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1.
Cell Mol Life Sci ; 81(1): 313, 2024 Jul 27.
Artículo en Inglés | MEDLINE | ID: mdl-39066826

RESUMEN

Bromodomain and extra-terminal (BET) proteins are relevant chromatin adaptors involved in the transcriptional control of thousands of genes. Two tandem N-terminal bromodomains are essential for chromatin attachment through acetyl-histone recognition. Recently, the BET proteins members BRD2 and BRD4 were found to interact with the SARS-CoV-2 envelope (E) protein, raising the question of whether the interaction constitutes a virus hijacking mechanism for transcription alteration in the host cell. To shed light on this question, we have compared the transcriptome of cells overexpressing E with that of cells treated with the BET inhibitor JQ1. Notably, E overexpression leads to a strong upregulation of natural immunity- and interferon response-related genes. However, BET inhibition results in the downregulation of most of these genes, indicating that these two conditions, far from causing a significant overlap of the altered transcriptomes, course with quite different outputs. Concerning the interaction of E protein with BET members, and differing from previous reports indicating that it occurs through BET bromodomains, we find that it relies on SEED and SEED-like domains, BET regions rich in Ser, Asp, and Glu residues. By taking advantage of this specific interaction, we have been able to direct selective degradation of E protein through a PROTAC system involving a dTAG-SEED fusion, highlighting the possible therapeutic use of this peptide for targeted degradation of a viral essential protein.


Asunto(s)
Proteínas de Ciclo Celular , SARS-CoV-2 , Factores de Transcripción , Triazoles , Humanos , Factores de Transcripción/metabolismo , Factores de Transcripción/genética , SARS-CoV-2/metabolismo , SARS-CoV-2/efectos de los fármacos , SARS-CoV-2/genética , Proteínas de Ciclo Celular/metabolismo , Proteínas de Ciclo Celular/genética , Triazoles/farmacología , Azepinas/farmacología , Proteínas Serina-Treonina Quinasas/metabolismo , Proteínas Serina-Treonina Quinasas/antagonistas & inhibidores , Proteínas Serina-Treonina Quinasas/genética , Dominios Proteicos , Transcripción Genética/efectos de los fármacos , COVID-19/virología , COVID-19/metabolismo , Células HEK293 , Unión Proteica , Proteínas que Contienen Bromodominio
2.
Nucleic Acids Res ; 50(17): 9838-9857, 2022 09 23.
Artículo en Inglés | MEDLINE | ID: mdl-36124662

RESUMEN

High mobility group (HMG) proteins are chromatin regulators with essential functions in development, cell differentiation and cell proliferation. The protein HMG20A is predicted by the AlphaFold2 software to contain three distinct structural elements, which we have functionally characterized: i) an amino-terminal, intrinsically disordered domain with transactivation activity; ii) an HMG box with higher binding affinity for double-stranded, four-way-junction DNA than for linear DNA; and iii) a long coiled-coil domain. Our proteomic study followed by a deletion analysis and structural modeling demonstrates that HMG20A forms a complex with the histone reader PHF14, via the establishment of a two-stranded alpha-helical coiled-coil structure. siRNA-mediated knockdown of either PHF14 or HMG20A in MDA-MB-231 cells causes similar defects in cell migration, invasion and homotypic cell-cell adhesion ability, but neither affects proliferation. Transcriptomic analyses demonstrate that PHF14 and HMG20A share a large subset of targets. We show that the PHF14-HMG20A complex modulates the Hippo pathway through a direct interaction with the TEAD1 transcription factor. PHF14 or HMG20A deficiency increases epithelial markers, including E-cadherin and the epithelial master regulator TP63 and impaired normal TGFß-trigged epithelial-to-mesenchymal transition. Taken together, these data indicate that PHF14 and HMG20A cooperate in regulating several pathways involved in epithelial-mesenchymal plasticity.


Asunto(s)
Proteínas del Grupo de Alta Movilidad/metabolismo , Histonas , Proteínas Nucleares/metabolismo , Factores de Transcripción/metabolismo , Factor de Crecimiento Transformador beta , Cadherinas/genética , Cadherinas/metabolismo , Línea Celular Tumoral , Cromatina , Vía de Señalización Hippo , Histonas/metabolismo , Humanos , Proteómica , ARN Interferente Pequeño , Factores de Transcripción/genética , Factor de Crecimiento Transformador beta/genética
3.
Nucleic Acids Res ; 49(11): 6267-6280, 2021 06 21.
Artículo en Inglés | MEDLINE | ID: mdl-34096575

