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1.
DNA Repair (Amst) ; 141: 103714, 2024 Sep.
Artículo en Inglés | MEDLINE | ID: mdl-38943827

RESUMEN

The Mediator complex is an essential coregulator of RNA polymerase II transcription. More recent developments suggest Mediator functions as a link between transcription regulation, genome organisation and DNA repair mechanisms including nucleotide excision repair, base excision repair, and homologous recombination. Dysfunctions of these processes are frequently associated with human pathologies, and growing evidence shows Mediator involvement in cancers, neurological, metabolic and infectious diseases. The detailed deciphering of molecular mechanisms of Mediator functions, using interdisciplinary approaches in different biological models and considering all functions of this complex, will contribute to our understanding of relevant human diseases.


Asunto(s)
Reparación del ADN , Complejo Mediador , Transcripción Genética , Humanos , Complejo Mediador/metabolismo , Complejo Mediador/genética , Neoplasias/genética , Neoplasias/metabolismo , Regulación de la Expresión Génica , ARN Polimerasa II/metabolismo , Animales
2.
PLoS Comput Biol ; 20(1): e1011799, 2024 Jan.
Artículo en Inglés | MEDLINE | ID: mdl-38266035

RESUMEN

In eukaryotic cells, the one-dimensional DNA molecules need to be tightly packaged into the spatially constraining nucleus. Folding is achieved on its lowest level by wrapping the DNA around nucleosomes. Their arrangement regulates other nuclear processes, such as transcription and DNA repair. Despite strong efforts to study nucleosome positioning using Next Generation Sequencing (NGS) data, the mechanism of their collective arrangement along the gene body remains poorly understood. Here, we classify nucleosome distributions of protein-coding genes in Saccharomyces cerevisiae according to their profile similarity and analyse their differences using functional Principal Component Analysis. By decomposing the NGS signals into their main descriptive functions, we compared wild type and chromatin remodeler-deficient strains, keeping position-specific details preserved whilst considering the nucleosome arrangement as a whole. A correlation analysis with other genomic properties, such as gene size and length of the upstream Nucleosome Depleted Region (NDR), identified key factors that influence the nucleosome distribution. We reveal that the RSC chromatin remodeler-which is responsible for NDR maintenance-is indispensable for decoupling nucleosome arrangement within the gene from positioning outside, which interfere in rsc8-depleted conditions. Moreover, nucleosome profiles in chd1Δ strains displayed a clear correlation with RNA polymerase II presence, whereas wild type cells did not indicate a noticeable interdependence. We propose that RSC is pivotal for global nucleosome organisation, whilst Chd1 plays a key role for maintaining local arrangement.


Asunto(s)
Proteínas de Saccharomyces cerevisiae , Saccharomyces cerevisiae , Saccharomyces cerevisiae/genética , Saccharomyces cerevisiae/metabolismo , Nucleosomas/genética , Proteínas de Saccharomyces cerevisiae/genética , Proteínas de Saccharomyces cerevisiae/metabolismo , ARN Polimerasa II/metabolismo , ADN , Ensamble y Desensamble de Cromatina/genética
3.
Cell Rep ; 42(5): 112465, 2023 05 30.
Artículo en Inglés | MEDLINE | ID: mdl-37133993

RESUMEN

Chromatin organization is crucial for transcriptional regulation in eukaryotes. Mediator is an essential and conserved co-activator thought to act in concert with chromatin regulators. However, it remains largely unknown how their functions are coordinated. Here, we provide evidence in the yeast Saccharomyces cerevisiae that Mediator establishes physical contact with RSC (Remodels the Structure of Chromatin), a conserved and essential chromatin remodeling complex that is crucial for nucleosome-depleted region (NDR) formation. We determine the role of Mediator-RSC interaction in their chromatin binding, nucleosome occupancy, and transcription on a genomic scale. Mediator and RSC co-localize on wide NDRs of promoter regions, and specific Mediator mutations affect nucleosome eviction and TSS-associated +1 nucleosome stability. This work shows that Mediator contributes to RSC remodeling function to shape NDRs and maintain chromatin organization on promoter regions. It will help in our understanding of transcriptional regulation in the chromatin context relevant for severe diseases.


