Transcription factor IIH: a key player in the cellular response to DNA damage

Lack of association between GTF2H4 genetic variants and AERD development and FEV1 decline by aspirin provocation

Aspirin-exacerbated respiratory disease (AERD) is prevalent in about 10% of asthma patients and is characterized by a severe decline in forced expiratory volume in 1-s (FEV(1) ), an important phenotype for total lung capacity, upon ingestion of aspirin. The general transcription factor IIH subunit 4 (GTF2H4) is positioned at 6p21.33, a part of the major histocompatibility complex (MHC) class II region that contains a number of genes that play an important role in the immune system. In addition, genetic variants in another general transcription factor IIH gene have revealed significant association with lung disease. To investigate whether GTF2H4 genetic variants could be a causative factor for AERD development and FEV(1) decline by aspirin provocation, five common single-nucleotide polymorphisms (SNPs) were genotyped in 93 patients with AERD and 96 aspirin-tolerant asthma (ATA) controls. As a result, when adjusted for age, gender, smoking status and atopy as covariates, the rs1264307 variant and two haplotypes showed nominal signals in the association with AERD (P = 0.02-0.04), but the significances disappeared after corrections for multiple testing (corrected P > 0.05). In further multiple regression analysis, no genetic variants of GTF2H4 showed significant associations with FEV(1) decline by aspirin provocation in asthmatics (P > 0.05). Despite the need for replications in larger cohorts, our preliminary findings suggest that GTF2H4 variants may not be associated with susceptibility to AERD and obstructive symptoms in asthmatics.

Characterization of ScMat1, a putative TFIIH subunit from sugarcane

The general transcription factor TFIIH is a multiprotein complex with different enzymatic activities such as helicase, protein kinase and DNA repair. MAT1 (ménage à trois 1) is one of the TFIIH subunits that has kinase activity and it is the third subunit of the cyclin-dependent kinase (CDK)-activating kinase (CAK), CDK7- cyclin H. The main objective of this work was to characterize ScMAT1, a sugarcane gene encoding a MAT1 homolog. Northern blots and in situ hybridization results showed that ScMAT1 was expressed in sugarcane mature leaf, leaf roll and inflorescence, and it was not differentially expressed in any of the other tissues analyzed such us bud and roots. In addition, ScMAT1 was not differentially expressed during different stress conditions and treatment with hormones. In situ hybridization analyses also showed that ScMAT1 was expressed in different cell types during leaf development. In order to identify proteins that interact with ScMAT1, a yeast two hybrid assay with ScMAT1 as bait was used to screen a sugarcane leaf cDNA library. The screening of yeast two hybrids yielded 14 positive clones. One of them is a cytochrome p450 family protein involved in oxidative degradation of toxic compounds. Other clones isolated are also related to plant responses to stress. To determine the subcellular localization of ScMAT1, a ScMAT1-GFP fusion was assayed in onion epidermal cell and the fluorescence was localized to the nucleus, in agreement with the putative role of ScMAT1 as a basal transcription factor.

Defective transcription/repair factor IIH recruitment to specific UV lesions in trichothiodystrophy syndrome

Most trichothiodystrophy (TTD) patients present mutations in the xeroderma pigmentosum D (XPD) gene, coding for a subunit of the transcription/repair factor IIH (TFIIH) complex involved in nucleotide excision repair (NER) and transcription. After UV irradiation, most TTD/XPD patients are more severely affected in the NER of cyclobutane pyrimidine dimers (CPD) than of 6-4-photoproducts (6-4PP). The reasons for this differential DNA repair defect are unknown. Here we report the first study of NER in response to CPDs or 6-4PPs separately analyzed in primary fibroblasts. This was done by using heterologous photorepair; recombinant adenovirus vectors carrying photolyases enzymes that repair CPD or 6-4PP specifically by using the energy of light were introduced in different cell lines. The data presented here reveal that some TTD/XPD mutations affect the recruitment of TFIIH specifically to CPDs, but not to 6-4PPs. This deficiency is further confirmed by the inability of TTD/XPD cells to recruit, specifically for CPDs, NER factors that arrive in a TFIIH-dependent manner later in the NER pathway. For 6-4PPs, we show that TFIIH complexes carrying an NH(2)-terminal XPD mutated protein are also deficient in recruitment of NER proteins downstream of TFIIH. Treatment with the histone deacetylase inhibitor trichostatin A allows the recovery of TFIIH recruitment to CPDs in the studied TTD cells and, for COOH-terminal XPD mutations, increases the repair synthesis and survival after UV, suggesting that this defect can be partially related with accessibility of DNA damage in closed chromatin regions.

Characterization of a TFIIH homologue from Trypanosoma brucei

Trypanosomes are protozoans showing unique transcription characteristics. We describe in Trypanosoma brucei a complex homologous to TFIIH, a multisubunit transcription factor involved in the control of transcription by RNA Pol I and RNA Pol II, but also in DNA repair and cell cycle control. Bioinformatics analyses allowed the detection of five genes encoding four putative core TFIIH subunits (TbXPD, TbXPB, Tbp44, Tbp52), including a novel XPB variant, TbXPBz. In all cases sequences known to be important for TFIIH functions were conserved. We performed a molecular analysis of this core complex, focusing on the two subunits endowed with a known enzymatic (helicase) activity, XPD and XPB. The involvement of these T. brucei proteins in a bona fide TFIIH core complex was supported by (i) colocalization by immunofluorescence in the nucleus, (ii) direct physical interaction of TbXPD and its interacting regulatory subunit Tbp44 as determined by double-hybrid assay and tandem affinity purification of the core TFIIH, (iii) involvement of the core proteins in a high molecular weight complex and (iv) occurrence of transcription, cell cycle and DNA repair phenotypes upon either RNAi knock-down or overexpression of essential subunits.

