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1.
Nat Commun ; 15(1): 3490, 2024 Apr 25.
Artículo en Inglés | MEDLINE | ID: mdl-38664429

RESUMEN

Congenital nucleotide excision repair (NER) deficiency gives rise to several cancer-prone and/or progeroid disorders. It is not understood how defects in the same DNA repair pathway cause different disease features and severity. Here, we show that the absence of functional ERCC1-XPF or XPG endonucleases leads to stable and prolonged binding of the transcription/DNA repair factor TFIIH to DNA damage, which correlates with disease severity and induces senescence features in human cells. In vivo, in C. elegans, this prolonged TFIIH binding to non-excised DNA damage causes developmental arrest and neuronal dysfunction, in a manner dependent on transcription-coupled NER. NER factors XPA and TTDA both promote stable TFIIH DNA binding and their depletion therefore suppresses these severe phenotypical consequences. These results identify stalled NER intermediates as pathogenic to cell functionality and organismal development, which can in part explain why mutations in XPF or XPG cause different disease features than mutations in XPA or TTDA.


Asunto(s)
Caenorhabditis elegans , Daño del ADN , Reparación del ADN , Proteínas de Unión al ADN , Endonucleasas , Factor de Transcripción TFIIH , Caenorhabditis elegans/metabolismo , Caenorhabditis elegans/genética , Humanos , Animales , Factor de Transcripción TFIIH/metabolismo , Factor de Transcripción TFIIH/genética , Proteínas de Unión al ADN/metabolismo , Proteínas de Unión al ADN/genética , Endonucleasas/metabolismo , Endonucleasas/genética , Proteínas de Caenorhabditis elegans/metabolismo , Proteínas de Caenorhabditis elegans/genética , Proteína de la Xerodermia Pigmentosa del Grupo A/metabolismo , Proteína de la Xerodermia Pigmentosa del Grupo A/genética , Unión Proteica , Factores de Transcripción/metabolismo , Factores de Transcripción/genética , Mutación , Proteínas Nucleares/metabolismo , Proteínas Nucleares/genética
2.
Mol Cell ; 84(9): 1699-1710.e6, 2024 May 02.
Artículo en Inglés | MEDLINE | ID: mdl-38604172

RESUMEN

The transition from transcription initiation to elongation is highly regulated in human cells but remains incompletely understood at the structural level. In particular, it is unclear how interactions between RNA polymerase II (RNA Pol II) and initiation factors are broken to enable promoter escape. Here, we reconstitute RNA Pol II promoter escape in vitro and determine high-resolution structures of initially transcribing complexes containing 8-, 10-, and 12-nt ordered RNAs and two elongation complexes containing 14-nt RNAs. We suggest that promoter escape occurs in three major steps. First, the growing RNA displaces the B-reader element of the initiation factor TFIIB without evicting TFIIB. Second, the rewinding of the transcription bubble coincides with the eviction of TFIIA, TFIIB, and TBP. Third, the binding of DSIF and NELF facilitates TFIIE and TFIIH dissociation, establishing the paused elongation complex. This three-step model for promoter escape fills a gap in our understanding of the initiation-elongation transition of RNA Pol II transcription.


Asunto(s)
Fosfoproteínas , Regiones Promotoras Genéticas , ARN Polimerasa II , Proteína de Unión a TATA-Box , Factor de Transcripción TFIIB , Factores de Transcripción , ARN Polimerasa II/metabolismo , ARN Polimerasa II/genética , Humanos , Factor de Transcripción TFIIB/metabolismo , Factor de Transcripción TFIIB/genética , Proteína de Unión a TATA-Box/metabolismo , Proteína de Unión a TATA-Box/genética , Factores de Transcripción/metabolismo , Factores de Transcripción/genética , Iniciación de la Transcripción Genética , Factor de Transcripción TFIIH/metabolismo , Factor de Transcripción TFIIH/genética , Factor de Transcripción TFIIH/química , Proteínas Nucleares/metabolismo , Proteínas Nucleares/genética , Unión Proteica , Factor de Transcripción TFIIA/metabolismo , Factor de Transcripción TFIIA/genética , Transcripción Genética , Elongación de la Transcripción Genética , ARN/metabolismo , ARN/genética , Factores de Transcripción TFII/metabolismo , Factores de Transcripción TFII/genética
3.
Environ Mol Mutagen ; 65 Suppl 1: 72-81, 2024 Apr.
Artículo en Inglés | MEDLINE | ID: mdl-37545038