RESUMEN

Prefoldin is a heterohexameric complex conserved from archaea to humans that plays a cochaperone role during the co-translational folding of actin and tubulin monomers. Additional functions of prefoldin have been described, including a positive contribution to transcription elongation and chromatin dynamics in yeast. Here we show that prefoldin perturbations provoked transcriptional alterations across the human genome. Severe pre-mRNA splicing defects were also detected, particularly after serum stimulation. We found impairment of co-transcriptional splicing during transcription elongation, which explains why the induction of long genes with a high number of introns was affected the most. We detected genome-wide prefoldin binding to transcribed genes and found that it correlated with the negative impact of prefoldin depletion on gene expression. Lack of prefoldin caused global decrease in Ser2 and Ser5 phosphorylation of the RNA polymerase II carboxy-terminal domain. It also reduced the recruitment of the CTD kinase CDK9 to transcribed genes, and the association of splicing factors PRP19 and U2AF65 to chromatin, which is known to depend on CTD phosphorylation. Altogether the reported results indicate that human prefoldin is able to act locally on the genome to modulate gene expression by influencing phosphorylation of elongating RNA polymerase II, and thereby regulating co-transcriptional splicing.


Asunto(s)
Chaperonas Moleculares/fisiología , Empalme del ARN , ARN Mensajero/metabolismo , Transcripción Genética , Línea Celular , Humanos , Intrones , ARN Polimerasa II/metabolismo , Precursores del ARN/metabolismo , Factores de Empalme de ARN/metabolismo , Proteínas Represoras/fisiología , Transcriptoma
4.
PLoS Comput Biol ; 13(9): e1005708, 2017 Sep.
Artículo en Inglés | MEDLINE | ID: mdl-28902867

RESUMEN

Gene order is not random in eukaryotic chromosomes, and co-regulated genes tend to be clustered. The mechanisms that determine co-regulation of large regions of the genome and its connection with chromatin three-dimensional (3D) organization are still unclear however. Here we have adapted a recently described method for identifying chromatin topologically associating domains (TADs) to identify coexpression domains (which we term "CODs"). Using human normal breast and breast cancer RNA-seq data, we have identified approximately 500 CODs. CODs in the normal and breast cancer genomes share similar characteristics but differ in their gene composition. COD genes have a greater tendency to be coexpressed with genes that reside in other CODs than with non-COD genes. Such inter-COD coexpression is maintained over large chromosomal distances in the normal genome but is partially lost in the cancer genome. Analyzing the relationship between CODs and chromatin 3D organization using Hi-C contact data, we find that CODs do not correspond to TADs. In fact, intra-TAD gene coexpression is the same as random for most chromosomes. However, the contact profile is similar between gene pairs that reside either in the same COD or in coexpressed CODs. These data indicate that co-regulated genes in the genome present similar patterns of contacts irrespective of the frequency of physical chromatin contacts between them.


Asunto(s)
Cromatina/metabolismo , Cromatina/ultraestructura , Regulación de la Expresión Génica/genética , Redes Reguladoras de Genes/genética , Mama/química , Mama/metabolismo , Neoplasias de la Mama/genética , Neoplasias de la Mama/metabolismo , Cromatina/química , Cromatina/genética , Ensamble y Desensamble de Cromatina , Análisis por Conglomerados , Biología Computacional , Femenino , Perfilación de la Expresión Génica , Genoma/genética , Humanos
5.
Proc Natl Acad Sci U S A ; 112(48): 14840-5, 2015 Dec 01.
Artículo en Inglés | MEDLINE | ID: mdl-26578803

RESUMEN

RNA polymerase II (RNAPII) transcription elongation is a highly regulated process that greatly influences mRNA levels as well as pre-mRNA splicing. Despite many studies in vitro, how chromatin modulates RNAPII elongation in vivo is still unclear. Here, we show that a decrease in the level of available canonical histones leads to more accessible chromatin with decreased levels of canonical histones and variants H2A.X and H2A.Z and increased levels of H3.3. With this altered chromatin structure, the RNAPII elongation rate increases, and the kinetics of pre-mRNA splicing is delayed with respect to RNAPII elongation. Consistent with the kinetic model of cotranscriptional splicing, the rapid RNAPII elongation induced by histone depletion promotes the skipping of variable exons in the CD44 gene. Indeed, a slowly elongating mutant of RNAPII was able to rescue this defect, indicating that the defective splicing induced by histone depletion is a direct consequence of the increased elongation rate. In addition, genome-wide analysis evidenced that histone reduction promotes widespread alterations in pre-mRNA processing, including intron retention and changes in alternative splicing. Our data demonstrate that pre-mRNA splicing may be regulated by chromatin structure through the modulation of the RNAPII elongation rate.


