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1.
Genome Biol ; 22(1): 82, 2021 03 11.
Artigo em Inglês | MEDLINE | ID: mdl-33706811

RESUMO

BACKGROUND: Alternative polyadenylation (APA) refers to the regulated selection of polyadenylation sites (PASs) in transcripts, which determines the length of their 3' untranslated regions (3'UTRs). We have recently shown that SRSF3 and SRSF7, two closely related SR proteins, connect APA with mRNA export. The mechanism underlying APA regulation by SRSF3 and SRSF7 remained unknown. RESULTS: Here we combine iCLIP and 3'-end sequencing and find that SRSF3 and SRSF7 bind upstream of proximal PASs (pPASs), but they exert opposite effects on 3'UTR length. SRSF7 enhances pPAS usage in a concentration-dependent but splicing-independent manner by recruiting the cleavage factor FIP1, generating short 3'UTRs. Protein domains unique to SRSF7, which are absent from SRSF3, contribute to FIP1 recruitment. In contrast, SRSF3 promotes distal PAS (dPAS) usage and hence long 3'UTRs directly by counteracting SRSF7, but also indirectly by maintaining high levels of cleavage factor Im (CFIm) via alternative splicing. Upon SRSF3 depletion, CFIm levels decrease and 3'UTRs are shortened. The indirect SRSF3 targets are particularly sensitive to low CFIm levels, because here CFIm serves a dual function; it enhances dPAS and inhibits pPAS usage by binding immediately downstream and assembling unproductive cleavage complexes, which together promotes long 3'UTRs. CONCLUSIONS: We demonstrate that SRSF3 and SRSF7 are direct modulators of pPAS usage and show how small differences in the domain architecture of SR proteins can confer opposite effects on pPAS regulation.


Assuntos
Regiões 3' não Traduzidas , Fator de Especificidade de Clivagem e Poliadenilação/genética , Regulação da Expressão Gênica , Poli A , Fatores de Processamento de Serina-Arginina/metabolismo , Processamento Alternativo , Animais , Sequência de Bases , Camundongos , Modelos Biológicos , Proteínas Monoméricas de Ligação ao GTP/metabolismo , Neurônios , Fosforilação , Proteínas de Ligação a Poli(A)/metabolismo , Poliadenilação , Ligação Proteica , Domínios e Motivos de Interação entre Proteínas , RNA Mensageiro/genética , RNA Mensageiro/metabolismo
2.
Adv Exp Med Biol ; 1203: 83-112, 2019.
Artigo em Inglês | MEDLINE | ID: mdl-31811631

RESUMO

Serine- and arginine-rich proteins (SR proteins) are a family of multitasking RNA-binding proteins (RBPs) that are key determinants of messenger ribonucleoprotein (mRNP) formation, identity and fate. Apart from their essential functions in pre-mRNA splicing, SR proteins display additional pre- and post-splicing activities and connect nuclear and cytoplasmic gene expression machineries. Through changes in their post-translational modifications (PTMs) and their subcellular localization, they provide functional specificity and adjustability to mRNPs. Transcriptome-wide UV crosslinking and immunoprecipitation (CLIP-Seq) studies revealed that individual SR proteins are present in distinct mRNPs and act in specific pairs to regulate different gene expression programmes. Adopting an mRNP-centric viewpoint, we discuss the roles of SR proteins in the assembly, maturation, quality control and turnover of mRNPs and describe the mechanisms by which they integrate external signals, coordinate their multiple tasks and couple subsequent mRNA processing steps.


Assuntos
Splicing de RNA , Proteínas de Ligação a RNA , Ribonucleoproteínas , Regulação da Expressão Gênica , Proteínas de Ligação a RNA/metabolismo , Ribonucleoproteínas/metabolismo
3.
Microbiology (Reading) ; 164(4): 646-658, 2018 04.
Artigo em Inglês | MEDLINE | ID: mdl-29469690

RESUMO

Translation initiation in 50-70 % of transcripts in Escherichia coli requires base pairing between the Shine-Dalgarno (SD) motif in the mRNA and the anti-SD motif at the 3' end of the 16S rRNA. However, 30-50 % of E. coli transcripts are non-canonical and are not preceded by an SD motif. The 5' ends of 44 E. coli transcripts were determined, all of which contained a 5'-UTR (no leaderless transcripts), but only a minority contained an SD motif. The 5'-UTR lengths were compared with those listed in RegulonDB and reported in previous publications, and the identities and differences were obtained in all possible combinations. We aimed to quantify the translational efficiencies of non-canonical 5'-UTRs using GusA reporter gene assays and Northern blot analyses. Ten non-canonical 5'-UTRs and two control 5'-UTRs with an SD motif were cloned upstream of the gusA gene. The translational efficiencies were quantified under five different conditions (different growth rates via two different temperatures and two different carbon sources, and heat shock). The translational efficiencies of the non-canonical 5'-UTRs varied widely, from 5 to 384 % of the positive control. In addition, the non-canonical transcripts did not exhibit a common regulatory pattern with changing environmental parameters. No correlation could be observed between the translational efficiencies of the non-canonical 5'-UTRs and their lengths, sequences, GC content, or predicted secondary structures. The introduction of an SD motif enhanced the translational efficiency of a poorly translated non-canonical transcript, while the efficiency of a well-translated non-canonical transcript remained unchanged. Taken together, the mechanisms of translation initiation at non-canonical transcripts in E. coli still need to be elucidated.


