Molecular biology of the cell

Journal of Education Health and Sport, Год журнала: 2022, Номер 12(8), С. 730 - 926

Опубликована: Авг. 23, 2022

The book is intended for students studying medical and biological specialties. CHAPTER I. EPIGENETICS INTRODUCTION science of epigenetics looks at the mechanisms molecular modifications histones DNA that can regulate gene activity without affecting nucleotide sequences in molecule. Recognized epigenetic regulators are methylation, post-translational histones, non-coding RNAs (nkRNAs). One most important differences between eukaryotic cells prokaryotes presence a complex nucleo-protein chromatin eukaryotes. It this form molecule stored our cells. On one hand, structural organization provides compact arrangement cell nucleus. other directly involved process regulating expression. At same time, nucleosome depicted Fig. 1 (a functional unit chromatin) considered as key component processes nucleus 8 histone proteins (octamers). consists two copies each H2A, H2B, H3 H4. chain, which includes 147 nucleotides, folds 1.65 times around octamer histones. nucleosomes arranged linear array along "beads on string". linker section connecting adjacent (transcriptionally inactive) sealed with H1-histone protein. length 30 nm. Moreover, site beginning transcription usually located inside nucleosome. Consequently, serves repressor, preventing initiation transcription. That is, total repression genes. In contrast, becomes possible result remodeling factors enable "dismantling" or otherwise alter their structure organization. Thus, (inactivation) genes begins wrapping nucleosome, liberation from (activation) involves freeing binding to unfolding by (Lorch Y., Kornberg R. D., 2017). Thanks mechanism, selective expression only those needed given time tissue possible. should be emphasized extends not transcription, but also associated molecule, such replication, mitotic division, repair double-strand breaks, maintenance telomeres. control various physiological pathological corresponding changing availability systems chromatin. scope application research methods rapidly expanding. Currently, we witnessing active introduction approaches field practical medicine aimed diagnosing treating dangerous human diseases. II. TRANSCRIPTION FACTORS For first existence was revealed basis discovery made it establish vitro purified RNA polymerase-II initiate template extract (Weil P. A. et al., 1979). Further fractionation identification general (GTF) required has identified similar rats, Drosophila, yeast substantiated assumption GTFs indeed "common" necessary transcribed polymerase highly conserved number organisms (Matsui T. 1980). We mention II because type enzyme ability synthesize mRNA. Whereas I responsible synthesis pro-rRNA, III tRNA RNAs. Meanwhile, regulation eukaryotes quite complex, since depends complexes (Burns L. G., Peterson C. L., 1997) covalent modification (Natsume-Kitatani Mamitsuka H., 2016). initiation, immediate target GTF well-defined promo zone gene. promotra eukaryotes, main elements regulatory distinguished. (bark promoter, see 2.1) attributed assembling (PIC), including TATA sequence above start (TSS ), an initiating (Inr) covering site. Promoters may include unit, initiator (Inr), both (Hampsey M., 1998). A third major element, downstream promoter element (DPE), originally described Drosophila about p.p. below TSS. DPE appears function conjunction Inr factor TFIID non-TATA promoters. According current research, cellular (main) promoters multicellular contain short nucleotides called cow (motifs) (e.g., block, lower (DPE)) recruit through common mechanism (Dreos 2021). authors report classes Inr+DPE present genome humans structurally other, different species organisms. studied box, box found 10-20% cortical Therefore, sequence, name known elements, include: BRE, MTE, TST sequences. BRE (TFIIB recognition element) motifs either (BREu) (BREd) box. TBP, demonstrate high levels conservatism range archaebacteria (Kadonaga J. T., 2012). doing so, BREu well BREd have positive negative effects activity. core (DPE) detected analysis Drosophila. MTE (motif ten element), front DPE, overrepresented "motif 10" then discovered, promoter. exhibit humans, appear recognized subunits TFIID, TAF resemble structure. turn, TCT regulates ribosomal protein humans. Although