Asunto(s)
Histonas/metabolismo , ARN Polimerasa II/metabolismo , Precursores del ARN/biosíntesis , Empalme del ARN/fisiología , Elongación de la Transcripción Genética/fisiología , Línea Celular Tumoral , Histonas/genética , Humanos , Receptores de Hialuranos/biosíntesis , Receptores de Hialuranos/genética , ARN Polimerasa II/genética , Precursores del ARN/genética
6.
PLoS Genet ; 11(4): e1005174, 2015 Apr.
Artículo en Inglés | MEDLINE | ID: mdl-25894978

RESUMEN

While the importance of gene enhancers in transcriptional regulation is well established, the mechanisms and the protein factors that determine enhancers activity have only recently begun to be unravelled. Recent studies have shown that progesterone receptor (PR) binds regions that display typical features of gene enhancers. Here, we show by ChIP-seq experiments that the chromatin remodeler CHD8 mostly binds promoters under proliferation conditions. However, upon progestin stimulation, CHD8 re-localizes to PR enhancers also enriched in p300 and H3K4me1. Consistently, CHD8 depletion severely impairs progestin-dependent gene regulation. CHD8 binding is PR-dependent but independent of the pioneering factor FOXA1. The SWI/SNF chromatin-remodelling complex is required for PR-dependent gene activation. Interestingly, we show that CHD8 interacts with the SWI/SNF complex and that depletion of BRG1 and BRM, the ATPases of SWI/SNF complex, impairs CHD8 recruitment. We also show that CHD8 is not required for H3K27 acetylation, but contributes to increase accessibility of the enhancer to DNaseI. Furthermore, CHD8 was required for RNAPII recruiting to the enhancers and for transcription of enhancer-derived RNAs (eRNAs). Taken together our data demonstrate that CHD8 is involved in late stages of PR enhancers activation.


Asunto(s)
Proteínas de Unión al ADN/genética , Elementos de Facilitación Genéticos , Receptores de Progesterona/genética , Factores de Transcripción/genética , Transcripción Genética , Acetilación , Cromatina/genética , Ensamble y Desensamble de Cromatina/genética , Proteínas Cromosómicas no Histona/genética , Proteínas Cromosómicas no Histona/metabolismo , ADN Helicasas/genética , Proteínas de Unión al ADN/metabolismo , Regulación de la Expresión Génica , Factor Nuclear 3-alfa del Hepatocito/genética , Factor Nuclear 3-alfa del Hepatocito/metabolismo , Humanos , Regiones Promotoras Genéticas , Unión Proteica , ARN Polimerasa II/genética , Receptores de Progesterona/metabolismo , Factores de Transcripción/metabolismo
7.
RNA Biol ; 14(3): 281-286, 2017 03 04.
Artículo en Inglés | MEDLINE | ID: mdl-27211514

RESUMEN

Histone proteins are main structural components of the chromatin and major determinants of gene regulation. Expression of canonical histone genes is strictly controlled during the cell cycle in order to couple DNA replication with histone deposition. Indeed, reductions in the levels of canonical histones or defects in chromatin assembly cause genetic instability. Early data from yeast demonstrated that severe histone depletion also causes strong gene expression changes. We have recently reported that a moderated depletion of canonical histones in human cells leads to an open chromatin configuration, which in turn increases RNA polymerase II elongation rates and causes pre-mRNA splicing defects. Interestingly, some of the observed defects accompany the scheduled histone depletion that is associated with several senescence and aging processes. Thus, our comparison of induced and naturally-occurring histone depletion processes suggests that a programmed reduction of the level of canonical histones might be a strategy to control gene expression during specific physiological processes.


Asunto(s)
Regulación de la Expresión Génica , Histonas/metabolismo , Animales , Ciclo Celular/genética , Senescencia Celular/genética , Humanos , Precursores del ARN/genética , Precursores del ARN/metabolismo , Empalme del ARN , Transcripción Genética
8.
Nucleic Acids Res ; 43(6): 3068-78, 2015 Mar 31.
Artículo en Inglés | MEDLINE | ID: mdl-25735750

RESUMEN

Chromatin distribution is not uniform along the human genome. In most genes there is a promoter-associated nucleosome free region (NFR) followed by an array of nucleosomes towards the gene body in which the first (+1) nucleosome is strongly positioned. The function of this characteristic chromatin distribution in transcription is not fully understood. Here we show in vivo that the +1 nucleosome plays a role in modulating RNA polymerase II (RNAPII) promoter-proximal pausing. When a +1 nucleosome is strongly positioned, elongating RNAPII has a tendency to stall at the promoter-proximal region, recruits more negative elongation factor (NELF) and produces less mRNA. The nucleosome-induced pause favors pre-mRNA quality control by promoting the addition of the cap to the nascent RNA. Moreover, the uncapped RNAs produced in the absence of a positioned nucleosome are degraded by the 5'-3' exonuclease XRN2. Interestingly, reducing the levels of the chromatin remodeler ISWI factor SNF2H decreases +1 nucleosome positioning and increases RNAPII pause release. This work demonstrates a function for +1 nucleosome in regulation of transcription elongation, pre-mRNA processing and gene expression.


