science (80- ). 2015 Aug 21;349(6250):882–5.
Danson AE, Jovanovic M, Buck M, Zhang X. Mechanisms of σ54-Dependent Transcription Initiation and Regulation. J Mol Biol . 2019 Sep;431(20):3960–74.
Wigneshweraraj SR, Casaz P, Buck M. Correlating protein footprinting with mutational analysis in the bacterial transcription factor sigma54 (sigmaN). Nucleic Acids Res. 2002 Feb 15;30(4):1016–28.
Coulon A, Chow CC, Singer RH, Larson DR. Eukaryotic transcriptional dynamics: from single molecules to cell populations. Nat Rev Genet. 2013 Aug 9;14(8):572–84.
Weirauch MT, Yang A, Albu M, Cote AG, Montenegro-Montero A, Drewe P, et al. Determination and Inference of Eukaryotic Transcription Factor Sequence Specificity. Cell. 2014 Sep;158(6):1431–43.
de Mendoza A, Sebé-Pedrós A, Šestak MS, Matejčić M, Torruella G, Domazet-Lošo T, et al. Transcription factor evolution in eukaryotes and the assembly of the regulatory toolkit in multicellular lineages. Proc Natl Acad Sci. 2013 Dec 10;110(50).
Lelli KM, Slattery M, Mann RS. Disentangling the Many Layers of Eukaryotic Transcriptional Regulation. Annu Rev Genet. 2012 Dec 15;46(1):43–68.
Reese JC. Basal transcription factors. Curr Opin Genet Dev. 2003 Apr;13(2):114–8.
Wen ZT, Burne RA. Analysis of cis- and trans- Acting Factors Involved in Regulation of the Streptococcus mutans Fructanase Gene ( fruA ). J Bacteriol. 2002 Jan;184(1):126–33.
Miyagawa R, Tano K, Mizuno R, Nakamura Y, Ijiri K, Rakwal R, et al. Identification of cis - and trans -acting factors involved in the localization of MALAT-1 noncoding RNA to nuclear speckles. RNA. 2012 Apr;18(4):738–51.
Vannini A, Cramer P. Conservation between the RNA Polymerase I, II, and III Transcription Initiation Machineries. Mol Cell. 2012 Feb;45(4):439–46.
Archambault J, Friesen JD. Genetics of eukaryotic RNA polymerases I, II, and III. Microbiol Rev. 1993;57(3):703–24.
Struhl K. Helix-turn-helix, zinc-finger, and leucine-zipper motifs for eukaryotic transcriptional regulatory proteins. Trends Biochem Sci. 1989 Apr;14(4):137–40.
Ellenberger T. Getting a grip on DNA recognition: structures of the basic region leucine zipper, and the basic region helix-loop-helix DNA-binding domains. Curr Opin Struct Biol. 1994 Jan;4(1):12–21.
Chen HP, Zhao YT, Zhao TC. Histone Deacetylases and Mechanisms of Regulation of Gene Expression. Crit Rev Oncog. 2015;20(1–2):35–47.
Hassig CA, Schreiber SL. Nuclear histone acetylases and deacetylases and transcriptional regulation: HATs off to HDACs. Curr Opin Chem Biol. 1997 Oct;1(3):300–8.
Jaenisch R, Bird A. Epigenetic regulation of gene expression: how the genome integrates intrinsic and environmental signals. Nat Genet. 2003 Mar;33(S3):245–54.
Mata J, Marguerat S, Bähler J. Post-transcriptional control of gene expression: a genome-wide perspective. Trends Biochem Sci. 2005 Sep;30(9):506–14.
Byszewska M, Śmietański M, Purta E, Bujnicki JM. RNA methyltransferases involved in 5′ cap biosynthesis. RNA Biol. 2014 Dec 2;11(12):1597–607.
Sheets MD, Wickens M. Two phases in the addition of a poly(A) tail. Genes Dev. 1989 Sep;3(9):1401–12.
Mishra SK, Thakran P. Intron specificity in pre-mRNA splicing. Curr Genet. 2018 Aug 3;64(4):777–84.
Kelemen O, Convertini P, Zhang Z, Wen Y, Shen M, Falaleeva M, et al. Function of alternative splicing. Gene. 2013 Feb;514(1):1–30.
Referanslar
Burnside K, Rajagopal L. Regulation of prokaryotic gene expression by eukaryotic-like enzymes. Curr Opin Microbiol. 2012 Apr;15(2):125–31.
Kreuzer KN. DNA Damage Responses in Prokaryotes: Regulating Gene Expression, Modulating Growth Patterns, and Manipulating Replication Forks. Cold Spring Harb Perspect Biol. 2013 Nov 1;5(11):a012674–a012674.
Ruff E, Record M, Artsimovitch I. Initial Events in Bacterial Transcription Initiation. Biomolecules. 2015 May 27;5(2):1035–62.
Feklístov A, Sharon BD, Darst SA, Gross CA. Bacterial Sigma Factors: A Historical, Structural, and Genomic Perspective. Annu Rev Microbiol. 2014 Sep 8;68(1):357–76.
Bae B, Feklistov A, Lass-Napiorkowska A, Landick R, Darst SA. Structure of a bacterial RNA polymerase holoenzyme open promoter complex. Elife. 2015 Sep 8;4.