RESUMEN

DNA damage occurs throughout life from a variety of sources, and it is imperative to repair damage in a timely manner to maintain genome stability. Thus, DNA repair mechanisms are a fundamental part of life. Nucleotide excision repair (NER) plays an important role in the removal of bulky DNA adducts, such as cyclobutane pyrimidine dimers from ultraviolet light or DNA crosslinking damage from platinum-based chemotherapeutics, such as cisplatin. A main component for the NER pathway is transcription factor IIH (TFIIH), a multifunctional, 10-subunit protein complex with crucial roles in both transcription and NER. In transcription, TFIIH is a component of the pre-initiation complex and is important for promoter opening and the phosphorylation of RNA Polymerase II (RNA Pol II). During repair, TFIIH is important for DNA unwinding, recruitment of downstream repair factors, and verification of the bulky lesion. Several different disease states can arise from mutations within subunits of the TFIIH complex. Most strikingly are xeroderma pigmentosum (XP), XP combined with Cockayne syndrome (CS), and trichothiodystrophy (TTD). Here, we summarize the recruitment and functions of TFIIH in the two NER subpathways, global genomic (GG-NER) and transcription-coupled NER (TC-NER). We will also discuss how TFIIH's roles in the two subpathways lead to different genetic disorders.


Asunto(s)
Reparación por Escisión , Xerodermia Pigmentosa , Humanos , Reparación del ADN/genética , Xerodermia Pigmentosa/genética , Factor de Transcripción TFIIH/genética , Factor de Transcripción TFIIH/metabolismo , Daño del ADN/genética , ADN/genética , Nucleótidos , Transcripción Genética
4.
Int J Mol Sci ; 24(24)2023 Dec 11.
Artículo en Inglés | MEDLINE | ID: mdl-38139171

RESUMEN

The interaction between mRNA and ribosomal RNA (rRNA) transcription in cancer remains unclear. RNAP I and II possess a common N-terminal tail (NTT), RNA polymerase subunit RPB6, which interacts with P62 of transcription factor (TF) IIH, and is a common target for the link between mRNA and rRNA transcription. The mRNAs and rRNAs affected by FUBP1-interacting repressor (FIR) were assessed via RNA sequencing and qRT-PCR analysis. An FIR, a c-myc transcriptional repressor, and its splicing form FIRΔexon2 were examined to interact with P62. Protein interaction was investigated via isothermal titration calorimetry measurements. FIR was found to contain a highly conserved region homologous to RPB6 that interacts with P62. FIRΔexon2 competed with FIR for P62 binding and coactivated transcription of mRNAs and rRNAs. Low-molecular-weight chemical compounds that bind to FIR and FIRΔexon2 were screened for cancer treatment. A low-molecular-weight chemical, BK697, which interacts with FIRΔexon2, inhibited tumor cell growth with rRNA suppression. In this study, a novel coactivation pathway for cancer-related mRNA and rRNA transcription through TFIIH/P62 by FIRΔexon2 was proposed. Direct evidence in X-ray crystallography is required in further studies to show the conformational difference between FIR and FIRΔexon2 that affects the P62-RBP6 interaction.


Asunto(s)
Neoplasias , Proteínas Represoras , Humanos , Factores de Empalme de ARN/genética , ARN Mensajero/genética , ARN Mensajero/metabolismo , Proteínas Represoras/genética , Empalme Alternativo , Neoplasias/tratamiento farmacológico , Neoplasias/genética , Factor de Transcripción TFIIH/genética , Factor de Transcripción TFIIH/metabolismo , Proteínas de Unión al ADN/genética , Proteínas de Unión al ADN/metabolismo , Proteínas de Unión al ARN/metabolismo
5.
Enzymes ; 54: 273-304, 2023.
Artículo en Inglés | MEDLINE | ID: mdl-37945175

RESUMEN

Nucleotide excision repair (NER) is a major DNA repair pathway conserved from bacteria to humans. Various DNA helicases, a group of enzymes capable of separating DNA duplex into two strands through ATP binding and hydrolysis, are required by NER to unwind the DNA duplex around the lesion to create a repair bubble and for damage verification and removal. In prokaryotes, UvrB helicase is required for repair bubble formation and damage verification, while UvrD helicase is responsible for the removal of the excised damage containing single-strand (ss) DNA fragment. In addition, UvrD facilitates transcription-coupled repair (TCR) by backtracking RNA polymerase stalled at the lesion. In eukaryotes, two helicases XPB and XPD from the transcription factor TFIIH complex fulfill the helicase requirements of NER. Interestingly, homologs of all these four helicases UvrB, UvrD, XPB, and XPD have been identified in archaea. This review summarizes our current understanding about the structure, function, and mechanism of these four helicases.