p8/TTD-A as a repair-specific TFIIH subunit

How subunits of the transcription/repair factor TFIIH cooperate to allow for the removal of DNA lesions or for the transcription of genes is crucial to understand the functioning of this complex. Here, we reveal that p8/TTD-A, the tenth subunit of TFIIH, has a critical role in DNA repair where it triggers DNA opening by stimulating XPB ATPase activity together with the damage recognition factor XPC-hHR23B. Fluorescent antibody labeling shows that such opening is needed for the recruitment of XPA to the site of the damage. By contrast, p8 is dispensable for RNA synthesis and doesn't interfere with the transcriptional function of CAK, although both interact with the XPD subunit. Interestingly, p8 overexpression in TTD-XPD cells counteracts the detrimental effect of XPD mutations by restoring the cellular TFIIH concentration. These findings resolve the primary functions of p8 and unveil how TFIIH components specifically direct the complex toward repair or transcription.

Human hair keratin-associated proteins (KAPs)

Elucidation of the genes encoding structural proteins of the human hair follicle has advanced rapidly during the last decade, complementing nearly three previous decades of research on this subject in other species. Primary among these advances was both the characterization of human hair keratins, as well as the hair keratin associated proteins (KAPs). This review describes the currently known human KAP families, their genomic organization, and their characteristics of expression. Furthermore, this report delves into further aspects, such as polymorphic variations in human KAP genes, the role that KAP proteins might play in hereditary hair diseases, as well as their modulation in several different transgenic mouse models displaying hair abnormalities.

TFIIH enzymatic activities in transcription and nucleotide excision repair

Transcription and nucleotide excision repair (NER) are two major mechanisms in which the transcription factor TFIIH plays a crucial role. In order to investigate its function, we first described a fast and efficient purification protocol of TFIIH from either HeLa cells or patient cell lines, as well as various in vitro enzymatic assays set up in our laboratory. All these enzymatic assays have been adapted to work on immobilized DNA, a powerful tool allowing for sequential protein incubations in various buffer conditions, without destabilizing protein complexes bound to the DNA. Runoff transcription assays performed with either whole cell extract or highly purified factors underline the role of TFIIH helicases (XPB and XPD) in the RNA synthesis. Moreover, the requirement of XPB and XPD in NER can also be investigated with various assays corresponding to the different steps of this process. The DNA opening assay (permanganate footprint) highlights DNA unwinding of the double-stranded DNA fragment within the repair complex, whereas the dual incision assay allows for detection of the double cut on both sides of the lesion. The gap-filling reaction following the cuts can be monitored as well with a DNA resynthesis assay. Futhermore, the use of immobilized DNA is of great interest to study the detailed mechanism in which TFIIH plays a central role. This chapter describes the ATP-independent recruitment of TFIIH on the damaged DNA previously recognized by XPC-hHR23B and the sequential arrival and departure of the repair proteins within the NER complex.

Making myc

Myc regulates to some degree every major process in the cell. Proliferation, growth, differentiation, apoptosis, and metabolism are all under myc control. In turn, these processes feed back to adjust the level of c-myc expression. Although Myc is regulated at every level from RNA synthesis to protein degradation, c-myc transcription is particularly responsive to multiple diverse physiological and pathological signals. These signals are delivered to the c-myc promoter by a wide variety of transcription factors and chromatin remodeling complexes. How these diverse and sometimes disparate signals are processed to manage the output of the c-myc promoter involves chromatin, recruitment of the transcription machinery, post-initiation transcriptional regulation, and mechanisms to provide dynamic feedback. Understanding these mechanisms promises to add new dimensions to models of transcriptional control and to reveal new strategies to manipulate Myc levels.

Solution Structure of the C-terminal Domain of TFIIH P44 Subunit Reveals a Novel Type of C4C4 Ring Domain Involved in Protein-Protein Interactions

The human general transcription factor TFIIH is involved in both transcription and DNA nucleotide excision repair. Among the 10 subunits of the complex, p44 subunit plays a crucial role in both mechanisms. Its N-terminal domain interacts with the XPD helicase, whereas its C-terminal domain is involved specifically in the promoter escape activity. By mutating an exposed and non-conserved cysteine residue into a serine, we produced a soluble mutant of p44-(321-395) suitable for solution structure determination. The domain adopts a C4C4 RING domain structure with sequential organization of beta-strands that is related to canonical RING domains by a circular permutation of the beta-sheet elements. Analysis of the molecular surface and mutagenesis experiments suggests that the binding of p44-(321-395) to TFIIH p34 subunit is not mediated by electrostatic interactions and, thus, differs from previously reported interaction mechanisms involving RING domains.