Marbach A, Bettenbrock K. lac operon induction in Escherichia coli: Systematic comparison of IPTG and TMG induction and influence of the transacetylase LacA. J Biotechnol. 2012 Jan;157(1):82–8.
Lewis M. Allostery and the lac Operon. J Mol Biol. 2013 Jul;425(13):2309–16.
Howe JA, Wang H, Fischmann TO, Balibar CJ, Xiao L, Galgoci AM, et al. Selective small-molecule inhibition of an RNA structural element. Nature. 2015 Oct 30;526(7575):672–7.
Wang B, Barahona M, Buck M. Amplification of small molecule-inducible gene expression via tuning of intracellular receptor densities. Nucleic Acids Res. 2015 Feb 18;43(3):1955–64.
Worthington RJ, Richards JJ, Melander C. Small molecule control of bacterial biofilms. Org Biomol Chem. 2012;10(37):7457.
Paget M. Bacterial Sigma Factors and Anti-Sigma Factors: Structure, Function and Distribution. Biomolecules. 2015 Jun 26;5(3):1245–65.
Yang Y, Darbari VC, Zhang N, Lu D, Glyde R, Wang Y-P, et al. Structures of the RNA polymerase-σ 54 reveal new and conserved regulatory strategies. Science (80- ). 2015 Aug 21;349(6250):882–5.
Danson AE, Jovanovic M, Buck M, Zhang X. Mechanisms of σ54-Dependent Transcription Initiation and Regulation. J Mol Biol . 2019 Sep;431(20):3960–74.
Wigneshweraraj SR, Casaz P, Buck M. Correlating protein footprinting with mutational analysis in the bacterial transcription factor sigma54 (sigmaN). Nucleic Acids Res. 2002 Feb 15;30(4):1016–28.
Coulon A, Chow CC, Singer RH, Larson DR. Eukaryotic transcriptional dynamics: from single molecules to cell populations. Nat Rev Genet. 2013 Aug 9;14(8):572–84.
Weirauch MT, Yang A, Albu M, Cote AG, Montenegro-Montero A, Drewe P, et al. Determination and Inference of Eukaryotic Transcription Factor Sequence Specificity. Cell. 2014 Sep;158(6):1431–43.
de Mendoza A, Sebé-Pedrós A, Šestak MS, Matejčić M, Torruella G, Domazet-Lošo T, et al. Transcription factor evolution in eukaryotes and the assembly of the regulatory toolkit in multicellular lineages. Proc Natl Acad Sci. 2013 Dec 10;110(50).
Lelli KM, Slattery M, Mann RS. Disentangling the Many Layers of Eukaryotic Transcriptional Regulation. Annu Rev Genet. 2012 Dec 15;46(1):43–68.
Reese JC. Basal transcription factors. Curr Opin Genet Dev. 2003 Apr;13(2):114–8.
Wen ZT, Burne RA. Analysis of cis- and trans- Acting Factors Involved in Regulation of the Streptococcus mutans Fructanase Gene ( fruA ). J Bacteriol. 2002 Jan;184(1):126–33.
Miyagawa R, Tano K, Mizuno R, Nakamura Y, Ijiri K, Rakwal R, et al. Identification of cis - and trans -acting factors involved in the localization of MALAT-1 noncoding RNA to nuclear speckles. RNA. 2012 Apr;18(4):738–51.
Vannini A, Cramer P. Conservation between the RNA Polymerase I, II, and III Transcription Initiation Machineries. Mol Cell. 2012 Feb;45(4):439–46.
Archambault J, Friesen JD. Genetics of eukaryotic RNA polymerases I, II, and III. Microbiol Rev. 1993;57(3):703–24.
Struhl K. Helix-turn-helix, zinc-finger, and leucine-zipper motifs for eukaryotic transcriptional regulatory proteins. Trends Biochem Sci. 1989 Apr;14(4):137–40.
Ellenberger T. Getting a grip on DNA recognition: structures of the basic region leucine zipper, and the basic region helix-loop-helix DNA-binding domains. Curr Opin Struct Biol. 1994 Jan;4(1):12–21.
Chen HP, Zhao YT, Zhao TC. Histone Deacetylases and Mechanisms of Regulation of Gene Expression. Crit Rev Oncog. 2015;20(1–2):35–47.
Hassig CA, Schreiber SL. Nuclear histone acetylases and deacetylases and transcriptional regulation: HATs off to HDACs. Curr Opin Chem Biol. 1997 Oct;1(3):300–8.
Jaenisch R, Bird A. Epigenetic regulation of gene expression: how the genome integrates intrinsic and environmental signals. Nat Genet. 2003 Mar;33(S3):245–54.
Mata J, Marguerat S, Bähler J. Post-transcriptional control of gene expression: a genome-wide perspective. Trends Biochem Sci. 2005 Sep;30(9):506–14.
Byszewska M, Śmietański M, Purta E, Bujnicki JM. RNA methyltransferases involved in 5′ cap biosynthesis. RNA Biol. 2014 Dec 2;11(12):1597–607.
Sheets MD, Wickens M. Two phases in the addition of a poly(A) tail. Genes Dev. 1989 Sep;3(9):1401–12.
Mishra SK, Thakran P. Intron specificity in pre-mRNA splicing. Curr Genet. 2018 Aug 3;64(4):777–84.
Kelemen O, Convertini P, Zhang Z, Wen Y, Shen M, Falaleeva M, et al. Function of alternative splicing. Gene. 2013 Feb;514(1):1–30.