Asunto(s)
Nucleosomas , Proteínas de Saccharomyces cerevisiae , Nucleosomas/metabolismo , Proteínas de Unión al ADN/genética , Proteínas de Unión al ADN/metabolismo , Ensamble y Desensamble de Cromatina , Proteínas de Saccharomyces cerevisiae/genética , Proteínas de Saccharomyces cerevisiae/metabolismo , Factores de Transcripción/genética , Factores de Transcripción/metabolismo , Cromatina/metabolismo , Saccharomyces cerevisiae/genética , Saccharomyces cerevisiae/metabolismo , Regiones Promotoras Genéticas/genética
4.
PLoS Comput Biol ; 18(9): e1010488, 2022 09.
Artículo en Inglés | MEDLINE | ID: mdl-36094963

RESUMEN

The great advances of sequencing technologies allow the in vivo measurement of nuclear processes-such as DNA repair after UV exposure-over entire cell populations. However, data sets usually contain only a few samples over several hours, missing possibly important information in between time points. We developed a data-driven approach to analyse CPD repair kinetics over time in Saccharomyces cerevisiae. In contrast to other studies that consider sequencing signals as an average behaviour, we understand them as the superposition of signals from independent cells. By motivating repair as a stochastic process, we derive a minimal model for which the parameters can be conveniently estimated. We correlate repair parameters to a variety of genomic features that are assumed to influence repair, including transcription rate and nucleosome density. The clearest link was found for the transcription unit length, which has been unreported for budding yeast to our knowledge. The framework hence allows a comprehensive analysis of nuclear processes on a population scale.


Asunto(s)
Nucleosomas , Proteínas de Saccharomyces cerevisiae , Daño del ADN/genética , Reparación del ADN , Saccharomyces cerevisiae/genética , Saccharomyces cerevisiae/metabolismo , Proteínas de Saccharomyces cerevisiae/metabolismo , Rayos Ultravioleta
5.
Genome Res ; 2022 Jun 23.
Artículo en Inglés | MEDLINE | ID: mdl-35738899

RESUMEN

Mediator is a conserved coregulator playing a key role in RNA polymerase (Pol) II transcription. Mediator also links transcription and nucleotide excision repair (NER) via a direct contact with Rad2/ERCC5(XPG) endonuclease. In this work, we analyzed the genome-wide distribution of Rad26/ERCC6(CSB) and Rad1-Rad10/ERCC4(XPF)-ERCC1, addressing the question of a potential link of these proteins with Mediator and Pol II in yeast Saccharomyces cerevisiae Our genomic analyses reveal that Rad1-Rad10 and Rad26 are present on the yeast genome in the absence of genotoxic stress, especially at highly transcribed regions, with Rad26 binding strongly correlating with that of Pol II. Moreover, we show that Rad1-Rad10 and Rad26 colocalize with Mediator at intergenic regions and physically interact with this complex. Using kin28 TFIIH mutant, we found that Mediator stabilization on core promoters leads to an increase in Rad1-Rad10 chromatin binding, whereas Rad26 occupancy follows mainly a decrease in Pol II transcription. Combined with multivariate analyses, our results show the relationships between Rad1-Rad10, Rad26, Mediator, and Pol II, modulated by the changes in binding dynamics of Mediator and Pol II transcription. In conclusion, we extend the Mediator link to Rad1-Rad10 and Rad26 NER proteins and reveal important differences in their dependence on Mediator and Pol II. Rad2 is the most dependent on Mediator, followed by Rad1-Rad10, whereas Rad26 is the most closely related to Pol II. Our work thus contributes to new concepts of the functional interplay between transcription and DNA repair machineries, which are relevant for human diseases including cancer and XP/CS syndromes.

6.
Lab Chip ; 21(12): 2407-2416, 2021 06 15.
Artículo en Inglés | MEDLINE | ID: mdl-33960358

RESUMEN

Mutations in DNA have large-ranging consequences, from evolution to disease. Many mechanisms contribute to mutational processes such as dysfunctions in DNA repair pathways and exogenous or endogenous mutagen exposures. Model organisms and mutation accumulation (MA) experiments are indispensable to study mutagenesis. Classical MA is, however, time consuming and laborious. To fill the need for more efficient approaches to characterize mutational profiles, we have developed an innovative microfluidic-based system that automatizes MA culturing over many generations in budding yeast. This unique experimental tool, coupled with high-throughput sequencing, reduces by one order of magnitude the time required for genome-wide measurements of mutational profiles, while also parallelizing and simplifying the cell culture. To validate our approach, we performed microfluidic MA experiments on two different genetic backgrounds, a wild-type strain and a base-excision DNA repair ung1 mutant characterized by a well-defined mutational profile. We show that the microfluidic device allows for mutation accumulation comparable to the traditional method on plate. Our approach thus paves the way to massively-parallel MA experiments with minimal human intervention that can be used to investigate mutational processes at the origin of human diseases and to identify mutagenic compounds relevant for medical and environmental research.


