Gen İfadesinin Düzenlenmesi

Reznikoff WS. The lactose operon-controlling elements: a complex paradigm. Mol Microbiol. 1992;6(17):2419-22. doi: 10.1111/j.1365-2958.1992.tb01416.x.

Sanganeria T, Bordoni B. Genetics, Inducible Operon. In: StatPearls (Internet). Treasure Island (FL): StatPearls Publishing; 2026. https://www.ncbi.nlm.nih.gov/books/NBK564361/

Clug WS, Cumming MR, Spencer C. Genetik Kavramlar. Cihan Öner Çev. Ed. Ankara: Nobel Yayınları; 2011

de Gunzburg J. Mode of action of cyclic amp in prokaryotes and eukaryotes, CAP and cAMP-dependent protein kinases. Biochimie. 198567(6):563-82. doi: 10.1016/s0300-9084(85)80196-6

Passner JM, Schultz SC, Steitz TA. Modeling the cAMP-induced allosteric transition using the crystal structure of CAP-cAMP at 2.1 A resolution. J Mol Biol. 2000 Dec 15;304(5):847-59. doi: 10.1006/jmbi.2000.4231. PMID: 11124031

Merino E, Jensen RA, Yanofsky C. Evolution of bacterial trp operons and their regulation. Curr Opin Microbiol. 2008;11(2):78-86. doi: 10.1016/j.mib.2008.02.005

Topaktaş M. Genetik. 2.basım. Ankara: Nobel Yayınları; 2021.

Bédard AV, Hien EDM, Lafontaine DA. Riboswitch regulation mechanisms: RNA, metabolites and regulatory proteins. Biochim Biophys Acta Gene Regul Mech. 2020;1863(3):194501. doi: 10.1016/j.bbagrm.2020.194501

Mandal M, Lee M, Barrick JE, Weinberg Z, Emilsson GM, Ruzzo WL, Breaker RR. A glycine-dependent riboswitch that uses cooperative binding to control gene expression. Science. 2004;306:275-279

Mccown PJ, Corbino KA, Stav S, Sherlock ME, Breaker RR. Riboswitch diversity and distribution. RNA. 2017; 23:995-1011

Serganov A, Nudler E. A decade of riboswitches. Cell. 2013;152:17-24

Panne D. The enhanceosome. Curr Opin Struct Biol. 2008;18(2):236-42. doi: 10.1016/j.sbi.2007.12.002.

Halfon MS. Silencers, Enhancers, and the Multifunctional Regulatory Genome. Trends Genet. 2020;36(3):149-151. doi: 10.1016/j.tig.2019.12.005

Niessing D, Blanke S, Jäckle H. Bicoid associates with the 5'-cap-bound complex of caudal mRNA and represses translation. Genes Dev. 2002;16(19):2576-82

Passmore LA, Coller J. Roles of mRNA poly(A) tails in regulation of eukaryotic gene expression. Nat Rev Mol Cell Biol. 2022;23(2):93-106. doi: 10.1038/s41580-021-00417-y

Chen CY, Shyu AB. Mechanisms of deadenylation-dependent decay. Wiley Interdiscip Rev RNA. 2011 Mar-Apr;2(2):167-83. doi: 10.1002/wrna.40. Epub 2010 Sep 15. PMID: 21957004; PMCID: PMC3624885.

Li L, Chang SS, Liu Y. RNA interference pathways in filamentous fungi. Cell Mol Life Sci. 2010;67(22):3849-63. doi: 10.1007/s00018-010-0471-y

Agrawal N, Dasaradhi PV, Mohmmed A, Malhotra P, Bhatnagar RK, Mukherjee SK. RNA interference: biology, mechanism, and applications. Microbiol Mol Biol Rev. 2003;67(4):657-85. doi: 10.1128/MMBR.67.4.657-685.2003

Halder K, Chaudhuri A, Abdin MZ, Majee M, Datta A. RNA Interference for Improving Disease Resistance in Plants and Its Relevance in This Clustered Regularly Interspaced Short Palindromic Repeats-Dominated Era in Terms of dsRNA-Based Biopesticides. Front Plant Sci. 202213;13:885128. doi: 10.3389/fpls.2022.885128