Retracted: In vivopotentiation of human oestrogen receptor α by Cdk7-mediated phosphorylation

Phosphorylation of the Ser(118) residue in the N-terminal A/B domain of the human oestrogen receptor alpha (hERalpha) by mitogen-activated protein kinase (MAPK), stimulated via growth factor signalling pathways, is known to potentiate ERalpha ligand-induced transactivation function. Besides MAPK, cyclin dependent kinase 7 (Cdk7) in the TFIIH complex has also been found to potentiate hERalpha transactivation in vitro through Ser(118) phosphorylation. To investigate an impact of Cdk7 on hERalpha transactivation in vivo, we assessed activity of hERalpha in a wild-type and cdk7 inactive mutant Drosophila that ectopically expressed hERalpha in the eye disc. Ectopic expression of the wild-type or mutant receptors, together with a green fluorescent protein (GFP) reporter gene, allowed us to demonstrate that hERalpha expressed in the fly tissues was transcriptionally functional and adequately responded to hERalpha ligands in the patterns similar to those observed in mammalian cells. Replacement of Ser(118) with alanine in hERalpha (S118A mutant) significantly reduced the ligand-induced hERalpha transactivation function. Importantly, while in cdk7 inactive mutant Drosophila the wild-type hERalpha exhibited reduced response to the ligand; levels of transactivation by the hERalpha S118A mutant were not affected in these inactive cdk7 mutant flies. Furthermore, phosphorylation of hERalpha at Ser(118) has been observed in vitro by both human and Drosophila Cdk7. Our findings demonstrate that Cdk7 is involved in regulation of the ligand-induced transactivation function of hERalphain vivo via Ser(118) phosphorylation.

Activation of gene expression by triplex-directed psoralen crosslinks

Psoralen-conjugated triplex-forming oligonucleotides (pso-TFOs) can target photochemical adducts to specific DNA sequences. Here, we have used pso-TFOs to activate gene expression on a plasmid. We designed a pso-TFO adapter, consisting of a single-stranded TFO for targeting DNA, linked to a double-stranded hairpin segment that contains a hybrid ecdysone response element (E/GRE) enhancer for binding activated ecdysone receptors. When targeted to the 5' flanking region of a minimal promoter, this pso-TFO adapter increased the expression of a downstream reporter gene three- to four-fold. Gene activation, however, was independent of both the E/GRE hairpin of the adapter and ecdysone receptors, suggesting it was due to an intrinsic effect of triplex. Gene activation was dependent on psoralen photo-crosslinking. Gene activation by pso-TFOs in which the psoralen was linked to the TFO via a disulfide bond was similar before and after detachment of the TFO and its release from the triplex. These results indicate that psoralen photo-crosslinks play a prominent role in activation. Gene activation was undiminished in XPA, XPD and XPG human cell lines, indicating that activation was not dependent on the complete nucleotide excision repair (NER) pathway. Collectively, these results demonstrate that TFOs can be used to direct psoralen crosslinks adjacent to a gene as a way of activating gene expression.

Interaction of estrogen receptor alpha with 3-methyladenine DNA glycosylase modulates transcription and DNA repair

Estrogen receptor alpha (ERalpha) interacts with basal transcription factors, coregulatory proteins, and chromatin modifiers to initiate transcription of the target genes. We have identified a novel interaction between ERalpha and the DNA repair protein 3-methyladenine DNA glycosylase (MPG) thereby providing a functional link between gene expression and DNA repair. Interestingly, the ERalpha-MPG interaction was enhanced by the presence of estrogen response element (ERE)-containing DNA. In vitro pull-down assays indicated that the interaction of ERalpha with MPG was direct and occurred through the DNA- and ligand-binding domains and the hinge region of the receptor. More importantly, endogenously expressed ERalpha and MPG from MCF-7 cells coimmunoprecipitated with ERalpha- and MPG-specific antibodies. The ERalpha-MPG interaction had functional consequences on the activities of both proteins. ERalpha increased MPG acetylation, stabilized the binding of MPG with hypoxanthine-containing oligos, and enhanced MPG-catalyzed removal of hypoxanthine from DNA. In turn, MPG dramatically stabilized the interaction of ERalpha with ERE-containing oligos, decreased p300-mediated acetylation of the receptor, and reduced transcription of simple and complex ERE-containing reporter plasmids in a dose-dependent manner. Our studies suggest that recruitment of MPG to ERE-containing genes influences transcription and plays a role in maintaining integrity of the genome by recruiting DNA repair proteins to actively transcribing DNA.

TFIIH Transcription Factor, a Target for the Rift Valley Hemorrhagic Fever Virus

The Rift Valley fever virus (RVFV) is the causative agent of fatal hemorrhagic fever in humans and acute hepatitis in ruminants. We found that infection by RVFV leads to a rapid and drastic suppression of host cellular RNA synthesis that parallels a decrease of the TFIIH transcription factor cellular concentration. Using yeast two hybrid system, recombinant technology, and confocal microscopy, we further demonstrated that the nonstructural viral NSs protein interacts with the p44 component of TFIIH to form nuclear filamentous structures that also contain XPB subunit of TFIIH. By competing with XPD, the natural partner of p44 within TFIIH, and sequestering p44 and XPB subunits, NSs prevents the assembly of TFIIH subunits, thus destabilizing the normal host cell life. These observations shed light on the mechanism utilized by RVFV to evade the host response.

The transcriptional complexity of the TFIIH complex

Mutations in some subunits of the basal DNA repair and transcription factor II H (TFIIH) are involved in several human genetic disorders. Transcription factor II H interacts with a variety of factors during transcription, including nuclear receptors, tissue-specific transcription factors, chromatin remodeling complexes and RNA, suggesting that, in addition to its essential role in transcription initiation, it also participates as a regulatory factor. Interpretation of the phenotypes produced by mutations in TFIIH is complicated by the recent finding that TFIIH plays a role in RNA polymerase I (RNA Pol I)-mediated transcription. In vitro reconstituted systems and genetic analysis suggest two possible explanations for the transcriptional phenotypes of TFIIH mutations that are not mutually excluding. The first is that different sets of genes require different levels of transcription to maintain a wild-type phenotype. The second suggests that mutations in TFIIH produce specific phenotypes arising from differential interactions of this complex with different transcription regulatory factors.