Asunto(s)
Acumulación de Mutaciones , Saccharomyces cerevisiae , Humanos , Microfluídica , Mutagénesis , Mutación , Saccharomyces cerevisiae/genética
7.
Trends Genet ; 37(3): 224-234, 2021 03.
Artículo en Inglés | MEDLINE | ID: mdl-32921511

RESUMEN

Dysfunctions of nuclear processes including transcription and DNA repair lead to severe human diseases. Gaining an understanding of how these processes operate in the crowded context of chromatin can be particularly challenging. Mediator is a large multiprotein complex conserved in eukaryotes with a key coactivator role in the regulation of RNA polymerase (Pol) II transcription. Despite intensive studies, the molecular mechanisms underlying Mediator function remain to be fully understood. Novel findings have provided insights into the relationship between Mediator and chromatin architecture, revealed its role in connecting transcription with DNA repair and proposed an emerging mechanism of phase separation involving Mediator condensates. Recent developments in the field suggest multiple functions of Mediator going beyond transcriptional processes per se that would explain its involvement in various human pathologies.


Asunto(s)
Cromatina/genética , Complejo Mediador/genética , ARN Polimerasa II/genética , Transcripción Genética/genética , Cromatina/ultraestructura , Reparación del ADN/genética , Humanos , Complejo Mediador/ultraestructura , ARN Polimerasa II/ultraestructura
8.
Mol Cell ; 81(1): 183-197.e6, 2021 01 07.
Artículo en Inglés | MEDLINE | ID: mdl-33278361

RESUMEN

Mre11-Rad50-Xrs2 (MRX) is a highly conserved complex with key roles in various aspects of DNA repair. Here, we report a new function for MRX in limiting transcription in budding yeast. We show that MRX interacts physically and colocalizes on chromatin with the transcriptional co-regulator Mediator. MRX restricts transcription of coding and noncoding DNA by a mechanism that does not require the nuclease activity of Mre11. MRX is required to tether transcriptionally active loci to the nuclear pore complex (NPC), and it also promotes large-scale gene-NPC interactions. Moreover, MRX-mediated chromatin anchoring to the NPC contributes to chromosome folding and helps to control gene expression. Together, these findings indicate that MRX has a role in transcription and chromosome organization that is distinct from its known function in DNA repair.


Asunto(s)
Cromosomas Fúngicos/metabolismo , Proteínas de Unión al ADN/metabolismo , Endodesoxirribonucleasas/metabolismo , Exodesoxirribonucleasas/metabolismo , Regulación Fúngica de la Expresión Génica , Proteínas de Saccharomyces cerevisiae/metabolismo , Saccharomyces cerevisiae/metabolismo , Cromosomas Fúngicos/genética , Proteínas de Unión al ADN/genética , Endodesoxirribonucleasas/genética , Exodesoxirribonucleasas/genética , Complejos Multiproteicos/metabolismo , Saccharomyces cerevisiae/genética , Proteínas de Saccharomyces cerevisiae/genética
9.
Cell ; 178(5): 1036-1038, 2019 08 22.
Artículo en Inglés | MEDLINE | ID: mdl-31442397

RESUMEN

In this issue of Cell, Casellas and colleagues provide insights into the structural and functional aspects of the mammalian multi-subunit Mediator complex, a conserved and essential transcriptional coregulator. Combining cryo-EM, genetic, and genomic analyses, the work sheds light on Mediator's mode of action as a functional bridge between enhancers and promoters.