Asunto(s)
Daño del ADN , Reparación del ADN , Humanos , ADN Helicasas/metabolismo , Factor de Transcripción TFIIH/metabolismo , ADN/química
6.
DNA Repair (Amst) ; 132: 103568, 2023 Dec.
Artículo en Inglés | MEDLINE | ID: mdl-37977600

RESUMEN

The heterodecameric transcription factor IIH (TFIIH) functions in multiple cellular processes, foremost in nucleotide excision repair (NER) and transcription initiation by RNA polymerase II. TFIIH is essential for life and hereditary mutations in TFIIH cause the devastating human syndromes xeroderma pigmentosum, Cockayne syndrome or trichothiodystrophy, or combinations of these. In NER, TFIIH binds to DNA after DNA damage is detected and, using its translocase and helicase subunits XPB and XPD, opens up the DNA and checks for the presence of DNA damage. This central activity leads to dual incision and removal of the DNA strand containing the damage, after which the resulting DNA gap is restored. In this review, we discuss new structural and mechanistic insights into the central function of TFIIH in NER. Moreover, we provide an elaborate overview of all currently known patients and diseases associated with inherited TFIIH mutations and describe how our understanding of TFIIH function in NER and transcription can explain the different disease features caused by TFIIH deficiency.


Asunto(s)
Proteína de la Xerodermia Pigmentosa del Grupo D , Xerodermia Pigmentosa , Humanos , Factor de Transcripción TFIIH/genética , Factor de Transcripción TFIIH/metabolismo , Proteína de la Xerodermia Pigmentosa del Grupo D/genética , Proteína de la Xerodermia Pigmentosa del Grupo D/metabolismo , Reparación del ADN , Xerodermia Pigmentosa/genética , ADN/genética
7.
Mol Cell ; 83(11): 1763-1764, 2023 06 01.
Artículo en Inglés | MEDLINE | ID: mdl-37267901

RESUMEN

In this issue of Molecular Cell, Abril-Garrido et al.1 used cryo-EM to uncover that the +1 nucleosome inhibits transcription by interfering with the function of the TFIIH translocase via mechanisms that depend on its position relative to the transcription start site.


Asunto(s)
Nucleosomas , Transcripción Genética , Nucleosomas/genética , Factor de Transcripción TFIIH/genética , Factor de Transcripción TFIIH/metabolismo
8.
Biosci Rep ; 43(7)2023 07 26.
Artículo en Inglés | MEDLINE | ID: mdl-37340985

RESUMEN

The general transcription factor TFIIH is a multi-subunit complex involved in transcription, DNA repair, and cell cycle in eukaryotes. In the human p62 subunit and the budding yeast Saccharomyces cerevisiae Tfb1 subunit of TFIIH, the pleckstrin homology (PH) domain (hPH/scPH) recruits TFIIH to transcription-start and DNA-damage sites by interacting with an acidic intrinsically disordered region in transcription and repair factors. Whereas metazoan PH domains are highly conserved and adopt a similar structure, fungal PH domains are divergent and only the scPH structure is available. Here, we have determined the structure of the PH domain from Tfb1 of fission yeast Schizosaccharomyces pombe (spPH) by NMR. spPH holds an architecture, including the core and external backbone structures, that is closer to hPH than to scPH despite having higher amino acid sequence identity to scPH. In addition, the predicted target-binding site of spPH shares more amino acid similarity with scPH, but spPH contains several key residues identified in hPH as required for specific binding. Using chemical shift perturbation, we have identified binding modes of spPH to spTfa1, a homologue of hTFIIEα, and to spRhp41, a homologue of the repair factors hXPC and scRad4. Both spTfa1 and spRhp41 bind to a similar but distinct surface of spPH by modes that differ from those of target proteins binding to hPH and scPH, revealing that the PH domain of TFIIH interacts with its target proteins in a polymorphic manner in Metazoa, and budding and fission yeasts.


Asunto(s)
Dominios Homólogos a Pleckstrina , Proteínas de Saccharomyces cerevisiae , Animales , Humanos , Estructura Terciaria de Proteína , Factor de Transcripción TFIIH/genética , Factor de Transcripción TFIIH/química , Factor de Transcripción TFIIH/metabolismo , Sitios de Unión , Dominios Proteicos , Saccharomyces cerevisiae/genética , Saccharomyces cerevisiae/metabolismo , Proteínas de Saccharomyces cerevisiae/metabolismo
9.
Curr Opin Struct Biol ; 80: 102605, 2023 06.
Artículo en Inglés | MEDLINE | ID: mdl-37150041

RESUMEN

Nucleotide excision repair (NER) is unique in its ability to identify and remove vastly different lesions from DNA. Recent advances in the structural characterization of complexes involved in detection, verification, and excision of damaged DNA have reshaped our understanding of the molecular architecture of this efficient and accurate machinery. Initial damage recognition achieved through transcription coupled repair (TC-NER) or global genome repair (GG-NER) has been addressed by complexes of RNA Pol II with different TC-NER factors and XPC/RAD23B/Centrin-2 with TFIIH, respectively. Moreover, transcription factor IIH (TFIIH), one of the core repair factors and a central NER hub was resolved in different states, providing important insights how this complex facilitates DNA opening and damage verification. Combined, these recent advances led to a highly improved understanding of the molecular landscape of NER core processes, sharpening our view on how NER is successfully achieved.