Xeroderma pigmentosum group A protein loads as a separate factor onto DNA lesions

Nucleotide excision repair (NER) is the main DNA repair pathway in mammals for removal of UV-induced lesions. NER involves the concerted action of more than 25 polypeptides in a coordinated fashion. The xeroderma pigmentosum group A protein (XPA) has been suggested to function as a central organizer and damage verifier in NER. How XPA reaches DNA lesions and how the protein is distributed in time and space in living cells are unknown. Here we studied XPA in vivo by using a cell line stably expressing physiological levels of functional XPA fused to green fluorescent protein and by applying quantitative fluorescence microscopy. The majority of XPA moves rapidly through the nucleoplasm with a diffusion rate different from those of other NER factors tested, arguing against a preassembled XPA-containing NER complex. DNA damage induced a transient ( approximately 5-min) immobilization of maximally 30% of XPA. Immobilization depends on XPC, indicating that XPA is not the initial lesion recognition protein in vivo. Moreover, loading of replication protein A on NER lesions was not dependent on XPA. Thus, XPA participates in NER by incorporation of free diffusing molecules in XPC-dependent NER-DNA complexes. This study supports a model for a rapid consecutive assembly of free NER factors, and a relatively slow simultaneous disassembly, after repair.

Xpd/Ercc2 regulates CAK activity and mitotic progression

General transcription factor IIH (TFIIH) consists of nine subunits: cyclin-dependent kinase 7 (Cdk7), cyclin H and MAT1 (forming the Cdk-activating-kinase or CAK complex), the two helicases Xpb/Hay and Xpd, and p34, p44, p52 and p62 (refs 1-3). As the kinase subunit of TFIIH, Cdk7 participates in basal transcription by phosphorylating the carboxy-terminal domain of the largest subunit of RNA polymerase II. As part of CAK, Cdk7 also phosphorylates other Cdks, an essential step for their activation. Here we show that the Drosophila TFIIH component Xpd negatively regulates the cell cycle function of Cdk7, the CAK activity. Excess Xpd titrates CAK activity, resulting in decreased Cdk T-loop phosphorylation, mitotic defects and lethality, whereas a decrease in Xpd results in increased CAK activity and cell proliferation. Moreover, Xpd is downregulated at the beginning of mitosis when Cdk1, a cell cycle target of Cdk7, is most active. Downregulation of Xpd thus seems to contribute to the upregulation of mitotic CAK activity and to regulate mitotic progression positively. Simultaneously, the downregulation of Xpd might be a major mechanism of mitotic silencing of basal transcription.

Regulation of RelA (p65) function by the large subunit of replication factor C

The RelA (p65) subunit of NF-kappaB is an important regulator of inflammation, proliferation, and apoptosis. We have discovered that the large subunit, p140, of replication factor C (RFC) can function as a regulator of RelA. RFC is a clamp loader, facilitating the addition and removal of proliferating-cell nuclear antigen from DNA during replication and repair but can also interact directly with the retinoblastoma tumor suppressor protein and the transcription factor C/EBPalpha. We find that RFC (p140) interacts with RelA both in vitro and in vivo and stimulates RelA transactivation. In contrast, coexpression of fragments of RFC (p140) that mediate the interaction with RelA results in transcriptional inhibition. The significance of this regulation was confirmed by using short interfering RNA oligonucleotides targeted to RFC (p140). Down regulation of endogenous RFC (p140) inhibits expression from a chromosomally integrated reporter plasmid induced by endogenous, TNF-alpha-activated NF-kappaB. Dominant negative fragments of RFC (p140) also cooperate with overexpressed RelA to induce cell death. Interestingly, RFC (p140) also interacts with the tumor suppressor p53. Taken together, these observations suggest that, in addition to its previously described function in DNA replication and repair, RFC (p140) has an important role as a regulator of transcription and NF-kappaB activity.

Mutations in the RING domain of TFB3, a subunit of yeast transcription factor IIH, reveal a role in cell cycle progression

The RNA polymerase II general transcription factor TFIIH is composed of 9 known subunits and possesses DNA helicase and protein kinase activities. The kinase subunits of TFIIH in animal cells, Cdk7, cyclin H, and MAT1, were independently isolated as an activity termed CAK (Cdk-activating kinase), which phosphorylates and activates cell cycle kinases. However, CAK activity of TFIIH subunits could not be demonstrated in budding yeast. TFB3, the 38-kDa subunit of yeast TFIIH, is the homolog of mammalian MAT1. By random mutagenesis we have isolated a temperature-sensitive mutation in the conserved RING domain. The mutant Tfb3 protein associates less efficiently with the kinase moiety of TFIIH than the wild type protein. In contrast to lethal mutants in other subunits of TFIIH, this mutation does not impair general transcription. Transcription of CLB2, and possibly other genes, is reduced in the mutant. At the restrictive temperature, the cells display a defect in cell cycle progression, which is manifest at more than one phase of the cycle. To conclude, in the present study we bring another demonstration of the multifunctional nature of TFIIH.

Linking activators and basals in transcription: it is all in one family

Analysis of nuclear hormone receptor function in cells derived from xeroderma pigmentosum patients reveals novel links between DNA repair and transcription and points to novel mechanisms of regulating transcriptional regulators.