Asunto(s)
Complejo Mediador , Animales , Regiones Promotoras Genéticas
10.
Nucleic Acids Res ; 47(17): 8988-9004, 2019 09 26.
Artículo en Inglés | MEDLINE | ID: mdl-31299084

RESUMEN

Transcription and maintenance of genome integrity are fundamental cellular functions. Deregulation of transcription and defects in DNA repair lead to serious pathologies. The Mediator complex links RNA polymerase (Pol) II transcription and nucleotide excision repair via Rad2/XPG endonuclease. However, the functional interplay between Rad2/XPG, Mediator and Pol II remains to be determined. In this study, we investigated their functional dynamics using genomic and genetic approaches. In a mutant affected in Pol II phosphorylation leading to Mediator stabilization on core promoters, Rad2 genome-wide occupancy shifts towards core promoters following that of Mediator, but decreases on transcribed regions together with Pol II. Specific Mediator mutations increase UV sensitivity, reduce Rad2 recruitment to transcribed regions, lead to uncoupling of Rad2, Mediator and Pol II and to colethality with deletion of Rpb9 Pol II subunit involved in transcription-coupled repair. We provide new insights into the functional interplay between Rad2, Mediator and Pol II and propose that dynamic interactions with Mediator and Pol II are involved in Rad2 loading to the chromatin. Our work contributes to the understanding of the complex link between transcription and DNA repair machineries, dysfunction of which leads to severe diseases.


Asunto(s)
Cromatina/metabolismo , Proteínas de Unión al ADN/metabolismo , Endodesoxirribonucleasas/metabolismo , Complejo Mediador/metabolismo , ARN Polimerasa II/metabolismo , Proteínas de Saccharomyces cerevisiae/metabolismo , Reparación del ADN , Proteínas de Unión al ADN/genética , Endodesoxirribonucleasas/genética , Genoma Fúngico , Humanos , Complejo Mediador/genética , Modelos Moleculares , Regiones Promotoras Genéticas , Proteínas Serina-Treonina Quinasas/genética , ARN Polimerasa II/genética , Saccharomyces cerevisiae/genética , Saccharomyces cerevisiae/metabolismo , Proteínas de Saccharomyces cerevisiae/genética
11.
Nat Rev Mol Cell Biol ; 19(4): 262-274, 2018 04.
Artículo en Inglés | MEDLINE | ID: mdl-29209056

RESUMEN

Alterations in the regulation of gene expression are frequently associated with developmental diseases or cancer. Transcription activation is a key phenomenon in the regulation of gene expression. In all eukaryotes, mediator of RNA polymerase II transcription (Mediator), a large complex with modular organization, is generally required for transcription by RNA polymerase II, and it regulates various steps of this process. The main function of Mediator is to transduce signals from the transcription activators bound to enhancer regions to the transcription machinery, which is assembled at promoters as the preinitiation complex (PIC) to control transcription initiation. Recent functional studies of Mediator with the use of structural biology approaches and functional genomics have revealed new insights into Mediator activity and its regulation during transcription initiation, including how Mediator is recruited to transcription regulatory regions and how it interacts and cooperates with PIC components to assist in PIC assembly. Novel roles of Mediator in the control of gene expression have also been revealed by showing its connection to the nuclear pore and linking Mediator to the regulation of gene positioning in the nuclear space. Clear links between Mediator subunits and disease have also encouraged studies to explore targeting of this complex as a potential therapeutic approach in cancer and fungal infections.


Asunto(s)
Complejo Mediador/genética , Complejo Mediador/metabolismo , Transcripción Genética , Animales , Quinasa 8 Dependiente de Ciclina/antagonistas & inhibidores , Evolución Molecular , Regulación de la Expresión Génica , Humanos , Complejo Mediador/química , Modelos Biológicos , Modelos Genéticos , Micosis/genética , Micosis/metabolismo , Micosis/terapia , Neoplasias/genética , Neoplasias/metabolismo , Neoplasias/terapia , Poro Nuclear/genética , Poro Nuclear/metabolismo , ARN Polimerasa II/metabolismo , Secuencias Reguladoras de Ácidos Nucleicos , Transducción de Señal , Iniciación de la Transcripción Genética , Activación Transcripcional
12.
Transcription ; 8(5): 328-342, 2017.
Artículo en Inglés | MEDLINE | ID: mdl-28841352

RESUMEN

Mediator is a multisubunit complex conserved in eukaryotes that plays an essential coregulator role in RNA polymerase (Pol) II transcription. Despite intensive studies of the Mediator complex, the molecular mechanisms of its function in vivo remain to be fully defined. In this review, we will discuss the different aspects of Mediator function starting with its interactions with specific transcription factors, its recruitment to chromatin and how, as a coregulator, it contributes to the assembly of transcription machinery components within the preinitiation complex (PIC) in vivo and beyond the PIC formation.


