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1.
Mol Cell ; 83(21): 3801-3817.e8, 2023 Nov 02.
Artículo en Inglés | MEDLINE | ID: mdl-37922872

RESUMEN

Histones shape chromatin structure and the epigenetic landscape. H1, the most diverse histone in the human genome, has 11 variants. Due to the high structural similarity between the H1s, their unique functions in transferring information from the chromatin to mRNA-processing machineries have remained elusive. Here, we generated human cell lines lacking up to five H1 subtypes, allowing us to characterize the genomic binding profiles of six H1 variants. Most H1s bind to specific sites, and binding depends on multiple factors, including GC content. The highly expressed H1.2 has a high affinity for exons, whereas H1.3 binds intronic sequences. H1s are major splicing regulators, especially of exon skipping and intron retention events, through their effects on the elongation of RNA polymerase II (RNAPII). Thus, H1 variants determine splicing fate by modulating RNAPII elongation.


Asunto(s)
Histonas , ARN Polimerasa II , Humanos , Histonas/genética , Histonas/metabolismo , ARN Polimerasa II/genética , ARN Polimerasa II/metabolismo , Empalme del ARN , Transcripción Genética , Cromatina/genética , Empalme Alternativo
2.
Mol Cell ; 82(5): 1021-1034.e8, 2022 03 03.
Artículo en Inglés | MEDLINE | ID: mdl-35182478

RESUMEN

How the splicing machinery defines exons or introns as the spliced unit has remained a puzzle for 30 years. Here, we demonstrate that peripheral and central regions of the nucleus harbor genes with two distinct exon-intron GC content architectures that differ in the splicing outcome. Genes with low GC content exons, flanked by long introns with lower GC content, are localized in the periphery, and the exons are defined as the spliced unit. Alternative splicing of these genes results in exon skipping. In contrast, the nuclear center contains genes with a high GC content in the exons and short flanking introns. Most splicing of these genes occurs via intron definition, and aberrant splicing leads to intron retention. We demonstrate that the nuclear periphery and center generate different environments for the regulation of alternative splicing and that two sets of splicing factors form discrete regulatory subnetworks for the two gene architectures. Our study connects 3D genome organization and splicing, thus demonstrating that exon and intron definition modes of splicing occur in different nuclear regions.


Asunto(s)
Empalme Alternativo , Empalme del ARN , Composición de Base , Exones/genética , Intrones/genética
3.
J Invest Dermatol ; 143(12): 2494-2506.e4, 2023 12.
Artículo en Inglés | MEDLINE | ID: mdl-37236596

RESUMEN

Skin pigmentation is paused after sun exposure; however, the mechanism behind this pausing is unknown. In this study, we found that the UVB-induced DNA repair system, led by the ataxia telangiectasia mutated (ATM) protein kinase, represses MITF transcriptional activity of pigmentation genes while placing MITF in DNA repair mode, thus directly inhibiting pigment production. Phosphoproteomics analysis revealed ATM to be the most significantly enriched pathway among all UVB-induced DNA repair systems. ATM inhibition in mouse or human skin, either genetically or chemically, induces pigmentation. Upon UVB exposure, MITF transcriptional activation is blocked owing to ATM-dependent phosphorylation of MITF on S414, which modifies MITF activity and interactome toward DNA repair, including binding to TRIM28 and RBBP4. Accordingly, MITF genome occupancy is enriched in sites of high DNA damage that are likely repaired. This suggests that ATM harnesses the pigmentation key activator for the necessary rapid, efficient DNA repair, thus optimizing the chances of the cell surviving. Data are available from ProteomeXchange with the identifier PXD041121.


Asunto(s)
Ataxia Telangiectasia , Humanos , Animales , Ratones , Pigmentación de la Piel/genética , Reparación del ADN , Proteínas de la Ataxia Telangiectasia Mutada/genética , Proteínas de la Ataxia Telangiectasia Mutada/metabolismo , Transducción de Señal , Daño del ADN , Fosforilación , Proteínas de Ciclo Celular/genética , Proteínas de Ciclo Celular/metabolismo , Factor de Transcripción Asociado a Microftalmía/genética , Factor de Transcripción Asociado a Microftalmía/metabolismo
4.
Nat Commun ; 12(1): 4545, 2021 07 27.
Artículo en Inglés | MEDLINE | ID: mdl-34315864

RESUMEN

In the earliest step of spliceosome assembly, the two splice sites flanking an intron are brought into proximity by U1 snRNP and U2AF along with other proteins. The mechanism that facilitates this intron looping is poorly understood. Using a CRISPR interference-based approach to halt RNA polymerase II transcription in the middle of introns in human cells, we discovered that the nascent 5' splice site base pairs with a U1 snRNA that is tethered to RNA polymerase II during intron synthesis. This association functionally corresponds with splicing outcome, involves bona fide 5' splice sites and cryptic intronic sites, and occurs transcriptome-wide. Overall, our findings reveal that the upstream 5' splice sites remain attached to the transcriptional machinery during intron synthesis and are thus brought into proximity of the 3' splice sites; potentially mediating the rapid splicing of long introns.


Asunto(s)
Intrones/genética , Sitios de Empalme de ARN/genética , Transcripción Genética , Emparejamiento Base/genética , Secuencia de Bases , Exones/genética , Células HEK293 , Células HeLa , Humanos , Proteínas de Microfilamentos/genética , ARN Polimerasa II/metabolismo , Precursores del ARN/genética , Precursores del ARN/metabolismo , ARN Nuclear Pequeño/genética , ARN Nuclear Pequeño/metabolismo , Proteínas de Unión al ARN/genética , Ribonucleoproteína Nuclear Pequeña U1/metabolismo , Transcriptoma/genética
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