The founding members of xeroderma pigmentosum group G produce XPG protein with severely impaired endonuclease activity

Of the eight human genes implicated in xeroderma pigmentosum, defects in XPG produce some of the most clinically diverse symptoms. These range from mild freckling to severe skeletal and neurologic abnormalities characteristic of Cockayne syndrome. Mildly affected xeroderma pigmentosum group G patients have diminished XPG endonuclease activity in nucleotide excision repair, whereas severely affected xeroderma pigmentosum group G/Cockayne syndrome patients produce truncated XPG proteins that are unable to function in either nucleotide excision repair or the transcription-coupled repair of oxidative lesions. The first two xeroderma pigmentosum group G patients, XP2BI and XP3BR, were reported before the relationship between xeroderma pigmentosum group G and Cockayne syndrome was appreciated. Here we provide evidence that both patients produce truncated proteins from one XPG allele. From the second allele, XP2BI generates full-length XPG of 1186 amino acids containing a single L858P substitution that has reduced stability and greatly impaired endonuclease activity. In XP3BR, a single base deletion and alternative splicing at a rare noncanonical AT-AC intron produces a 1185 amino acid protein containing 44 internal non-XPG residues. This protein is stably expressed but it also has greatly impaired endonuclease activity. These four XPG products can thus account for the severe ultraviolet sensitivity of XP2BI and XP3BR fibroblasts. These cells, unlike those from xeroderma pigmentosum group G/Cockayne syndrome patients, are capable of limited transcription-coupled repair of oxidative lesions. Our results suggest that the L858P protein in XP2BI and the almost full-length XPG protein in XP3BR are responsible for this activity and for the absence of severe early onset Cockayne syndrome symptoms in these patients.

Mechanisms of transcription-coupled DNA repair

Several types of helix-distorting DNA lesions block the passage of elongating RNA polymerase II. Surprisingly, such transcription-blocking lesions are usually repaired considerably faster than non-obstructive lesions in the non-transcribed strand or in the genome overall. In this review, our knowledge of eukaryotic transcription-coupled repair (TCR) will be considered from the point of view of transcription, and current models for the mechanism of TCR will be discussed.

TFIIH inhibits CDK9 phosphorylation during human immunodeficiency virus type 1 transcription

Tat stimulates human immunodeficiency virus, type 1 (HIV-1), transcription elongation by recruitment of the human transcription elongation factor P-TEFb, consisting of CDK9 and cyclin T1, to the TAR RNA structure. It has been demonstrated further that CDK9 phosphorylation is required for high affinity binding of Tat/P-TEFb to the TAR RNA structure and that the state of P-TEFb phosphorylation may regulate Tat transactivation. We now demonstrate that CDK9 phosphorylation is uniquely regulated in the HIV-1 preinitiation and elongation complexes. The presence of TFIIH in the HIV-1 preinitiation complex inhibits CDK9 phosphorylation. As TFIIH is released from the elongation complex between +14 and +36, CDK9 phosphorylation is observed. In contrast to the activity in the "soluble" complex, phosphorylation of CDK9 is increased by the presence of Tat in the transcription complexes. Consistent with these observations, we have demonstrated that purified TFIIH directly inhibits CDK9 autophosphorylation. By using recombinant TFIIH subcomplexes, our results suggest that the XPB subunit of TFIIH is responsible for this inhibition of CDK9 phosphorylation. Interestingly, our results further suggest that the phosphorylated form of CDK9 is the active kinase for RNA polymerase II carboxyl-terminal domain phosphorylation.

Early postnatal ataxia and abnormal cerebellar development in mice lacking Xeroderma pigmentosum Group A and Cockayne syndrome Group B DNA repair genes

Xeroderma pigmentosum (XP) and Cockayne syndrome (CS) are rare autosomal recessive disorders associated with a defect in the nucleotide excision repair (NER) pathway required for the removal of DNA damage induced by UV light and distorting chemical adducts. Although progressive neurological dysfunction is one of the hallmarks of CS and of some groups of XP patients, the causative mechanisms are largely unknown. Here we show that mice lacking both the XPA (XP-group A) and CSB (CS-group B) genes in contrast to the single mutants display severe growth retardation, ataxia, and motor dysfunction during early postnatal development. Their cerebella are hypoplastic and showed impaired foliation and stunted Purkinje cell dendrites. Reduced neurogenesis and increased apoptotic cell death occur in the cerebellar external granular layer. These findings suggest that XPA and CSB have additive roles in the mouse nervous system and support a crucial role for these genes in normal brain development.

Effects of XPD mutations on ultraviolet-induced apoptosis in relation to skin cancer-proneness in repair-deficient syndromes