Asunto(s)
Complejo Mediador/metabolismo , Iniciación de la Transcripción Genética , Animales , Cromatina/genética , Cromatina/metabolismo , Humanos , ARN Polimerasa II/metabolismo , Factores de Transcripción/metabolismo
13.
Genes Dev ; 30(18): 2119-2132, 2016 09 15.
Artículo en Inglés | MEDLINE | ID: mdl-27688401

RESUMEN

Mediator is a large coregulator complex conserved from yeast to humans and involved in many human diseases, including cancers. Together with general transcription factors, it stimulates preinitiation complex (PIC) formation and activates RNA polymerase II (Pol II) transcription. In this study, we analyzed how Mediator acts in PIC assembly using in vivo, in vitro, and in silico approaches. We revealed an essential function of the Mediator middle module exerted through its Med10 subunit, implicating a key interaction between Mediator and TFIIB. We showed that this Mediator-TFIIB link has a global role on PIC assembly genome-wide. Moreover, the amplitude of Mediator's effect on PIC formation is gene-dependent and is related to the promoter architecture in terms of TATA elements, nucleosome occupancy, and dynamics. This study thus provides mechanistic insights into the coordinated function of Mediator and TFIIB in PIC assembly in different chromatin contexts.


Asunto(s)
Complejo Mediador/metabolismo , Regiones Promotoras Genéticas/fisiología , Saccharomyces cerevisiae/fisiología , Factor de Transcripción TFIIB/metabolismo , Cromatina/metabolismo , Complejo Mediador/genética , Mutación , Unión Proteica/genética , Multimerización de Proteína/genética , Saccharomyces cerevisiae/genética , Proteínas de Saccharomyces cerevisiae/metabolismo
14.
Nucleic Acids Res ; 43(19): 9214-31, 2015 Oct 30.
Artículo en Inglés | MEDLINE | ID: mdl-26240385

RESUMEN

Mediator is a large multiprotein complex conserved in all eukaryotes, which has a crucial coregulator function in transcription by RNA polymerase II (Pol II). However, the molecular mechanisms of its action in vivo remain to be understood. Med17 is an essential and central component of the Mediator head module. In this work, we utilised our large collection of conditional temperature-sensitive med17 mutants to investigate Mediator's role in coordinating preinitiation complex (PIC) formation in vivo at the genome level after a transfer to a non-permissive temperature for 45 minutes. The effect of a yeast mutation proposed to be equivalent to the human Med17-L371P responsible for infantile cerebral atrophy was also analyzed. The ChIP-seq results demonstrate that med17 mutations differentially affected the global presence of several PIC components including Mediator, TBP, TFIIH modules and Pol II. Our data show that Mediator stabilizes TFIIK kinase and TFIIH core modules independently, suggesting that the recruitment or the stability of TFIIH modules is regulated independently on yeast genome. We demonstrate that Mediator selectively contributes to TBP recruitment or stabilization to chromatin. This study provides an extensive genome-wide view of Mediator's role in PIC formation, suggesting that Mediator coordinates multiple steps of a PIC assembly pathway.


Asunto(s)
Complejo Mediador/fisiología , Proteínas de Saccharomyces cerevisiae/genética , Iniciación de la Transcripción Genética , Cromatina/metabolismo , Galactoquinasa/genética , Regulación Fúngica de la Expresión Génica , Genoma Fúngico , Complejo Mediador/genética , Mutación , ARN Polimerasa II/metabolismo , ARN Mensajero/metabolismo , Saccharomyces cerevisiae/genética , Proteína de Unión a TATA-Box/metabolismo , Factor de Transcripción TFIIH/metabolismo
15.
PLoS One ; 9(7): e102464, 2014.
Artículo en Inglés | MEDLINE | ID: mdl-25029256