Asunto(s)
Nucleosomas/genética , Nucleosomas/metabolismo , Regiones Promotoras Genéticas , Adenosina Trifosfatasas/metabolismo , Animales , Ensamble y Desensamble de Cromatina , Proteínas Cromosómicas no Histona/metabolismo , Exorribonucleasas/metabolismo , Genes myc , Genoma Humano , Células HEK293 , Humanos , Ratones , Caperuzas de ARN/genética , Caperuzas de ARN/metabolismo , ARN Polimerasa II/metabolismo , ARN Mensajero/genética , ARN Mensajero/metabolismo , Factores de Transcripción/metabolismo
9.
Nucleic Acids Res ; 42(4): 2185-96, 2014 Feb.
Artículo en Inglés | MEDLINE | ID: mdl-24265227

RESUMEN

The precise regulation of S-phase-specific genes is critical for cell proliferation. How the repressive chromatin configuration mediated by the retinoblastoma protein and repressor E2F factors changes at the G1/S transition to allow transcription activation is unclear. Here we show ChIP-on-chip studies that reveal that the chromatin remodeller CHD8 binds ∼ 2000 transcriptionally active promoters. The spectrum of CHD8 target genes was enriched in E2F-dependent genes. We found that CHD8 binds E2F-dependent promoters at the G1/S transition but not in quiescent cells. Consistently, CHD8 was required for G1/S-specific expression of these genes and for cell cycle re-entry on serum stimulation of quiescent cells. We also show that CHD8 interacts with E2F1 and, importantly, loading of E2F1 and E2F3, but not E2F4, onto S-specific promoters, requires CHD8. However, CHD8 recruiting is independent of these factors. Recruiting of MLL histone methyltransferase complexes to S-specific promoters was also severely impaired in the absence of CHD8. Furthermore, depletion of CHD8 abolished E2F1 overexpression-dependent S-phase stimulation of serum-starved cells, highlighting the essential role of CHD8 in E2F-dependent transcription activation.


Asunto(s)
Proteínas de Unión al ADN/metabolismo , Factores de Transcripción E2F/metabolismo , Fase S/genética , Factores de Transcripción/metabolismo , Activación Transcripcional , Animales , Línea Celular , Factor de Transcripción E2F1/metabolismo , Factor de Transcripción E2F3/metabolismo , Humanos , Regiones Promotoras Genéticas
10.
Proc Natl Acad Sci U S A ; 109(21): 8085-90, 2012 May 22.
Artículo en Inglés | MEDLINE | ID: mdl-22570500

RESUMEN

The LSD1-CoREST histone demethylase complex is required to repress neuronal genes in nonneuronal tissues. Here we show that sumoylation of Braf35, one of the subunits of the complex, is required to maintain full repression of neuron-specific genes and for occupancy of the LSD1-CoREST complex at its gene targets. Interestingly, expression of Braf35 was sufficient to prevent neuronal differentiation induced by bHLH neurogenic transcription factors in P19 cells and in neuronal progenitors of the chicken embryo neural tube. Sumoylation of Braf35 is required for this antineurogenic activity. We also show that iBraf, a paralogue of Braf35, forms heterodimers with Braf35. Braf35-iBraf heterodimerization impairs Braf35 interaction with the LSD1-CoREST complex and inhibits Braf35 sumoylation. Consistent with these results, iBraf prevents the antineurogenic activity of Braf35 in vivo. Our data uncover a mechanism of regulation of the LSD1-CoREST complex and provide a molecular explanation for the antagonism between Braf35 and iBraf in neuronal differentiation.


Asunto(s)
Proteínas del Grupo de Alta Movilidad/metabolismo , Proteínas del Tejido Nervioso/metabolismo , Neurogénesis/fisiología , Neuronas/citología , Oxidorreductasas N-Desmetilantes/metabolismo , Proteínas Represoras/metabolismo , Animales , Proteínas de Ciclo Celular , Diferenciación Celular/fisiología , Embrión de Pollo , Pollos , Proteínas Co-Represoras , Proteínas de Unión al ADN , Dimerización , Células Madre de Carcinoma Embrionario/citología , Regulación de la Expresión Génica/fisiología , Células HEK293 , Células HeLa , Proteínas del Grupo de Alta Movilidad/química , Proteínas del Grupo de Alta Movilidad/genética , Histona Demetilasas/química , Histona Demetilasas/metabolismo , Humanos , Ratones , Complejos Multiproteicos/química , Complejos Multiproteicos/metabolismo , Proteínas del Tejido Nervioso/química , Oxidorreductasas N-Desmetilantes/química , Proteínas Represoras/química , Sumoilación/fisiología
11.
Cell Rep ; 43(3): 113855, 2024 Mar 26.
Artículo en Inglés | MEDLINE | ID: mdl-38427563