there no universal all promoters, concept nuclear defined minimum stretch sufficient accurately 2012; Haberle V., Stark A., 2018). noted results modern will constantly supplement list new components example, DNA-replicatedrelated (DRE), Ohler 1,6 7 (Danino Y. M. 2015; authors, bark transformed course evolution. Due this, modulated composition elements. Such modulation achieved emergence combinations additional level realized. To summarize facts, initiated specific position, Transcription Initiation Site (TSS), 5' end TSS embedded spanning 50 base pairs platform related (GTFs). Regulatory low basal activity, further activated, generally more distally enhancers (discussed below). Enhancers bind factors, cofactors, enhance III. CELL SIGNALING PATHWAYS organism, work regulated large signals. These signals formed organism itself, reflecting needs living (metabolic state, stages development, differentiation, reproduction), reaction external environment. implementation these encompasses biochemical lead cell's perception signal response. something receptor, turn response signal. receptor recognizes signal, interprets specificity translates into intracellular signaling molecules, cascade phosphorylation, pathways. soon (ligand) binds its – complementary transmembrane cell. Growth hormones, cytokines, neurotransmitters, extracellular matrix, etc. chemical nature ligands diverse, small molecules lipids (prostaglandins, steroid hormones), (for peptide cytokines chemokines, growth factors)., polymers sugars β-glucan zymosan) proteoglycans), nucleic acids, Binding ligand induces conformational changes translated activating cascades secondary messengers (kinases, phosphatases, GTPases, ions cAMP, cGMP, diacylglycerol, etc.). message transmitted membrane nucleus, where expression, subsequent translation targeting organelles triggered. There types receptors (transmembrane) receptors. Membrane plasma separate domain ligand, hydrophobic nature, cytoplasmic domain. Cell surface divided G-protein-bound receptors, tyrosine kinase-bound ionotropic When binds, undergo activate enzymatic domain, kinases, phosphatases adapter proteins. covalently bound capable producing transmission. Intracellular (estrogen glucocorticoid progesterone retinoic acid thyroid hormone etc.), membranes (mitochondria, endoplasmic reticulum Golgi apparatus). information received receptor) targets. All path transmission However, certain set effector proteins, enzymes substrates implement pathway (signaling cascade). Recently, however, been growing evidence themselves play extremely role signaling, theso-called scaffold ("platform proteins", adaptor proteins), coordinate assembly multicomponent complexes. Scaffold several single thereby modulating efficiency bringing closer together, direct flow cell, activating, coordinating events networks (Skovorodnikova P.A. literature, described, cover wide functions. This group three categories (Fig. 1): simple functionally dependent (adaptors), larger multi-domain designed (scaffold⁄anchoring proteins) specialized localizing proteins-components pathways (docking ( Buday Tompa P, 2010) platforms increases selectivity pathway, allows formation feedback. e ultimate ultimately allow resulting converted change (Brivanlou Darnell E., 2002). Most eventually activation repressors sequence. Eukaryotic like takes place cytoplasm. Signal multifactorial system, based nodular special cascades. none isolation. interaction inevitable complexes, when system perceives combination stimuli (hormones, pathogenic ligands), preserves accuracy (Saini N., Sarin relatively development mammals Combinations action determine decisions fate differentiation ontogenesis (Li R., Elowitz M.V., 2019; de Roo Staal F. 2020) malignancy (Dreesen O., Brivanlou A.N., 2007; Skovorodnikova Consider some medically important. IV. MOLECULAR BIOLOGY OF THE TUMOR: MECHANISMS INITIATION, PROMOTION AND PROGRESSION Tumor diseases occupy leading place, terms morbidity mortality. despite advances study genetic patterns, many unresolved questions remain. spectrum markers makes diagnose, predict course, degree malignancy, rate tumor progression therapy. occur characterized stability, they dynamic profile - appearance clones properties. heterogeneity simultaneously complicates strategy managing patients, creating prerequisites characteristics