Asunto(s)
Daño del ADN , Reparación del ADN , Factor de Transcripción TFIIH/metabolismo , ADN/genética
10.
Int J Neuropsychopharmacol ; 26(6): 396-411, 2023 Jun 23.
Artículo en Inglés | MEDLINE | ID: mdl-37235790

RESUMEN

BACKGROUND: Major depressive disorder (MDD) is a type of emotional dysfunction, and its pathogenesis has not been fully elucidated. Specifically, the key molecules in depression-related brain regions involved in this disease and their contributions to this disease are currently unclear. METHODS: GSE53987 and GSE54568 were selected from the Gene Expression Omnibus database. The data were standardized to identify the common differentially expressed genes (DEGs) in the cortex of MDD patients in the 2 datasets. The DEGs were subjected to Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway analyses. The STRING database was used to build protein-protein interaction networks, and the cytoHubba plugin was used to identify hub genes. Furthermore, we selected another blood transcriptome dataset that included 161 MDD and 169 control samples to explore the changes in the screened hub genes. Mice were subjected to 4 weeks of chronic unpredictable mild stress to establish an animal model of depression, and the expression of these hub genes in tissues of the prefrontal cortex was then detected by quantitative real time polymerase chain reaction (qRT-PCR). We subsequently predicted the possible posttranscriptional regulatory networks and traditional Chinese medicine according to the hub genes using a few online databases. RESULTS: The analysis identified 147 upregulated genes and 402 downregulated genes were identified in the cortex of MDD patients compared with that of the controls. Enrichment analyses revealed that DEGs were predominantly enriched in synapse-related cell functions, linoleic acid metabolism, and other pathways. Protein-protein interaction analysis identified 20 hub genes based on the total score. The changes in KDM6B, CUX2, NAAA, PHKB, NFYA, GTF2H1, CRK, CCNG2, ACER3, and SLC4A2 in the peripheral blood of MDD patients were consistent with those in the brain. Furthermore, the prefrontal cortex of mice with depressive-like behaviors showed significantly increased Kdm6b, Aridb1, Scaf11, and Thoc2 expression and decreased Ccng2 expression compared with that of normal mice, which was consistent with the results found for the human brain. Potential therapeutic candidates, such as citron, fructus citri, leaves of Panax Notoginseng, sanchi flower, pseudoginseng, and dan-shen root, were selected via traditional Chinese medicine screening. CONCLUSIONS: This study identified several novel hub genes in specific brain regions involved in the pathogenesis of MDD, which may not only deepen our understanding of depression but may also provide new ideas for its diagnosis and treatment.


Asunto(s)
Trastorno Depresivo Mayor , Humanos , Animales , Ratones , Trastorno Depresivo Mayor/genética , Redes Reguladoras de Genes , Perfilación de la Expresión Génica/métodos , Mapas de Interacción de Proteínas , Encéfalo , Biología Computacional/métodos , Factor de Transcripción TFIIH/genética , Histona Demetilasas con Dominio de Jumonji/genética , Antiportadores de Cloruro-Bicarbonato/genética
11.
Mol Cell ; 83(11): 1798-1809.e7, 2023 06 01.
Artículo en Inglés | MEDLINE | ID: mdl-37148879

RESUMEN

At active human genes, the +1 nucleosome is located downstream of the RNA polymerase II (RNA Pol II) pre-initiation complex (PIC). However, at inactive genes, the +1 nucleosome is found further upstream, at a promoter-proximal location. Here, we establish a model system to show that a promoter-proximal +1 nucleosome can reduce RNA synthesis in vivo and in vitro, and we analyze its structural basis. We find that the PIC assembles normally when the edge of the +1 nucleosome is located 18 base pairs (bp) downstream of the transcription start site (TSS). However, when the nucleosome edge is located further upstream, only 10 bp downstream of the TSS, the PIC adopts an inhibited state. The transcription factor IIH (TFIIH) shows a closed conformation and its subunit XPB contacts DNA with only one of its two ATPase lobes, inconsistent with DNA opening. These results provide a mechanism for nucleosome-dependent regulation of transcription initiation.