RESUMEN

SWI/SNF complexes are evolutionarily conserved, ATP-dependent chromatin remodeling machines. Here, we characterize the features of SWI/SNF-dependent genes using BRM014, an inhibitor of the ATPase activity of the complexes. We find that SWI/SNF activity is required to maintain chromatin accessibility and nucleosome occupancy for most enhancers but not for most promoters. SWI/SNF activity is needed for expression of genes with low to medium levels of expression that have promoters with (1) low chromatin accessibility, (2) low levels of active histone marks, (3) high H3K4me1/H3K4me3 ratio, (4) low nucleosomal phasing, and (5) enrichment in TATA-box motifs. These promoters are mostly occupied by the canonical Brahma-related gene 1/Brahma-associated factor (BAF) complex. These genes are surrounded by SWI/SNF-dependent enhancers and mainly encode signal transduction, developmental, and cell identity genes (with almost no housekeeping genes). Machine-learning models trained with different chromatin characteristics of promoters and their surrounding regulatory regions indicate that the chromatin landscape is a determinant for establishing SWI/SNF dependency.


Asunto(s)
Cromatina , Factores de Transcripción , Cromatina/genética , Factores de Transcripción/metabolismo , Nucleosomas/genética , Ensamble y Desensamble de Cromatina
12.
Cell Death Discov ; 10(1): 116, 2024 Mar 06.
Artículo en Inglés | MEDLINE | ID: mdl-38448406

RESUMEN

Serine protease inhibitor clade E member 1 (SERPINE1) inhibits extracellular matrix proteolysis and cell detachment. However, SERPINE1 expression also promotes tumor progression and plays a crucial role in metastasis. Here, we solve this apparent paradox and report that Serpine1 mRNA per se, independent of its protein-coding function, confers mesenchymal properties to the cell, promoting migration, invasiveness, and resistance to anoikis and increasing glycolytic activity by sequestering miRNAs. Expression of Serpine1 mRNA upregulates the expression of the TRA2B splicing factor without affecting its mRNA levels. Through transcriptional profiling, we found that Serpine1 mRNA expression downregulates through TRA2B the expression of genes involved in the immune response. Analysis of human colon tumor samples showed an inverse correlation between SERPINE1 mRNA expression and CD8+ T cell infiltration, unveiling the potential value of SERPINE1 mRNA as a promising therapeutic target for colon tumors.

13.
Plant Physiol ; 159(4): 1806-18, 2012 Aug.
Artículo en Inglés | MEDLINE | ID: mdl-22715108

RESUMEN

Photosynthetic organisms need copper for cytochrome oxidase and for plastocyanin in the fundamental processes of respiration and photosynthesis. However, excess of free copper is detrimental inside the cells and therefore organisms have developed homeostatic mechanisms to tightly regulate its acquisition, sequestration, and efflux. Herein we show that the CopRS two-component system (also known as Hik31-Rre34) is essential for copper resistance in Synechocystis sp. PCC 6803. It regulates expression of a putative heavy-metal efflux-resistance nodulation and division type copper efflux system (encoded by copBAC) as well as its own expression (in the copMRS operon) in response to the presence of copper in the media. Mutants in this two-component system or the efflux system render cells more sensitive to the presence of copper in the media and accumulate more intracellular copper than the wild type. Furthermore, CopS periplasmic domain is able to bind copper, suggesting that CopS could be able to detect copper directly. Both operons (copMRS and copBAC) are also induced by the photosynthetic inhibitor 2,5-dibromo-3-methyl-6-isopropyl-p-benzoquinone but this induction requires the presence of copper in the media. The reduced response of two mutant strains to copper, one lacking plastocyanin and a second one impaired in copper transport to the thylakoid, due to the absence of the P(I)-type ATPases PacS and CtaA, suggests that CopS can detect intracellular copper. In addition, a tagged version of CopS with a triple HA epitope localizes to both the plasma and the thylakoid membranes, suggesting that CopS could be involved in copper detection in both the periplasm and the thylakoid lumen.


Asunto(s)
Adaptación Fisiológica/efectos de los fármacos , Proteínas Bacterianas/metabolismo , Cobre/toxicidad , Transducción de Señal/efectos de los fármacos , Synechocystis/efectos de los fármacos , Synechocystis/fisiología , Proteínas Bacterianas/química , Proteínas Bacterianas/genética , Transporte Biológico/efectos de los fármacos , Membrana Celular/efectos de los fármacos , Membrana Celular/metabolismo , Cobre/metabolismo , Espacio Intracelular/efectos de los fármacos , Espacio Intracelular/metabolismo , Modelos Biológicos , Oxidación-Reducción/efectos de los fármacos , Periplasma/efectos de los fármacos , Periplasma/metabolismo , Plastocianina/metabolismo , Regiones Promotoras Genéticas/genética , Unión Proteica/efectos de los fármacos , Estructura Terciaria de Proteína , Transporte de Proteínas/efectos de los fármacos , Tilacoides/efectos de los fármacos , Tilacoides/metabolismo
14.
EMBO Rep ; 11(10): 751-7, 2010 Oct.
Artículo en Inglés | MEDLINE | ID: mdl-20829883

RESUMEN

RNA polymerase II (RNAPII) transcribes genes in a chromatin context. We have designed a system to investigate the role of chromatin remodelling during elongation in vivo, which involves inserting a strong nucleosome-positioning sequence between a promoter and a reporter gene. Our data indicate that a nucleosome positioned in the body of a transcription unit impairs RNAPII progression, provokes RNAPII accumulation upstream to the positioned nucleosome and reduces transcription. By using this system, we show that BRG1, the enzymatic motor of the SWI-SNF chromatin-remodelling complex, is recruited to the positioned nucleosome in a transcription elongation-dependent manner and facilitates traversal of the nucleosome by RNAPII.