Язык: Английский

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CDK8 and CDK19: positive regulators of signal-induced transcription and negative regulators of Mediator complex proteins

Nucleic Acids Research, Год журнала: 2023, Номер 51(14), С. 7288 - 7313

Опубликована: Июнь 28, 2023

Abstract We have conducted a detailed transcriptomic, proteomic and phosphoproteomic analysis of CDK8 its paralog CDK19, alternative enzymatic components the kinase module associated with transcriptional Mediator complex implicated in development diseases. This was performed using genetic modifications selective CDK8/19 small molecule inhibitors potent PROTAC degrader. inhibition cells exposed to serum or agonists NFκB protein C (PKC) reduced induction signal-responsive genes, indicating pleiotropic role kinases signal-induced reprogramming. under basal conditions initially downregulated group most which were inducible by PKC stimulation. Prolonged mutagenesis upregulated larger gene set, along post-transcriptional increase proteins comprising core module. Regulation both RNA expression required activities but enzymes protected their binding partner cyclin from proteolytic degradation kinase-independent manner. Analysis isogenic cell populations expressing CDK8, CDK19 kinase-inactive mutants revealed that same qualitative effects on phosphorylation at levels, whereas differential versus knockouts attributable quantitative differences activity rather than different functions.

Язык: Английский

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Mediator kinase inhibition reverses castration resistance of advanced prostate cancer

Journal of Clinical Investigation, Год журнала: 2024, Номер 134(10)

Опубликована: Март 28, 2024

Mediator kinases CDK19 and CDK8, pleiotropic regulators of transcriptional reprogramming, are differentially regulated by androgen signaling but both upregulated in castration-resistant prostate cancer (CRPC). Genetic or pharmacological inhibition CDK8 reverses the phenotype restores sensitivity CRPC xenografts to deprivation vivo. Prolonged CDK8/19 inhibitor treatment combined with castration not only suppresses growth also induces tumor regression cures. Transcriptomic analysis revealed that kinase amplifies modulates effects on gene expression, disrupting adaptation deprivation. inactivation cells affects stromal indicating activity molds microenvironment. The combination downregulates MYC pathway, a MYC-driven model even without castration. inhibitors show efficacy patient-derived xenograft models CRPC, signature correlates progression overall survival clinical samples metastatic CRPC. These results indicate mediate androgen-independent vivo supporting development for this presently incurable disease.

Язык: Английский

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The Mediator kinase module enhances polymerase activity to regulate transcriptional memory after heat stress in Arabidopsis

The EMBO Journal, Год журнала: 2024, Номер 43(3), С. 437 - 461

Опубликована: Янв. 16, 2024

Abstract Plants are often exposed to recurring adverse environmental conditions in the wild. Acclimation high temperatures entails transcriptional responses, which prime plants better withstand subsequent stress events. Heat (HS)-induced memory results more efficient re-induction of transcription upon recurrence heat stress. Here, we identified CDK8 and MED12, two subunits kinase module co-regulator complex, Mediator, as promoters associated histone modifications Arabidopsis. is recruited heat-stress genes by HEAT SHOCK TRANSCRIPTION FACTOR A2 (HSFA2). Like HSFA2, largely dispensable for initial gene induction HS, its function thus independent primary activation. In addition promoter start region target genes, also binds their 3ʹ-region, where it may promote elongation, termination, or rapid re-initiation RNA polymerase II (Pol II) complexes during bursts. Our work presents a complex role Mediator multicellular eukaryotes, through interactions with factors, chromatin modifications, promotion Pol efficiency.

Язык: Английский

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Mechanisms of Interaction between Enhancers and Promoters in Three Drosophila Model Systems

International Journal of Molecular Sciences, Год журнала: 2023, Номер 24(3), С. 2855 - 2855

Опубликована: Фев. 2, 2023

In higher eukaryotes, the regulation of developmental gene expression is determined by enhancers, which are often located at a large distance from promoters they regulate. Therefore, architecture chromosomes and mechanisms that determine functional interaction between enhancers decisive importance in development organisms. Mammals model animal Drosophila have homologous key architectural proteins similar organization chromosome architecture. This review describes current progress understanding formation long-range interactions three well-studied regulatory loci Drosophila.

Язык: Английский

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MED12 and CDK8/19 modulate androgen receptor activity and enzalutamide response in prostate cancer

Endocrinology, Год журнала: 2024, Номер 165(10)

Опубликована: Авг. 27, 2024

Abstract Prostate cancer progression is driven by androgen receptor (AR) activity, which a target for therapeutic approaches. Enzalutamide an AR inhibitor that prolongs the survival of patients with advanced prostate cancer. However, resistance mechanisms arise and impair its efficacy. One these expression AR-V7, constitutively active splice variant. The Mediator complex multisubunit protein modulates gene on genome-wide scale. MED12 cyclin-dependent kinase (CDK)8, or paralog CDK19, are components module regulates proliferation cells. In this study, we investigated how CDK8/19 influence cancer-driven processes in cell lines, focusing activity enzalutamide response. We inhibited LNCaP (AR+, enzalutamide-sensitive), 22Rv1 (AR-V7+, enzalutamide-resistant), PC3 (AR−, enzalutamide-insensitive) Both inhibition reduced all respective 3D spheroids. knockdown significantly c-Myc signaling pathways. cells, it consistently response, prostate-specific antigen (PSA) secretion, genes, AR-V7 expression. Combined enzalutamide, additively decreased both PSA secretion cells and, when combined Our study revealed regulate their may modulate response to