Bofill-De Ros X, Vang Ørom UA. Recent progress in miRNA biogenesis and decay. RNA Biology.2004;21(1):36–43. https://doi.org/10.1080/15476286.2023.2288741

O'Brien J, Hayder H, Zayed Y, Peng C. Overview of MicroRNA Biogenesis, Mechanisms of Actions, and Circulation. Front Endocrinol (Lausanne). 2018;9:402. doi: 10.3389/fendo.2018.00402

Wilson RC, Doudna JA. Molecular mechanisms of RNA interference. Annu Rev Biophys. 2013;42:217-39. doi: 10.1146/annurev-biophys-083012-130404

Akkoç AN, Toplu N. RNA Interferens (RNAi). Animal Health Prod and Hyg. 2017;6(1):468-476

Bender O, Çelebi E, Atalay A. RNA İnterferans ve Güncel Klinik Uygulamaları, RNA Interference and Current Clinical Applications: Review, Turkiye Klinikleri J Med Sci. 2016;36(1):53-60 doi: 10.5336/medsci.2015-49055

Dağeri A, Güz N, Gürkan MO. Böceklerle mücadelede yeni bir strateji: RNA interferans A new approach to insect pest management: interference RNA. Türk. entomol. bült. 2012;2(3):223-230.

Gündoğdu R, Çelik V. RNA interferens (RNAi). Erciyes Üniversitesi Fen Bilimleri Enstitüsü Dergisi. 2009;25(1-2):34-47

Gebauer F, Hentze MW. Molecular mechanisms of translational control. Nature Reviews Molecular Cell Biology. 2004;5:827–835

Hinnebusch AG, Lorsch JR. The mechanism of eukaryotic translation initiation: new insights and challenges. Cold Spring Harb Perspect Biol. 2012;4(10):a011544. doi: 10.1101/cshperspect.a011544

Nandagopal N, Roux PP. Regulation of global and specific mRNA translation by the mTOR signaling pathway. Translation (Austin). 2015;3(1):e983402. doi: 10.4161/21690731.2014.983402

Grüner S, Weber R, Peter D, Chung MY, Igreja C, Valkov E, Izaurralde E. Structural motifs in eIF4G and 4E-BPs modulate their binding to eIF4E to regulate translation initiation in yeast. Nucleic Acids Res. 2018;46(13):6893-6908. doi: 10.1093/nar/gky542

Wu X, Brewer G. The regulation of mRNA stability in mammalian cells: 2.0. Gene. 2012;500(1):10-21. doi: 10.1016/j.gene.2012.03.021

Kim B, Seol J, Kim YK, Lee JB. Single-molecule visualization of mRNA circularization during translation. Exp Mol Med. 202355(2):283-289. doi: 10.1038/s12276-023-00933-1

Nelson MR, Leidal AM, Smibert CA. Drosophila Cup is an eIF4E-binding protein that functions in Smaug-mediated translational repression. EMBO J. 2004;23(1):150-9. doi: 10.1038/sj.emboj.7600026

Colombero C, Remy D, Antoine-Bally S, Macé AS, Monteiro P, ElKhatib N, Fournier M, Dahmani A, Montaudon E, Montagnac G, Marangoni E, Chavrier P. mTOR Repression in Response to Amino Acid Starvation Promotes ECM Degradation Through MT1-MMP Endocytosis Arrest. Adv Sci (Weinh). 20218(17):e2101614. doi: 10.1002/advs.202101614

Rong L, Livingstone M, Sukarieh R, Petroulakis E, Gingras AC, Crosby K, Smith B, Polakiewicz RD, Pelletier J, Ferraiuolo MA, Sonenberg N. Control of eIF4E cellular localization by eIF4E-binding proteins, 4E-BPs. RNA. 2008;14(7):1318-27. doi: 10.1261/rna.950608