Asunto(s)
ADN Helicasas/metabolismo , Proteínas Nucleares/metabolismo , Nucleosomas/metabolismo , ARN Polimerasa II/metabolismo , Factores de Transcripción/metabolismo , Factores de Elongación Transcripcional/metabolismo , Línea Celular , Ensamble y Desensamble de Cromatina , Genes Reporteros , Humanos
15.
PLoS Genet ; 5(8): e1000605, 2009 Aug.
Artículo en Inglés | MEDLINE | ID: mdl-19680533

RESUMEN

Dynamic regulation of chromatin structure is of fundamental importance for modulating genomic activities in higher eukaryotes. The opposing activities of Polycomb group (PcG) and trithorax group (trxG) proteins are part of a chromatin-based cellular memory system ensuring the correct expression of specific transcriptional programs at defined developmental stages. The default silencing activity of PcG proteins is counteracted by trxG proteins that activate PcG target genes and prevent PcG mediated silencing activities. Therefore, the timely expression and regulation of PcG proteins and counteracting trxG proteins is likely to be of fundamental importance for establishing cell identity. Here, we report that the chromodomain/helicase/DNA-binding domain CHD3 proteins PICKLE (PKL) and PICKLE RELATED2 (PKR2) have trxG-like functions in plants and are required for the expression of many genes that are repressed by PcG proteins. The pkl mutant could partly suppress the leaf and flower phenotype of the PcG mutant curly leaf, supporting the idea that CHD3 proteins and PcG proteins antagonistically determine cell identity in plants. The direct targets of PKL in roots include the PcG genes SWINGER and EMBRYONIC FLOWER2 that encode subunits of Polycomb repressive complexes responsible for trimethylating histone H3 at lysine 27 (H3K27me3). Similar to mutants lacking PcG proteins, lack of PKL and PKR2 caused reduced H3K27me3 levels and, therefore, increased expression of a set of PcG protein target genes in roots. Thus, PKL and PKR2 are directly required for activation of PcG protein target genes and in roots are also indirectly required for repression of PcG protein target genes. Reduced PcG protein activity can lead to cell de-differentiation and callus-like tissue formation in pkl pkr2 mutants. Thus, in contrast to mammals, where PcG proteins are required to maintain pluripotency and to prevent cell differentiation, in plants PcG proteins are required to promote cell differentiation by suppressing embryonic development.


Asunto(s)
Proteínas de Arabidopsis/metabolismo , Arabidopsis/citología , Arabidopsis/metabolismo , Diferenciación Celular , Regulación de la Expresión Génica de las Plantas , Proteínas Represoras/metabolismo , Transactivadores/metabolismo , Arabidopsis/genética , Arabidopsis/crecimiento & desarrollo , Proteínas de Arabidopsis/genética , Linaje de la Célula , ADN Helicasas , Regulación del Desarrollo de la Expresión Génica , Histonas/metabolismo , Raíces de Plantas/citología , Raíces de Plantas/genética , Raíces de Plantas/crecimiento & desarrollo , Raíces de Plantas/metabolismo , Proteínas del Grupo Polycomb , Unión Proteica , Proteínas Represoras/genética , Transactivadores/genética
16.
Commun Biol ; 5(1): 277, 2022 03 28.
Artículo en Inglés | MEDLINE | ID: mdl-35347226

RESUMEN

Differential splicing efficiency of specific introns is a mechanism that dramatically increases protein diversity, based on selection of alternative exons for the final mature mRNA. However, it is unclear whether splicing efficiency of introns within the same gene is coordinated and eventually regulated as a mechanism to control mature mRNA levels. Based on nascent chromatin-associated RNA-sequencing data, we now find that co-transcriptional splicing (CTS) efficiency tends to be similar between the different introns of a gene. We establish that two well-differentiated strategies for CTS efficiency exist, at the extremes of a gradient: short genes that produce high levels of pre-mRNA undergo inefficient splicing, while long genes with relatively low levels of pre-mRNA have an efficient splicing. Notably, we observe that genes with efficient CTS display a higher level of mature mRNA relative to their pre-mRNA levels. Further, we show that the TGFß signal transduction pathway regulates the general CTS efficiency, causing changes in mature mRNA levels. Taken together, our data indicate that CTS efficiency is a gene-specific characteristic that can be regulated to control gene expression.