To understand the relationship between DNA repair, apoptosis, transcription, and cancer-proneness, we have studied the apoptotic response and the recovery of RNA synthesis following ultraviolet C and ultraviolet B irradiation in nucleotide excision repair deficient diploid fibroblasts from the cancer-prone xeroderma pigmentosum (XP) syndrome patients and the non-cancer-prone trichothiodystrophy (TTD) patients. Analysis of four XPD and four TTD/XPD fibroblast strains presenting different mutations on the XPD gene has shown that XPD cells are more sensitive to ultraviolet-induced apoptosis than TTD/XPD cells, and this response seems to be modulated by the type and the location of the mutation on the XPD gene. Moreover, the other xeroderma pigmentosum fibroblast strains analyzed (groups A and C) are more sensitive to undergo apoptosis after ultraviolet irradiation than normal human fibroblasts, showing that the cancer-proneness of xeroderma pigmentosum patients is not due to a deficiency in the ultraviolet-induced apoptotic response. We have also found that cells from transcription-coupled repair deficient XPA, XPD, TTD/XPD, and Cockayne's syndrome patients undergo apoptosis at lower ultraviolet doses than transcription-coupled repair proficient cells (normal human fibroblasts and XPC), indicating that blockage of RNA polymerase II at unrepaired lesions on the transcribed strand is the trigger. Moreover, XPD and XPA cells are more sensitive to ultraviolet-induced apoptosis than trichothiodystrophy and Cockayne's syndrome fibroblasts, suggesting that both cyclobutane pyrimidine dimers and pyrimidine 6-4 pyrimidone on the transcribed strand trigger apoptosis. Finally, we show that apoptosis is directly proportional to the level of inhibition of transcription, which depends on the density of ultraviolet-induced lesions occurring on transcribed sequences.

A role of the C-terminal part of p44 in the promoter escape activity of transcription factor IIH

The p44 subunit plays a crucial role in the overall activity of the transcription/DNA repair factor TFIIH: on the one hand its N-terminal domain interacts with and regulates the XPD helicase (, ); on the other hand, as shown in the present study, it participates with the promoter escape reaction. Mutagenesis along with recombinant technology using the baculovirus/insect cells expression system allowed us to define the function of the two structural motifs of the C-terminal moiety of p44: mutations within the C4 zinc finger motif (residues 291-308) prevent incorporation of the p62 subunit within the core TFIIH. Double mutations in the RING finger motif (residues 345-385) allow the synthesis of the first phosphodiester bond by RNA polymerase II, but prevent its escape from the promoter. This highlights the role of transcription factor IIH in the various steps of the transcription initiation process.

The 14th Datta Lecture. TFIIH: from transcription to clinic

Once a large proportion of the genes responsible for genetic disorders are identified in the post-genome era, the fundamental challenge is to establish a genotype/phenotype relationship. Our aim is to explain how mutations in a given gene affect its enzymatic function and, in consequence, disturb the life of the cell. Genome integrity is continuously threatened by the occurrence of DNA damage arising from cellular exposure to irradiation and genotoxic chemicals. This mutagenic or potentially lethal DNA damage induces various cellular responses including cell cycle arrest, transcription alteration and processing by DNA repair mechanisms, such as the nucleotide excision repair (NER) pathway. Disruption of NER in response to genotoxic injuries results in autosomal recessive hereditary diseases such as Xeroderma pigmentosum (XP), Cockayne syndrome (CS) and trichothiodystrophy (TTD). One of the most immediate consequences of the induction of strand-distorting lesions is the arrest of transcription in which TFIIH plays a role in addition to its role in DNA repair. The observations made by clinicians close to XP, TTD and CS patients, suggested that transcription defects responsible for brittle hair and nails for TTD, or developmental abnormalities for CS, resulted from TFIIH mutations. Here a story will be related which could be called 'a multi-faceted factor named TFIIH'. As biochemists, we have characterized each component of TFIIH, three of which are XPB and XPD helicases and cdk7, a cyclin-dependent kinase. With the help of structural biologists, we have characterized most of the specific three-dimensional structures of TFIIH subunits and obtained its electron microscopy image. Together these approaches help us to propose a number of structure-function relationships for TFIIH. Through transfection and microinjection assays, cell biology allows us to determine the role of TFIIH in transcription and NER. We are thus in a position to explain, at least in part, transcription initiation mechanisms and their coupling to DNA repair. We now know how the XPB helicase opens the promoter region for RNA synthesis and that one of the roles of XPD helicase is to anchor the cdk7 kinase to the core-TFIIH. In XP and CS associated patients, we have demonstrated that some XPD mutations prevent an optimal phosphorylation of nuclear receptors by cdk7 with, as a consequence, a drop in the expression of genes sensitive to hormone action. We have thus shown that hormonal responses operate through TFIIH. Careful analysis of each TFIIH subunit also shows how the p44 Ring finger participates in certain promoter escape reactions. We are also able to localize the action of TFIIH in the sequence of events that lead to the elimination of DNA lesions. Thanks to the combination of these different approaches we are obtaining a much clearer picture of the TFIIH complex and its integration into the life of the cell.

Solution structure of the N-terminal domain of the human TFIIH MAT1 subunit: new insights into the RING finger family

The human MAT1 protein belongs to the cyclin-dependent kinase-activating kinase complex, which is functionally associated to the transcription/DNA repair factor TFIIH. The N-terminal region of MAT1 consists of a C3HC4 RING finger, which contributes to optimal TFIIH transcriptional activities. We report here the solution structure of the human MAT1 RING finger domain (Met(1)-Asp(65)) as determined by (1)H NMR spectroscopy. The MAT1 RING finger domain presents the expected betaalphabetabeta topology with two interleaved zinc-binding sites conserved among the RING family. However, the presence of an additional helical segment in the N-terminal part of the domain and a conserved hydrophobic central beta strand are the defining features of this new structure and more generally of the MAT1 RING finger subfamily. Comparison of electrostatic surfaces of RING finger structures shows that the RING finger domain of MAT1 presents a remarkable positively charged surface. The functional implications of these MAT1 RING finger features are discussed.