Paraskeva E, Gray NK, Schläger B, Wehr K, Hentze MW. Ribosomal pausing and scanning arrest as mechanisms of translational regulation from cap-distal iron-responsive elements. Mol Cell Biol. 1999;19(1):807-16. doi: 10.1128/MCB.19.1.807

Menotti E, Henderson BR, Kühn LC. Translational regulation of mRNAs with distinct IRE sequences by iron regulatory proteins 1 and 2. J Biol Chem. 1998;273(3):1821-4. doi: 10.1074/jbc.273.3.1821

Gosselin P, Oulhen N, Jam M, Ronzca J, Cormier P, Czjzek M, Cosson B. The translational repressor 4E-BP called to order by eIF4E: new structural insights by SAXS. Nucleic Acids Res. 2011;39(8):3496-503. doi: 10.1093/nar/gkq1306

Penalva LO, Sánchez L. RNA binding protein sex-lethal (Sxl) and control of Drosophila sex determination and dosage compensation. Microbiol Mol Biol Rev. 2003;67(3):343-59, table of contents. doi: 10.1128/MMBR.67.3.343-359.2003

Nandagopal N, Roux PP. Regulation of global and specific mRNA translation by the mTOR signaling pathway. Translation (Austin). 2015;3(1):e983402. doi: 10.4161/21690731.2014.983402

Wilkie GS, Dickson KS, Gray NK. Regulation of mRNA translation by 5'- and 3'-UTR-binding factors. Trends Biochem Sci. 2003;28(4):182-8. doi: 10.1016/S0968-0004(03)00051-3

Li Z, Li S, Luo M, Jhong JH, Li W, Yao L, Pang Y, Wang Z, Wang R, Ma R, Yu J, Huang Y, Zhu X, Cheng Q, Feng H, Zhang J, Wang C, Hsu JB, Chang WC, Wei FX, Huang HD, Lee TY. dbPTM in 2022: an updated database for exploring regulatory networks and functional associations of protein post-translational modifications. Nucleic Acids Res. 2022;50(D1):D471-D479. doi: 10.1093/nar/gkab1017

Schofield LC, Dialpuri JS, Murshudov GN, Agirre J. Post-translational modifications in the Protein Data Bank. Acta Crystallogr D Struct Biol. 2024;80(Pt 9):647-660. doi: 10.1107/S2059798324007794

Qin W, Ugur E, Mulholland CB, Bultmann S, Solovei I, Modic M, Smets M, Wierer M, Forné I, Imhof A, Cardoso MC, Leonhardt H. Phosphorylation of the HP1β hinge region sequesters KAP1 in heterochromatin and promotes the exit from naïve pluripotency. Nucleic Acids Res. 2021;49(13):7406-7423. doi: 10.1093/nar/gkab548

Małecki JM, Davydova E, Falnes PØ. Protein methylation in mitochondria. J Biol Chem. 2022;298(4):101791. doi: 10.1016/j.jbc.2022.101791

Wang YC, Huang SH, Chang CP, Li C. Identification and Characterization of Glycine- and Arginine-Rich Motifs in Proteins by a Novel GAR Motif Finder Program. Genes (Basel). 2023;14(2):330. doi: 10.3390/genes14020330

Bruick RK, McKnight SL. A conserved family of prolyl-4-hydroxylases that modify HIF. Science. 2001;294(5545):1337-40. doi: 10.1126/science.1066373

Ismail HD, Newman RH, Kc DB. RF-Hydroxysite: a random forest based predictor for hydroxylation sites. Mol Biosyst. 2016;12(8):2427-35. doi: 10.1039/c6mb00179c

Varma S, Orgel JPRO, Schieber JD. Contrasting Local and Macroscopic Effects of Collagen Hydroxylation. Int J Mol Sci. 2021;22(16):9068. doi: 10.3390/ijms22169068

Strocchi S, Reggiani F, Gobbi G, Ciarrocchi A, Sancisi V. The multifaceted role of EGLN family prolyl hydroxylases in cancer: going beyond HIF regulation. Oncogene. 2022;41(29):3665-3679. doi: 10.1038/s41388-022-02378-8