Asunto(s)
Precursores del ARN , Factor de Crecimiento Transformador beta , Intrones , Precursores del ARN/genética , Precursores del ARN/metabolismo , Empalme del ARN , ARN Mensajero/genética , ARN Mensajero/metabolismo , Factor de Crecimiento Transformador beta/genética , Factor de Crecimiento Transformador beta/metabolismo
17.
Noncoding RNA ; 8(5)2022 Sep 15.
Artículo en Inglés | MEDLINE | ID: mdl-36136852

RESUMEN

Long non-coding RNAs (lncRNAs) have emerged as key regulators in a wide range of biological processes. Here, we identified a mouse miRNA-host gene lncRNA (lnc-Nr6a1) upregulated early during epithelial-to-mesenchymal transition (EMT). We show that when lncRNA is processed, it gives rise to two abundant polyadenylated isoforms, lnc-Nr6a1-1 and lnc-Nr6a1-2, and a longer non-polyadenylated microprocessor-driven lnc-pri-miRNA containing clustered pre-miR-181a2 and pre-miR-181b2 hairpins. Ectopic expression of the lnc-Nr6a1-1 or lnc-Nr6a1-2 isoform enhanced cell migration and the invasive capacity of the cells, whereas the expression of the isoforms and miR-181a2 and miR-181b2 conferred anoikis resistance. Lnc-Nr6a1 gene deletion resulted in cells with lower adhesion capacity and reduced glycolytic metabolism, which are restored by lnc-Nr6a1-1 isoform expression. We performed identification of direct RNA interacting proteins (iDRIP) to identify proteins interacting directly with the lnc-Nr6a1-1 isoform. We defined a network of interacting proteins, including glycolytic enzymes, desmosome proteins and chaperone proteins; and we demonstrated that the lnc-Nr6a1-1 isoform directly binds and acts as a scaffold molecule for the assembly of ENO1, ALDOA, GAPDH, and PKM glycolytic enzymes, along with LDHA, supporting substrate channeling for efficient glycolysis. Our results unveil a role of Lnc-Nr6a1 as a multifunctional lncRNA acting as a backbone for multiprotein complex formation and primary microRNAs.

18.
RNA Biol ; 8(3): 389-93, 2011.
Artículo en Inglés | MEDLINE | ID: mdl-21445002

RESUMEN

The natural template for transcription is chromatin. In vitro and in vivo experiments demonstrate that positioned nucleosomes are obstacles for RNA polymerase II (RNAPII) elongation, raising the question of how RNAPII crosses a nucleosome. In fact, transcription elongation is accompanied by chromatin remodeling in the body of the genes. Numerous results evidence that chromatin remodelers such as histone chaperones and histone acetyl transferases contribute to transcription elongation. Recent data indicate that the SWI/SNF complex, an ATP-dependent chromatin remodeling machine, also helps RNAPII to overcome a nucleosomal barrier during elongation. Finally, the idea that remodeling of positioned nucleosomes in the coding regions would alter RNAPII elongation rate and, therefore, would regulate gene expression at different levels is discussed.


Asunto(s)
Nucleosomas/metabolismo , Extensión de la Cadena Peptídica de Translación , Cromatina/metabolismo , Ensamble y Desensamble de Cromatina , Proteínas Cromosómicas no Histona/metabolismo , Expresión Génica , Modelos Biológicos , ARN Polimerasa II/metabolismo , Factores de Transcripción/metabolismo
19.
Front Med (Lausanne) ; 8: 720128, 2021.
Artículo en Inglés | MEDLINE | ID: mdl-34869418

RESUMEN

Checkpoint with forkhead-associated and ring finger domains (CHFR) has been proposed as a predictive and prognosis biomarker for different tumor types, but its role in pancreatic ductal adenocarcinoma (PDAC) remains unknown. The aim of this study was two-pronged: to review the role of CHFR in PDAC and evaluating CHFR as a potential predictive biomarker in this disease. For this purpose, we first explored the CHFR messenger (m)RNA expression and promoter methylation through the TCGA database. Secondly, the CHFR expression and promoter methylation were prospectively evaluated in a cohort of patients diagnosed with borderline (n = 19) or resectable (n = 16) PDAC by immunohistochemistry (IHC), methylation specific-PCR (MSP), and pyrosequencing. The results from the TCGA database showed significant differences in terms of progression-free survival (PFS) and overall survival (OS) based on the CHFR mRNA expression, which was likely independent from the promoter methylation. Importantly, our results showed that in primarily resected patients and also the entire cohort, a higher CHFR expression as indicated by the higher IHC staining intensity might identify patients with longer disease-free survival (DFS) and OS, respectively. Similarly, in the same cohorts, patients with lower methylation levels by pyrosequencing showed significantly longer OS than patients without this pattern. Both, the CHFR expression intensity and its promoter methylation were established as independent prognostic factors for PFS and OS in the entire cohort. In contrast, no significant differences were found between different methylation patterns for CHFR and the response to taxane-based neoadjuvant treatment. These results suggest the potential role of the higher expression of CHFR and the methylation pattern of its promoter as potential prognostic biomarkers in PDAC, thus warranting further comprehensive studies to extend and confirm our preliminary findings.