Asunto(s)
Nucleosomas , ARN Polimerasa II , Humanos , Nucleosomas/genética , ARN Polimerasa II/metabolismo , Regiones Promotoras Genéticas , Factor de Transcripción TFIIH/metabolismo , ADN/genética , ADN/química , Transcripción Genética , Sitio de Iniciación de la Transcripción
12.
Nat Commun ; 14(1): 2758, 2023 05 13.
Artículo en Inglés | MEDLINE | ID: mdl-37179334

RESUMEN

Transcription factor IIH (TFIIH) is a protein assembly essential for transcription initiation and nucleotide excision repair (NER). Yet, understanding of the conformational switching underpinning these diverse TFIIH functions remains fragmentary. TFIIH mechanisms critically depend on two translocase subunits, XPB and XPD. To unravel their functions and regulation, we build cryo-EM based TFIIH models in transcription- and NER-competent states. Using simulations and graph-theoretical analysis methods, we reveal TFIIH's global motions, define TFIIH partitioning into dynamic communities and show how TFIIH reshapes itself and self-regulates depending on functional context. Our study uncovers an internal regulatory mechanism that switches XPB and XPD activities making them mutually exclusive between NER and transcription initiation. By sequentially coordinating the XPB and XPD DNA-unwinding activities, the switch ensures precise DNA incision in NER. Mapping TFIIH disease mutations onto network models reveals clustering into distinct mechanistic classes, affecting translocase functions, protein interactions and interface dynamics.


Asunto(s)
ADN Helicasas , Reparación del ADN , Factor de Transcripción TFIIH/genética , Factor de Transcripción TFIIH/metabolismo , ADN Helicasas/genética , ADN Helicasas/metabolismo , Conformación Molecular , ADN/metabolismo , Transcripción Genética
13.
Nature ; 617(7959): 170-175, 2023 05.
Artículo en Inglés | MEDLINE | ID: mdl-37076618

RESUMEN

Nucleotide excision repair removes DNA lesions caused by ultraviolet light, cisplatin-like compounds and bulky adducts1. After initial recognition by XPC in global genome repair or a stalled RNA polymerase in transcription-coupled repair, damaged DNA is transferred to the seven-subunit TFIIH core complex (Core7) for verification and dual incisions by the XPF and XPG nucleases2. Structures capturing lesion recognition by the yeast XPC homologue Rad4 and TFIIH in transcription initiation or DNA repair have been separately reported3-7. How two different lesion recognition pathways converge and how the XPB and XPD helicases of Core7 move the DNA lesion for verification are unclear. Here we report on structures revealing DNA lesion recognition by human XPC and DNA lesion hand-off from XPC to Core7 and XPA. XPA, which binds between XPB and XPD, kinks the DNA duplex and shifts XPC and the DNA lesion by nearly a helical turn relative to Core7. The DNA lesion is thus positioned outside of Core7, as would occur with RNA polymerase. XPB and XPD, which track the lesion-containing strand but translocate DNA in opposite directions, push and pull the lesion-containing strand into XPD for verification.


Asunto(s)
Daño del ADN , Reparación del ADN , Proteínas de Unión al ADN , ADN , Factor de Transcripción TFIIH , Proteína de la Xerodermia Pigmentosa del Grupo A , Humanos , ADN/química , ADN/metabolismo , ADN Helicasas/metabolismo , Proteínas de Unión al ADN/metabolismo , Factor de Transcripción TFIIH/metabolismo , Proteína de la Xerodermia Pigmentosa del Grupo A/metabolismo , Especificidad por Sustrato , ARN Polimerasas Dirigidas por ADN/metabolismo
14.
PLoS One ; 18(3): e0283186, 2023.
Artículo en Inglés | MEDLINE | ID: mdl-36961799

RESUMEN

MicroRNAs (miRNAs) are small non coding RNAs responsible for posttranscriptional regulation of gene expression. Even though almost 2000 precursors have been described so far, additional miRNAs are still being discovered in normal as well as malignant cells. Alike protein coding genes, miRNAs may acquire oncogenic properties in consequence of altered expression or presence of gain or loss of function mutations. In this study we mined datasets from miRNA expression profiling (miRNA-seq) of 7 classic Hodgkin Lymphoma (cHL) cell lines, 10 non-Hodgkin lymphoma (NHL) cell lines and 56 samples of germinal center derived B-cell lymphomas. Our aim was to discover potential novel cHL oncomiRs not reported in miRBase (release 22.1) and expressed in cHL cell lines but no other B-cell lymphomas. We identified six such miRNA candidates in cHL cell lines and verified the expression of two of them encoded at chr2:212678788-212678849 and chr5:168090507-168090561 (GRCh38). Interestingly, we showed that one of the validated miRNAs (located in an intron of the TENM2 gene) is expressed together with its host gene. TENM2 is characterized by hypomethylation and open chromatin around its TSS in cHL cell lines in contrast to NHL cell lines and germinal centre B-cells respectively. It indicates an epigenetic mechanism responsible for aberrant expression of both, the TENM2 gene and the novel miRNA in cHL cell lines. Despite the GO analysis performed with the input of the in silico predicted novel miRNA target genes did not reveal ontologies typically associated with cHL pathogenesis, it pointed to several interesting candidates involved in i.e. lymphopoiesis. These include the lymphoma related BCL11A gene, the IKZF2 gene involved in lymphocyte development or the transcription initiator GTF2H1.