Garrido Ruiz D, Sandoval-Perez A, Rangarajan AV, Gunderson EL, Jacobson MP. Cysteine Oxidation in Proteins: Structure, Biophysics, and Simulation. Biochemistry. 2022;61(20):2165-2176. doi: 10.1021/acs.biochem.2c00349

Chandran S, Binninger D. Role of Oxidative Stress, Methionine Oxidation and Methionine Sulfoxide Reductases (MSR) in Alzheimer's Disease. Antioxidants (Basel). 2023;13(1):21. doi: 10.3390/antiox13010021

Varki A, Cummings RD, Esko JD, Stanley P, Hart GW, Aebi M, Mohnen D, Kinoshita T, Packer NH, Prestegard JH, Schnaar RL, Seeberger PH, editors. Essentials of Glycobiology (Internet). 4th ed. Cold Spring Harbor (NY): Cold Spring Harbor Laboratory Press; 2022

Huang Y, Yang C, Xu XF, Xu W, Liu SW. Structural and functional properties of SARS-CoV-2 spike protein: potential antivirus drug development for COVID-19. Acta Pharmacol Sin. 2020;41(9):1141-1149. doi: 10.1038/s41401-020-0485-4.

Tanaka K, Mizushima T, Saeki Y. The proteasome: molecular machinery and pathophysiological roles. Biol Chem. 2012;393(4):217-34. doi: 10.1515/hsz-2011-0285

Waibl F, Liedl KR, Rupp B. Correcting cis-trans-transgressions in macromolecular structure models. FEBS J. 2022;289(10):2793-2804. doi: 10.1111/febs.15884

Hu M, He F, Thompson EW, Ostrikov KK, Dai X. Lysine Acetylation, Cancer Hallmarks and Emerging Onco-Therapeutic Opportunities. Cancers (Basel). 2022;14(2):346. doi: 10.3390/cancers14020346.

Varland S, Silva RD, Kjosås I, Faustino A, Bogaert A, Billmann M, Boukhatmi H, Kellen B, Costanzo M, Drazic A, Osberg C, Chan K, Zhang X, Tong AHY, Andreazza S, Lee JJ, Nedyalkova L, Ušaj M, Whitworth AJ, Andrews BJ, Moffat J, Myers CL, Gevaert K, Boone C, Martinho RG, Arnesen T. N-terminal acetylation shields proteins from degradation and promotes age-dependent motility and longevity. Nat Commun. 2023;14(1):6774. doi: 10.1038/s41467-023-42342-y

Deshaies RJ. Proteotoxic crisis, the ubiquitin-proteasome system, and cancer therapy. BMC Biol. 2014;12:94. doi: 10.1186/s12915-014-0094-0

Finley D. Recognition and processing of ubiquitin-protein conjugates by the proteasome. Annu Rev Biochem. 2009;78:477-513. doi: 10.1146/annurev.biochem.78.081507.101607

Saeki Y. Ubiquitin recognition by the proteasome. J Biochem. 2017;161(2):113-124. doi: 10.1093/jb/mvw091. PMID: 28069863

Ghosh S, Ramadas B, Manna D. Targeted protein degradation using the lysosomal pathway. RSC Med Chem. 2022;13(12):1476-1494. doi: 10.1039/d2md00273f

Yamamoto H, Matsui T. Molecular Mechanisms of Macroautophagy, Microautophagy, and Chaperone-Mediated Autophagy. J Nippon Med Sch. 2024;91(1):2-9. doi: 10.1272/jnms.JNMS.2024_91-102

Tuğrul B, Balcan E, Gürcü B. Otofaji ve Kanser Autophagy and Cancer. CBU-SBED. 2023;10(2):155-160.

Martini-Stoica H, Xu Y, Ballabio A, Zheng H. The Autophagy-Lysosomal Pathway in Neurodegeneration: A TFEB Perspective. Trends Neurosci. 2016;39(4):221-234. doi: 10.1016/j.tins.2016.02.002.