Assuntos
Escherichia coli/genética , Motivos de Nucleotídeos/fisiologia , Iniciação Traducional da Cadeia Peptídica/genética , RNA Bacteriano/genética , RNA Mensageiro/genética , Regiões 5' não Traduzidas/genética , Proteínas de Bactérias/biossíntese , Genes Reporter , Motivos de Nucleotídeos/genética , RNA Bacteriano/metabolismo , RNA Mensageiro/metabolismo
4.
Semin Cell Dev Biol ; 79: 131-142, 2018 07.
Artigo em Inglês | MEDLINE | ID: mdl-29102717

RESUMO

Nuclear retention of incompletely spliced or mature mRNAs emerges as a novel, previously underappreciated layer of gene regulation, which enables the cell to rapidly respond to stress, viral infection, differentiation cues or changing environmental conditions. Focusing on mammalian cells, we discuss recent insights into the mechanisms and functions of nuclear retention, describe retention-promoting features in protein-coding transcripts and propose mechanisms for their regulated release into the cytoplasm. Moreover, we discuss examples of how aberrant nuclear retention of mRNAs may lead to human diseases.


Assuntos
Núcleo Celular/genética , Doença/genética , Regulação da Expressão Gênica , RNA Mensageiro/genética , Transporte Ativo do Núcleo Celular , Animais , Núcleo Celular/metabolismo , Citoplasma/genética , Citoplasma/metabolismo , Humanos , Modelos Genéticos , Controle de Qualidade , RNA Mensageiro/metabolismo
5.
J Cell Biol ; 216(7): 1993-2009, 2017 07 03.
Artigo em Inglês | MEDLINE | ID: mdl-28592444

RESUMO

SR proteins function in nuclear pre-mRNA processing, mRNA export, and translation. To investigate their cellular dynamics, we developed a quantitative assay, which detects differences in nucleocytoplasmic shuttling among seven canonical SR protein family members. As expected, SRSF2 and SRSF5 shuttle poorly in HeLa cells but surprisingly display considerable shuttling in pluripotent murine P19 cells. Combining individual-resolution cross-linking and immunoprecipitation (iCLIP) and mass spectrometry, we show that elevated arginine methylation of SRSF5 and lower phosphorylation levels of cobound SRSF2 enhance shuttling of SRSF5 in P19 cells by modulating protein-protein and protein-RNA interactions. Moreover, SRSF5 is bound to pluripotency-specific transcripts such as Lin28a and Pou5f1/Oct4 in the cytoplasm. SRSF5 depletion reduces and overexpression increases their cytoplasmic mRNA levels, suggesting that enhanced mRNA export by SRSF5 is required for the expression of pluripotency factors. Remarkably, neural differentiation of P19 cells leads to dramatically reduced SRSF5 shuttling. Our findings indicate that posttranslational modification of SR proteins underlies the regulation of their mRNA export activities and distinguishes pluripotent from differentiated cells.


Assuntos
Diferenciação Celular , Núcleo Celular/metabolismo , Células-Tronco Pluripotentes/metabolismo , RNA Mensageiro/metabolismo , Fatores de Processamento de Serina-Arginina/metabolismo , Transporte Ativo do Núcleo Celular , Animais , Arginina , Proteínas de Ligação a DNA/genética , Proteínas de Ligação a DNA/metabolismo , Células HeLa , Humanos , Imunoprecipitação , Metilação , Camundongos , Neurogênese , Fenótipo , Fosforilação , Ligação Proteica , Processamento de Proteína Pós-Traducional , Interferência de RNA , RNA Mensageiro/genética , Proteínas de Ligação a RNA/genética , Proteínas de Ligação a RNA/metabolismo , Proteínas Repressoras/genética , Proteínas Repressoras/metabolismo , Fatores de Processamento de Serina-Arginina/genética , Espectrometria de Massas em Tandem , Fatores de Transcrição/genética , Fatores de Transcrição/metabolismo , Transfecção
6.
J Microbiol Methods ; 131: 181-187, 2016 12.
Artigo em Inglês | MEDLINE | ID: mdl-27794441

RESUMO

Reporter genes facilitate the characterization of promoter activities, transcript stabilities, translational efficiencies, or intracellular localization. Various reporter genes for Escherichia coli have been established, however, most of them have drawbacks like transcript instability or the inability to be used in genetic selections. Therefore, the glpD gene encoding glycerol-3-phosphate dehydrogenase was introduced as a novel reporter gene for E. coli. The enzymatic assay was optimized, and it was verified that growth on glycerol strictly depends on the presence of GlpD. The 5'-UTRs of three E. coli genes were chosen and cloned upstream of the new reporter gene glpD as well as the established reporter genes lacZ and gusA. Protein and transcript levels were quantified and translational efficiencies were calculated. The lacZ transcript was very unstable and its level highly depended on its translation, compromising its use as a reporter. The results obtained with gusA and glpD were similar, however, only glpD can be used for genetic selections. Therefore, glpD was found to be a superior novel reporter gene compared to the established reporter genes lacZ and gusA.


Assuntos
Escherichia coli/genética , Genes Reporter/genética , Glicerolfosfato Desidrogenase/genética , Óperon Lac/genética , Clonagem Molecular , DNA Bacteriano/genética , Ensaios Enzimáticos/métodos , Escherichia coli/enzimologia , Escherichia coli/crescimento & desenvolvimento , Regulação Bacteriana da Expressão Gênica , Fusão Gênica , Genes Bacterianos/genética , Glicerol/metabolismo , Glicerolfosfato Desidrogenase/metabolismo , Regiões Promotoras Genéticas , Transcrição Gênica
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