Asunto(s)
Enfermedad de Hodgkin , Linfoma de Células B , Linfoma no Hodgkin , MicroARNs , Humanos , MicroARNs/genética , MicroARNs/metabolismo , Enfermedad de Hodgkin/patología , Línea Celular , Centro Germinal/patología , Linfoma de Células B/genética , Linfoma no Hodgkin/genética , Regulación Neoplásica de la Expresión Génica , Factor de Transcripción TFIIH/genética , Factor de Transcripción TFIIH/metabolismo
15.
Proc Natl Acad Sci U S A ; 120(11): e2208860120, 2023 03 14.
Artículo en Inglés | MEDLINE | ID: mdl-36893274

RESUMEN

XPA is a central scaffold protein that coordinates the assembly of repair complexes in the global genome (GG-NER) and transcription-coupled nucleotide excision repair (TC-NER) subpathways. Inactivating mutations in XPA cause xeroderma pigmentosum (XP), which is characterized by extreme UV sensitivity and a highly elevated skin cancer risk. Here, we describe two Dutch siblings in their late forties carrying a homozygous H244R substitution in the C-terminus of XPA. They present with mild cutaneous manifestations of XP without skin cancer but suffer from marked neurological features, including cerebellar ataxia. We show that the mutant XPA protein has a severely weakened interaction with the transcription factor IIH (TFIIH) complex leading to an impaired association of the mutant XPA and the downstream endonuclease ERCC1-XPF with NER complexes. Despite these defects, the patient-derived fibroblasts and reconstituted knockout cells carrying the XPA-H244R substitution show intermediate UV sensitivity and considerable levels of residual GG-NER (~50%), in line with the intrinsic properties and activities of the purified protein. By contrast, XPA-H244R cells are exquisitely sensitive to transcription-blocking DNA damage, show no detectable recovery of transcription after UV irradiation, and display a severe deficiency in TC-NER-associated unscheduled DNA synthesis. Our characterization of a new case of XPA deficiency that interferes with TFIIH binding and primarily affects the transcription-coupled subpathway of nucleotide excision repair, provides an explanation of the dominant neurological features in these patients, and reveals a specific role for the C-terminus of XPA in TC-NER.


Asunto(s)
Neoplasias Cutáneas , Xerodermia Pigmentosa , Humanos , Proteínas de Unión al ADN/genética , Proteínas de Unión al ADN/metabolismo , Alelos , Proteína de la Xerodermia Pigmentosa del Grupo A/genética , Proteína de la Xerodermia Pigmentosa del Grupo A/metabolismo , Reparación del ADN/genética , Daño del ADN/genética , Xerodermia Pigmentosa/genética , Xerodermia Pigmentosa/metabolismo , Neoplasias Cutáneas/genética , Factor de Transcripción TFIIH/genética , Factor de Transcripción TFIIH/metabolismo
16.
Nat Struct Mol Biol ; 30(2): 226-232, 2023 02.
Artículo en Inglés | MEDLINE | ID: mdl-36411341

RESUMEN

The preinitiation complex (PIC) assembles on promoters of protein-coding genes to position RNA polymerase II (Pol II) for transcription initiation. Previous structural studies revealed the PIC on different promoters, but did not address how the PIC assembles within chromatin. In the yeast Saccharomyces cerevisiae, PIC assembly occurs adjacent to the +1 nucleosome that is located downstream of the core promoter. Here we present cryo-EM structures of the yeast PIC bound to promoter DNA and the +1 nucleosome located at three different positions. The general transcription factor TFIIH engages with the incoming downstream nucleosome and its translocase subunit Ssl2 (XPB in human TFIIH) drives the rotation of the +1 nucleosome leading to partial detachment of nucleosomal DNA and intimate interactions between TFIIH and the nucleosome. The structures provide insights into how transcription initiation can be influenced by the +1 nucleosome and may explain why the transcription start site is often located roughly 60 base pairs upstream of the dyad of the +1 nucleosome in yeast.