20.
Theranostics ; 11(14): 6983-7004, 2021.
Artículo en Inglés | MEDLINE | ID: mdl-34093866

RESUMEN

Rationale: We recently demonstrated that the 'Metabesity' factor HMG20A regulates islet beta-cell functional maturity and adaptation to physiological stress such as pregnancy and pre-diabetes. HMG20A also dictates central nervous system (CNS) development via inhibition of the LSD1-CoREST complex but its expression pattern and function in adult brain remains unknown. Herein we sought to determine whether HMG20A is expressed in the adult CNS, specifically in hypothalamic astrocytes that are key in glucose homeostasis and whether similar to islets, HMG20A potentiates astrocyte function in response to environmental cues. Methods: HMG20A expression profile was assessed by quantitative PCR (QT-PCR), Western blotting and/or immunofluorescence in: 1) the hypothalamus of mice exposed or not to either a high-fat diet or a high-fat high-sucrose regimen, 2) human blood leukocytes and adipose tissue obtained from healthy or diabetic individuals and 3) primary mouse hypothalamic astrocytes exposed to either high glucose or palmitate. RNA-seq and cell metabolic parameters were performed on astrocytes treated or not with a siHMG20A. Astrocyte-mediated neuronal survival was evaluated using conditioned media from siHMG20A-treated astrocytes. The impact of ORY1001, an inhibitor of the LSD1-CoREST complex, on HMG20A expression, reactive astrogliosis and glucose metabolism was evaluated in vitro and in vivo in high-fat high-sucrose fed mice. Results: We show that Hmg20a is predominantly expressed in hypothalamic astrocytes, the main nutrient-sensing cell type of the brain. HMG20A expression was upregulated in diet-induced obesity and glucose intolerant mice, correlating with increased transcript levels of Gfap and Il1b indicative of inflammation and reactive astrogliosis. Hmg20a transcript levels were also increased in adipose tissue of obese non-diabetic individuals as compared to obese diabetic patients. HMG20A silencing in astrocytes resulted in repression of inflammatory, cholesterol biogenesis and epithelial-to-mesenchymal transition pathways which are hallmarks of reactive astrogliosis. Accordingly, HMG20A depleted astrocytes exhibited reduced mitochondrial bioenergetics and increased susceptibility to apoptosis. Neuron viability was also hindered in HMG20A-depleted astrocyte-derived conditioned media. ORY1001 treatment rescued expression of reactive astrogliosis-linked genes in HMG20A ablated astrocytes while enhancing cell surface area, GFAP intensity and STAT3 expression in healthy astrocytes, mimicking the effect of HMG20A. Furthermore, ORY1001 treatment protected against obesity-associated glucose intolerance in mice correlating with a regression of hypothalamic HMG20A expression, indicative of reactive astrogliosis attenuation with improved health status. Conclusion: HMG20A coordinates the astrocyte polarization state. Under physiological pressure such as obesity and insulin resistance that induces low grade inflammation, HMG20A expression is increased to induce reactive astrogliosis in an attempt to preserve the neuronal network and re-establish glucose homeostasis. Nonetheless, a chronic metabesity state or functional mutations will result in lower levels of HMG20A, failure to promote reactive astrogliosis and increase susceptibility of neurons to stress-induced apoptosis. Such effects could be reversed by ORY1001 treatment both in vitro and in vivo, paving the way for a new therapeutic approach for Type 2 Diabetes Mellitus.


Asunto(s)
Astrocitos/metabolismo , Diabetes Mellitus Tipo 2/metabolismo , Gliosis/metabolismo , Proteínas del Grupo de Alta Movilidad/metabolismo , Hipotálamo/metabolismo , Neuronas/metabolismo , Obesidad/metabolismo , Tejido Adiposo/metabolismo , Adulto , Animales , Supervivencia Celular/efectos de los fármacos , Proteínas Co-Represoras/antagonistas & inhibidores , Dieta Alta en Grasa , Proteína Ácida Fibrilar de la Glía/metabolismo , Glucosa/metabolismo , Proteínas del Grupo de Alta Movilidad/antagonistas & inhibidores , Proteínas del Grupo de Alta Movilidad/genética , Histona Demetilasas/antagonistas & inhibidores , Humanos , Interleucina-1beta/metabolismo , Masculino , Ratones , Ratones Endogámicos C57BL , Persona de Mediana Edad , Mitocondrias/genética , Mitocondrias/metabolismo , Proteínas del Tejido Nervioso/antagonistas & inhibidores , ARN Interferente Pequeño , RNA-Seq
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