Codominance associated with overexpression of certain XPD mutations

Mutations in the XPD gene are associated with three complex clinical phenotypes, namely xeroderma pigmentosum (XP), XP in combination with Cockayne syndrome (XP-CS), and trichothiodystrophy (TTD). XP is caused by a deficiency in nucleotide excision repair (NER) that results in a high risk of skin cancer. TTD is characterized by severe developmental and neurological defects, with hallmark features of brittle hair and scaly skin, and sometimes has defective NER. We used CHO cells as a system to study how specific mutations alter the dominant/recessive behavior of XPD protein. Previously we identified the T46I and R75W mutations in two highly UV-sensitive hamster cell lines that were reported to have paradoxically high levels of unscheduled DNA synthesis. Here we report that these mutants have greatly reduced XPD helicase activity and fully defective NER in a cell-extract excision assay. We conclude that the unscheduled DNA synthesis seen in these mutants is caused by abortive "repair" that does not contribute to cell survival. These mutations, as well as the K48R canonical helicase-domain mutation, each produced codominant negative phenotypes when overexpressed in wild-type CHO cells. The common XP-specific R683W mutation also behaved in a codominant manner when overexpressed, which is consistent with the idea that this mutation may affect primarily the enzymatic activity of the protein rather than impairing protein interactions, which may underlie TTD. A C-terminal mutation uniquely found in TTD (R722W) was overexpressed but not to levels sufficiently high to rigorously test for a codominant phenotype. Overexpression of mutant XPD alleles may provide a simple means of producing NER deficiency in other cell lines.

Nuclear targeting determinants of the far upstream element binding protein, a c-myc transcription factor

FUSE binding protein (FBP) binds in vivo and in vitro with the single-stranded far upstream element (FUSE) upstream of the c-myc gene. In addition to its transcriptional role, FBP and its closely related siblings FBP2 (KSRP) and FBP3 have been reported to bind RNA and participate in various steps of RNA processing, transport or catabolism. To perform these diverse functions, FBP must traffic to different nuclear sites. To identify determinants of nuclear localization, full-length FBP or fragments thereof were fused to green fluorescent protein. Fluorescent-FBP localized in the nucleus in three patterns, diffuse, dots and spots. Each pattern was conferred by a distinct nuclear localization signal (NLS): a classical bipartite NLS in the N-terminal and two non-canonical signals, an alpha-helix in the third KH-motif of the nucleic acid binding domain and a tyrosine-rich motif in the C-terminal transcription activation domain. Upon treatment with the transcription inhibitor actinomycin D, FBP completely re-localized into dots, but did not exit from the nucleus. This is in contrast to many general RNA-binding proteins, which shuttle from the nucleus upon treatment with actinomycin D. Furthermore, FBP co-localized with transcription sites and with the general transcription factor TFIIH, but not with the splicing factor SC-35. Taken together, these data reveal complex intranuclear trafficking of FBP and support a transcriptional role for this protein.

Cytoplasmic and nuclear localization of the 130 and 160 kDa Bcr proteins

Formation of the Bcr-Abl chimeric protein is the molecular hallmark of Philadelphia-positive leukemia. Normal Bcr is a complex protein which has been found in the cytoplasm, has serine kinase activity, and has been implicated in cellular signal transduction. However, we have recently demonstrated that Bcr can also associate with condensed chromatin. Since two major Bcr proteins have been characterized (p160Bcr and p130Bcr), we sought to determine if different forms of Bcr localized to the nucleus vs the cytoplasm. Metabolic labeling and Western blotting experiments were performed using nuclear and cytoplasmic extracts of three human Philadelphia-negative leukemia/lymphoma cell lines (KG-1, HL-60, and Jurkat). Both methodologies showed that p160Bcr and p130Bcr localized to the cytoplasm, but the p130 form predominated in the nucleus. These results suggest that Bcr serves both nuclear and cytoplasmic functions, and that different forms of Bcr may be preferentially involved in these distinct activities.

Human pre-mRNA cleavage factor II(m) contains homologs of yeast proteins and bridges two other cleavage factors

Six different protein factors are required in vitro for 3' end formation of mammalian pre-mRNAs by endonucleolytic cleavage and polyadenylation. Five of the factors have been purified and most of their components cloned, but cleavage factor II(m) (CF II(m)) remained uncharacterized. We have purified CF II(m) from HeLa cell nuclear extract by several chromatographic steps. During purification, CF II(m) activity separated into two components, one essential (CF IIA(m)) and one stimulatory (CF IIB(m)) for the cleavage reaction. CF IIA(m) fractions contain the human homologs of two yeast 3' end processing factors, Pcf11p and Clp1p, as well as cleavage factor I(m) (CF I(m)) and several splicing and transcription factors. We report the cloning of hClp1 and show that it is a genuine subunit of CF IIA(m). Antibodies directed against hClp1 deplete cleavage activity, but not polyadenylation activity from HeLa cell nuclear extract. hClp1 interacts with CF I(m) and the cleavage and polyadenylation specificity factor CPSF, suggesting that it bridges these two 3' end processing factors within the cleavage complex.

p44/SSL1, the regulatory subunit of the XPD/RAD3 helicase, plays a crucial role in the transcriptional activity of TFIIH

In order to unravel the mechanism that regulates transcription of protein-coding genes, we investigated the function of the p44 subunit of TFIIH, a basal transcription factor that is also involved in DNA repair. We have shown previously that mutations in the C terminus of the XPD helicase, another subunit of TFIIH, prevent its regulation by p44 (Coin, F., Bergmann, E., Tremeau-Bravard, A., and Egly, J. M. (1999) EMBO 18, 1357-1366). By using a site-directed mutagenesis approach within the p44 region from amino acids 66 to 200, we indicate how a decrease in the interaction between p44 and XPD results in a decrease of the XPD helicase activity and leads to a defect in the first steps of the transcription reaction, namely the first phosphodiester bond formation and promoter clearance. We thus provide some explanation for the transcriptional defect found in SSL1 mutated yeast (Wang, Z., Buratowski, S., Svejstrup, J. Q., Feaver, W. J., Wu, X., Kornberg, R. D., Donahue, T. F., and Friedberg, E. C. (1995) Mol. Cell. Biol. 15, 2288-2293). Moreover, this study shows how the activity of the the cyclin-dependent kinase-activating kinase associated with TFIIH complex in stimulating transcription is mediated in part by p44/XPD interaction.