Asunto(s)
Proteínas de Saccharomyces cerevisiae , Saccharomyces cerevisiae , Humanos , Saccharomyces cerevisiae/genética , Saccharomyces cerevisiae/metabolismo , Nucleosomas/metabolismo , Proteínas de Saccharomyces cerevisiae/metabolismo , ARN Polimerasa II/metabolismo , ADN/química , Transcripción Genética , ADN Helicasas/metabolismo , Factor de Transcripción TFIIH/metabolismo
17.
Hum Mol Genet ; 32(7): 1102-1113, 2023 03 20.
Artículo en Inglés | MEDLINE | ID: mdl-36308430

RESUMEN

TFIIH is a complex essential for transcription of protein-coding genes by RNA polymerase II, DNA repair of UV-lesions and transcription of rRNA by RNA polymerase I. Mutations in TFIIH cause the cancer prone DNA-repair disorder xeroderma pigmentosum (XP) and the developmental and premature aging disorders trichothiodystrophy (TTD) and Cockayne syndrome. A total of 50% of the TTD cases are caused by TFIIH mutations. Using TFIIH mutant patient cells from TTD and XP subjects we can show that the stress-sensitivity of the proteome is reduced in TTD, but not in XP. Using three different methods to investigate the accuracy of protein synthesis by the ribosome, we demonstrate that translational fidelity of the ribosomes of TTD, but not XP cells, is decreased. The process of ribosomal synthesis and maturation is affected in TTD cells and can lead to instable ribosomes. Isolated ribosomes from TTD patients show an elevated error rate when challenged with oxidized mRNA, explaining the oxidative hypersensitivity of TTD cells. Treatment of TTD cells with N-acetyl cysteine normalized the increased translational error-rate and restored translational fidelity. Here we describe a pathomechanism that might be relevant for our understanding of impaired development and aging-associated neurodegeneration.


Asunto(s)
Síndromes de Tricotiodistrofia , Xerodermia Pigmentosa , Humanos , Factor de Transcripción TFIIH/genética , Factor de Transcripción TFIIH/metabolismo , Reparación del ADN/genética , Xerodermia Pigmentosa/genética , Xerodermia Pigmentosa/patología , Mutación , Síndromes de Tricotiodistrofia/genética , Síndromes de Tricotiodistrofia/patología , Ribosomas/genética , Ribosomas/metabolismo
18.
Nucleic Acids Res ; 51(3): 1019-1033, 2023 02 22.
Artículo en Inglés | MEDLINE | ID: mdl-36477609

RESUMEN

Nucleotide excision repair (NER) is critical for removing bulky DNA base lesions and avoiding diseases. NER couples lesion recognition by XPC to strand separation by XPB and XPD ATPases, followed by lesion excision by XPF and XPG nucleases. Here, we describe key regulatory mechanisms and roles of XPG for and beyond its cleavage activity. Strikingly, by combing single-molecule imaging and bulk cleavage assays, we found that XPG binding to the 7-subunit TFIIH core (coreTFIIH) stimulates coreTFIIH-dependent double-strand (ds)DNA unwinding 10-fold, and XPG-dependent DNA cleavage by up to 700-fold. Simultaneous monitoring of rates for coreTFIIH single-stranded (ss)DNA translocation and dsDNA unwinding showed XPG acts by switching ssDNA translocation to dsDNA unwinding as a likely committed step. Pertinent to the NER pathway regulation, XPG incision activity is suppressed during coreTFIIH translocation on DNA but is licensed when coreTFIIH stalls at the lesion or when ATP hydrolysis is blocked. Moreover, ≥15 nucleotides of 5'-ssDNA is a prerequisite for efficient translocation and incision. Our results unveil a paired coordination mechanism in which key lesion scanning and DNA incision steps are sequentially coordinated, and damaged patch removal is only licensed after generation of ≥15 nucleotides of 5'-ssDNA, ensuring the correct ssDNA bubble size before cleavage.


Nucleotide excision repair (NER) removes bulky DNA lesions and is thereby crucial in maintaining transcription and genomic integrity. Here, the authors show a dual function for the XPG nuclease that is critical for finding and excising the damage. During the separation of the damage-containing strand from the undamaged strand, XPG stimulates TFIIH dependent dsDNA unwinding 10 fold. In return, when TFIIH stalls at the damage it stimulates XPG nuclease activity 700 fold. Remarkably, this mutually exclusive coordination requires a bubble longer than 15 nucleotides. This study addressees why a bubble of a certain size is needed to facilitate NER and why XPG is recruited at the beginning of NER when its endonucleolytic activity is required at the very end.