Язык: Английский

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Transcriptional coupling of telomeric retrotransposons with the cell cycle

Science Advances, Год журнала: 2025, Номер 11(1)

Опубликована: Янв. 3, 2025

Unlike most species that use telomerase for telomere maintenance, many dipterans, including Drosophila , rely on three telomere-specific retrotransposons (TRs)— HeT-A TART and TAHRE —to form tandem repeats at chromosome ends. Although TR transcription is crucial in their life cycle, its regulation remains poorly understood. This study identifies the Mediator complex, E2F1-Dp, Scalloped/dTEAD as key regulators of transcription. Reducing activity or Sd/dTEAD increases expression length, while overexpressing E2F1-Dp depleting Rbf1 stimulates The regulate this process through E2F1-Dp. CUT&RUN (Cleavage under targets release using nuclease) analysis shows direct binding CDK8, Dp, to telomeric repeats, with motif enrichment revealing E2F- TEAD-binding sites. These findings uncover complex’s role controlling length Sd, coupling transcriptional cycle host cell-cycle machinery protect ends .

Язык: Английский

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Mediator kinase inhibition suppresses hyperactive interferon signaling in Down syndrome

eLife, Год журнала: 2025, Номер 13

Опубликована: Фев. 10, 2025

Hyperactive interferon (IFN) signaling is a hallmark of Down syndrome (DS), condition caused by Trisomy 21 (T21); strategies that normalize IFN could benefit this population. Mediator-associated kinases CDK8 and CDK19 drive inflammatory responses through incompletely understood mechanisms. Using sibling-matched cell lines with/without T21, we investigated Mediator kinase function in the context hyperactive DS over 75 min to 24 hr timeframe. Activation IFN-response genes was suppressed cells treated with CDK8/CDK19 inhibitor cortistatin A (CA), via rapid suppression IFN-responsive transcription factor (TF) activity. We also discovered affect splicing, novel means which control gene expression. To further probe function, completed cytokine screens metabolomics experiments. Cytokines are master regulators responses; screening 105 different proteins, show help IFN-dependent at least part transcriptional regulation receptors. Metabolomics revealed inhibition altered core metabolic pathways type-specific ways, broad upregulation anti-inflammatory lipid mediators occurred specifically kinase-inhibited during IFNγ signaling. subset these lipids (e.g. oleamide, desmosterol) serve as ligands for nuclear receptors PPAR LXR, activation CA-treated cells, revealing mechanistic links between kinases, metabolism, receptor function. Collectively, our results establish context-specific regulators, reveal expression not only TFs, but changes splicing. Moreover, antagonizes transcriptional, metabolic, responses, implications other chronic conditions.

Язык: Английский

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Chemical inhibitors of transcription-associated kinases

Current Opinion in Chemical Biology, Год журнала: 2022, Номер 70, С. 102186 - 102186

Опубликована: Авг. 1, 2022

Transcription by RNA polymerase II (pol II) is regulated kinases. In recent years, many selective and potent inhibitors of pol transcription-associated kinases have been developed, these molecules advanced understanding kinase function in mammalian cells. Here, we focus on chemical the CDK7, CDK8, CDK9, CDK12, CDK13, CDK19. We provide a brief overview common activation mechanisms. then highlight advantages compared with other basic research methods, describe caveats associated non-selective compounds (e.g. flavopiridol). conclude strategies recommendations for implementation experimental analysis

Язык: Английский

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Cyclin‐dependent kinases: Masters of the eukaryotic universe

Wiley Interdisciplinary Reviews - RNA, Год журнала: 2023, Номер 15(1)

Опубликована: Сен. 17, 2023

Abstract A family of structurally related cyclin‐dependent protein kinases (CDKs) drives many aspects eukaryotic cell function. Much the literature in this area has considered individual members to act primarily either as regulators cycle, context which CDKs were first discovered, or transcription. Until recently, CDK7 was only clear example a CDK that functions both processes. However, new data points several “cell‐cycle” having important roles transcription and some “transcriptional” cycle‐related targets. For example, novel have been demonstrated for archetypal cycle regulator CDK1. The increasing evidence overlap between these two types suggests they might play critical role coordinating Here we review canonical cell‐cycle transcriptional CDKs, provide an update on how collaborate perform cellular functions. We also brief overview dysregulation contributes carcinogenesis, possible treatment avenues. This article is categorized under: RNA Interactions with Proteins Other Molecules > RNA‐Protein Complexes Processing 3′ End Splicing Regulation/Alternative

Язык: Английский

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