RESUMEN

The BYpass of Ess1 (Bye1) protein is a putative S. cerevisiae transcription factor homologous to the human cancer-associated PHF3/DIDO family of proteins. Bye1 contains a Plant Homeodomain (PHD) and a TFIIS-like domain. The Bye1 PHD finger interacts with tri-methylated lysine 4 of histone H3 (H3K4me3) while the TFIIS-like domain binds to RNA polymerase (Pol) II. Here, we investigated the contribution of these structural features to Bye1 recruitment to chromatin as well as its function in transcriptional regulation. Genome-wide analysis of Bye1 distribution revealed at least two distinct modes of association with actively transcribed genes: within the core of Pol II- and Pol III-transcribed genes concomitant with the presence of the TFIIS transcription factor and, additionally, with promoters of a subset of Pol II-transcribed genes. Specific loss of H3K4me3 abolishes Bye1 association to gene promoters, but doesn't affect its binding within gene bodies. Genetic interactions suggested an essential role of Bye1 in cell fitness under stress conditions compensating the absence of TFIIS. Furthermore, BYE1 deletion resulted in the attenuation of GAL genes expression upon galactose-mediated induction indicating its positive role in transcription regulation. Together, these findings point to a bimodal role of Bye1 in regulation of Pol II transcription. It is recruited via its PHD domain to H3K4 tri-methylated promoters at early steps of transcription. Once Pol II is engaged into elongation, Bye1 binds directly to the transcriptional machinery, modulating its progression along the gene.


Asunto(s)
Cromatina/metabolismo , Regulación Fúngica de la Expresión Génica/fisiología , ARN Polimerasa II/metabolismo , Proteínas de Saccharomyces cerevisiae/química , Proteínas de Saccharomyces cerevisiae/metabolismo , Factores de Elongación Transcripcional/química , Factores de Elongación Transcripcional/metabolismo , Inmunoprecipitación de Cromatina , Histonas/metabolismo , Oligonucleótidos/genética , Unión Proteica , Estructura Terciaria de Proteína , Reacción en Cadena de la Polimerasa de Transcriptasa Inversa , Técnicas del Sistema de Dos Híbridos
17.
Genes Dev ; 27(23): 2549-62, 2013 Dec 01.
Artículo en Inglés | MEDLINE | ID: mdl-24298055

RESUMEN

Mediator is a large multiprotein complex conserved in all eukaryotes. The crucial function of Mediator in transcription is now largely established. However, we found that this complex also plays an important role by connecting transcription with DNA repair. We identified a functional contact between the Med17 Mediator subunit and Rad2/XPG, the 3' endonuclease involved in nucleotide excision DNA repair. Genome-wide location analyses revealed that Rad2 is associated with RNA polymerase II (Pol II)- and Pol III-transcribed genes and telomeric regions in the absence of exogenous genotoxic stress. Rad2 occupancy of Pol II-transcribed genes is transcription-dependent. Genome-wide Rad2 occupancy of class II gene promoters is well correlated with that of Mediator. Furthermore, UV sensitivity of med17 mutants is correlated with reduced Rad2 occupancy of class II genes and concomitant decrease of Mediator interaction with Rad2 protein. Our results suggest that Mediator is involved in DNA repair by facilitating Rad2 recruitment to transcribed genes.


Asunto(s)
Reparación del ADN/fisiología , Proteínas de Unión al ADN/metabolismo , Endodesoxirribonucleasas/metabolismo , Endonucleasas/metabolismo , Complejo Mediador/metabolismo , Proteínas Nucleares/metabolismo , Proteínas de Saccharomyces cerevisiae/metabolismo , Saccharomyces cerevisiae/genética , Saccharomyces cerevisiae/metabolismo , Factores de Transcripción/metabolismo , Reparación del ADN/genética , Proteínas de Unión al ADN/genética , Endodesoxirribonucleasas/genética , Endonucleasas/genética , Eliminación de Gen , Genoma , Humanos , Complejo Mediador/genética , Proteínas Nucleares/genética , Regiones Promotoras Genéticas/genética , Unión Proteica , Tolerancia a Radiación/genética , Saccharomyces cerevisiae/efectos de la radiación , Proteínas de Saccharomyces cerevisiae/genética , Factores de Transcripción/genética , Rayos Ultravioleta
18.
Nucleic Acids Res ; 40(1): 270-83, 2012 Jan.
Artículo en Inglés | MEDLINE | ID: mdl-21911356

RESUMEN

RNA polymerase (Pol) III synthesizes the tRNAs, the 5S ribosomal RNA and a small number of untranslated RNAs. In vitro, it also transcribes short interspersed nuclear elements (SINEs). We investigated the distribution of Pol III and its associated transcription factors on the genome of mouse embryonic stem cells using a highly specific tandem ChIP-Seq method. Only a subset of the annotated class III genes was bound and thus transcribed. A few hundred SINEs were associated with the Pol III transcription machinery. We observed that Pol III and its transcription factors were present at 30 unannotated sites on the mouse genome, only one of which was conserved in human. An RNA was associated with >80% of these regions. More than 2200 regions bound by TFIIIC transcription factor were devoid of Pol III. These sites were associated with cohesins and often located close to CTCF-binding sites, suggesting that TFIIIC might cooperate with these factors to organize the chromatin. We also investigated the genome-wide distribution of the ubiquitous TFIIS variant, TCEA1. We found that, as in Saccharomyces cerevisiae, TFIIS is associated with class III genes and also with SINEs suggesting that TFIIS is a Pol III transcription factor in mammals.