Distinct regions of MAT1 regulate cdk7 kinase and TFIIH transcription activities

The transcription/DNA repair factor TFIIH may be resolved into at least two subcomplexes: the core TFIIH and the cdk-activating kinase (CAK) complex. The CAK complex, which is also found free in the cell, is composed of cdk7, cyclin H, and MAT1. In the present work, we found that the C terminus of MAT1 binds to the cdk7 x cyclin H complex and activates the cdk7 kinase activity. The median portion of MAT1, which contains a coiled-coil motif, allows the binding of CAK to the TFIIH core through interactions with both XPD and XPB helicases. Furthermore, using recombinant TFIIH complexes, it is demonstrated that the N-terminal RING finger domain of MAT1 is crucial for transcription activation and participates to the phosphorylation of the C-terminal domain of the largest subunit of the RNA polymerase II.

Decreased DNA repair efficiency by loss or disruption of p53 function preferentially affects removal of cyclobutane pyrimidine dimers from non-transcribed strand and slow repair sites in transcribed strand

The tumor suppressor protein p53 plays a central role in modulating the cellular responses to DNA damage. Several recent studies, undertaken with the whole genomic DNA or full-length gene segments, have shown that p53 is involved in nucleotide excision repair and it selectively influences the adduct removal from the non-transcribed strand in the genome. In this study, we have analyzed the damage induction at nucleotide resolution by ligase-mediated polymerase chain reaction and compared the repair of ultraviolet radiation-induced cyclobutane pyrimidine dimers within exon 8 of p53 gene in normal and Li-Fraumeni syndrome fibroblasts as well as in normal and human papillomavirus 16 E6 and E7 protein-expressing human mammary epithelial cells. The results demonstrate that (i) loss or disruption of p53 function decreases efficiency of DNA repair, by preferentially affecting the repair of non-transcribed strand and of intrinsically slow repair sites in transcribed strand; (ii) mutant p53 protein affects DNA repair, at least of non-transcribed strand, in a dominant negative manner; and (iii) pRb does not have an effect on the repair of DNA damage within transcribed or non-transcribed strand. The overall data suggest that p53 could regulate excision repair or related events through direct protein-protein interaction.

Peeling by binding or twisting by cranking: models for promoter opening and transcription initiation by RNA polymerase II

The precise, sequence-specific regulation of RNA synthesis is the primary mechanism underlying differential gene expression. This general statement applies to both prokaryotic and eukaryotic organisms, as well as to their viral pathogens. Thus, it is not surprising that genomes use a substantial portion of their protein-coding content to regulate the process of RNA synthesis. Transcriptional regulation in bacterial systems is particularly well understood. In this essay, we build on this knowledge and propose two opposing models to describe promoter opening and transcription initiation in the eukaryotic RNA polymerase II system. Promoter opening in the "twisting by cranking" model is based on changes in the trajectory of DNA. In contrast, invasion of single-stranded DNA-binding proteins between the DNA strands drives the reaction in the "peeling by binding" model.

The FBP interacting repressor targets TFIIH to inhibit activated transcription

FUSE-binding protein (FBP) binds the single-stranded far upstream element of active c-myc genes, possesses potent transcription activation and repression domains, and is necessary for c-myc expression. A novel 60 kDa protein, the FBP interacting repressor (FIR), blocked activator-dependent, but not basal, transcription through TFIIH. Recruited through FBP's nucleic acid-binding domain, FIR formed a ternary complex with FBP and FUSE. FIR repressed a c-myc reporter via the FUSE. The amino terminus of FIR contained an activator-selective repression domain capable of acting in cis or even in trans in vivo and in vitro. The repression domain of FIR targeted only TFIIH's p89/XPB helicase, required at several stages in transcription, but not factors required for promoter selection. Thus, FIR locks TFIIH in an activation-resistant configuration that still supports basal transcription.

Phosphorylation in transcription: the CTD and more

Phosphorylation appears to be one mechanism in the regulation of transcription. Indeed, a multitude of factors involved in distinct steps of transcription, including RNA polymerase II, the general transcription factors, pre-mRNA processing factors, and transcription activators/repressors are phosphoproteins and serve as substrates for multiple kinases. Among these substrates, most attention has been paid in recent years to the phosphorylation of the carboxyl-terminal domain (CTD) of RNA polymerase II and its role in transcription regulation. Kinases responsible for such CTD phosphorylation that are associated with RNA polymerase II at distinct steps of transcription, such as cdk7 and cdk8, also phosphorylate some other components of the transcription machinery in a regulatory manner. These observations enlighten the pivotal role of such kinases in an entangled regulation of transcription by phosphorylation. Summarizing the phosphorylation of various components of the transcription machinery, we point out the variety of steps in transcription that are regulated by such protein modifications, envisioning an interconnection of the several stages of mRNA synthesis by phosphorylation.