Asunto(s)
Reparación del ADN , Factor de Transcripción TFIIH , ADN/metabolismo , Daño del ADN , ADN de Cadena Simple , Endonucleasas/metabolismo , Nucleótidos , Factor de Transcripción TFIIH/metabolismo
19.
BMC Cancer ; 22(1): 1181, 2022 Nov 16.
Artículo en Inglés | MEDLINE | ID: mdl-36384536

RESUMEN

BACKGROUND: Repair pathway genes play an important role in the development of lung cancer. The study aimed to assess the correlation between single nucleotide polymorphisms (SNPs) in DNA repair gene (GTF2H1 and RAD54L2) and the risk of lung cancer. METHODS: Five SNPs in GTF2H1 and four SNPs in RAD54L2 in 506 patients with lung cancer and 510 age-and gender-matched healthy controls were genotyped via the Agena MassARRAY platform. The influence of GTF2H1 and RAD54L2 polymorphisms on lung cancer susceptibility was assessed using logistic regression analysis by calculating odds ratios (ORs) and their corresponding 95% confidence intervals (CIs). RESULTS: RAD54L2 rs9864693 GC genotype increased the risk of lung cancer (OR = 1.33, 95%CI: 1.01-1.77, p = 0.045). Stratified analysis found that associations of RAD54L2 rs11720298, RAD54L2 rs4687592, RAD54L2 rs9864693 and GTF2H1 rs4150667 with lung cancer risk were found in subjects aged ≤ 59 years. Precisely, a protective effect of RAD54L2 rs11720298 on the occurrence of lung cancer was observed in non-smokers and drinkers. GTF2H1 rs4150667 was associated with a decreased risk of lung cancer in subjects with BMI ≤ 24 kg/m2. RAD54L2 rs4687592 was associated with an increased risk of lung cancer in drinkers. In addition, GTF2H1 rs3802967 was associated with a reduced risk of lung squamous cell carcinoma. CONCLUSION: Our study first revealed that RAD54L2 rs9864693 was associated with an increased risk of lung cancer in the Chinese Han population. This study may increase the understanding of the effect of RAD54L2 and GTF2H1 polymorphisms on lung cancer occurrence.


Asunto(s)
ADN Helicasas , Predisposición Genética a la Enfermedad , Neoplasias Pulmonares , Factor de Transcripción TFIIH , Humanos , Pueblo Asiatico/genética , China/epidemiología , Neoplasias Pulmonares/epidemiología , Neoplasias Pulmonares/genética , Polimorfismo de Nucleótido Simple , Factor de Transcripción TFIIH/genética , ADN Helicasas/genética
20.
Hum Mutat ; 43(12): 2222-2233, 2022 12.
Artículo en Inglés | MEDLINE | ID: mdl-36259739

RESUMEN

Trichothiodystrophy (TTD) is a rare hereditary disease whose prominent feature is brittle hair. Additional clinical signs are physical and neurodevelopmental abnormalities and in about half of the cases hypersensitivity to UV radiation. The photosensitive form of TTD (PS-TTD) is most commonly caused by mutations in the ERCC2/XPD gene encoding a subunit of the transcription/DNA repair complex TFIIH. Here we report novel ERCC2/XPD mutations affecting proper protein folding, which generate thermo-labile forms of XPD associated with thermo-sensitive phenotypes characterized by reversible aggravation of TTD clinical signs during episodes of fever. In patient cells, the newly identified XPD variants result in thermo-instability of the whole TFIIH complex and consequent temperature-dependent defects in DNA repair and transcription. Improving the protein folding process by exposing patient cells to low temperature or to the chemical chaperone glycerol allowed rescue of TFIIH thermo-instability and a concomitant recovery of the complex activities. Besides providing a rationale for the peculiar thermo-sensitive clinical features of these new cases, the present findings demonstrate how variations in the cellular concentration of mutated TFIIH impact the cellular functions of the complex and underlie how both quantitative and qualitative TFIIH alterations contribute to TTD clinical features.


Asunto(s)
Enfermedades del Cabello , Enfermedades de la Piel , Síndromes de Tricotiodistrofia , Xerodermia Pigmentosa , Humanos , Factor de Transcripción TFIIH/genética , Factor de Transcripción TFIIH/metabolismo , Síndromes de Tricotiodistrofia/genética , Síndromes de Tricotiodistrofia/complicaciones , Reparación del ADN , Enfermedades del Cabello/genética , Transcripción Genética , Xerodermia Pigmentosa/genética , Proteína de la Xerodermia Pigmentosa del Grupo D/genética , Proteína de la Xerodermia Pigmentosa del Grupo D/metabolismo
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