Asunto(s)
Células Madre Embrionarias/metabolismo , ARN Polimerasa III/metabolismo , Transcripción Genética , Factores de Elongación Transcripcional/metabolismo , Animales , Sitios de Unión , Factor 1 de Respuesta al Butirato , Línea Celular , Cromatina/metabolismo , Inmunoprecipitación de Cromatina/métodos , Genoma , Ratones , Proteínas Nucleares/metabolismo , ARN Polimerasa II/metabolismo , ARN Nuclear Pequeño/genética , ARN de Transferencia/genética , Proteínas de Unión al ARN/metabolismo , Análisis de Secuencia de ADN , Elementos de Nucleótido Esparcido Corto , Factor de Transcripción TFIIIB/metabolismo , Factores de Transcripción TFIII/metabolismo
19.
Science ; 331(6023): 1451-4, 2011 Mar 18.
Artículo en Inglés | MEDLINE | ID: mdl-21415355

RESUMEN

Gene transcription is highly regulated. Altered transcription can lead to cancer or developmental diseases. Mediator, a multisubunit complex conserved among eukaryotes, is generally required for RNA polymerase II (Pol II) transcription. An interaction between the two complexes is known, but its molecular nature and physiological role are unclear. We identify a direct physical interaction between the Rpb3 Pol II subunit of Saccharomyces cerevisiae and the essential Mediator subunit, Med17. Furthermore, we demonstrate a functional element in the Mediator-Pol II interface that is important for genome-wide Pol II recruitment in vivo. Our findings suggest that a direct interaction between Mediator and Pol II is generally required for transcription of class II genes in eukaryotes.


Asunto(s)
Complejo Mediador/metabolismo , ARN Polimerasa II/metabolismo , Proteínas de Saccharomyces cerevisiae/metabolismo , Saccharomyces cerevisiae/genética , Transcripción Genética , Inmunoprecipitación de Cromatina , Galactoquinasa/genética , Genes Fúngicos , Genoma Fúngico , Complejo Mediador/genética , Mutación , Regiones Promotoras Genéticas , Unión Proteica , Saccharomyces cerevisiae/metabolismo , Proteínas de Saccharomyces cerevisiae/genética , Temperatura
20.
Curr Biol ; 20(12): 1053-64, 2010 Jun 22.
Artículo en Inglés | MEDLINE | ID: mdl-20605454

RESUMEN

BACKGROUND: The switch from cellular proliferation to differentiation occurs to a large extent through specific programs of gene expression. In fission yeast, the master regulator of sexual differentiation, ste11, is induced by environmental conditions leading to mating and meiosis. RESULTS: We show that phosphorylation of serine 2 (S2P) in the C-terminal domain of the largest subunit of the RNA polymerase II (PolII) enzyme by the Lsk1 cyclin-dependent kinase has only a minor impact on global gene expression during vegetative growth but is critical for the induction of ste11 transcription during sexual differentiation. The recruitment of the Lsk1 kinase initiates in the vicinity of the transcription start site of ste11, resulting in a marked increase of S2P on the ste11 unit, including an extended 5' untranslated region (5'UTR). This pattern contrasts with the classical gradient of S2P toward the 3' region. In the absence of S2P, both PolII occupancy at the ste11 locus and ste11 expression are impaired. This results in sterility, which is rescued by expression of the ste11 coding sequence from the adh1 promoter. CONCLUSION: Thus, the S2P polymerase plays a specific, regulatory role in cell differentiation through the induction of ste11.


Asunto(s)
ARN Polimerasa II/metabolismo , Schizosaccharomyces/enzimología , Electroforesis en Gel de Poliacrilamida , Regulación Fúngica de la Expresión Génica , Fosforilación , Schizosaccharomyces/citología
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