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1.
Anticancer Res ; 39(11): 6273-6282, 2019 Nov.
Artigo em Inglês | MEDLINE | ID: mdl-31704857

RESUMO

BACKGROUND/AIM: We have yet to understand why JAK2-positive myeloproliferative neoplasms (MPN) patients manifest different phenotypes despite harboring JAK2 mutations and what drives secondary transformations. PATIENTS AND METHODS: Using targeted sequencing, we analyzed mutational status of 17 polycythemia vera (PV), 16 essential thrombocythemia (ET), 8 primary myelofibrosis (PMF) patients who tested positive for JAK by polymerase chain reaction. RESULTS: The somatic mutations in JAK2 influence the clinical behavior of the disease. We found that ASXL1 or EZH2 mutation acquisition after JAK2 leads to PV, while ASXL1 mutation acquisition before JAK2 leads to ET or PMF. Mutations in TP53, ASXL1, and splicing genes are associated with the prognosis of MPN. PMF was more frequently associated with splicing mutations, while PV was more closely related to mutations in chromatin modifiers. The presence of these mutations influenced hemogram at MPN diagnosis. CONCLUSION: Each subtype of MPN harbors distinct patterns of somatic mutations and acquisition order, while mutations in TP53, ASXL1, and splicing genes may be associated with the prognosis of MPN.


Assuntos
Proteína Potenciadora do Homólogo 2 de Zeste/genética , Genes p53 , Janus Quinase 2/genética , Mutação , Policitemia Vera/genética , Mielofibrose Primária/genética , Proteínas Repressoras/genética , Trombocitemia Essencial/genética , Adulto , Idoso , Feminino , Humanos , Masculino , Pessoa de Meia-Idade , Fenótipo , Prognóstico , Processamento de RNA
2.
J Agric Food Chem ; 67(40): 11077-11088, 2019 Oct 09.
Artigo em Inglês | MEDLINE | ID: mdl-31525039

RESUMO

Cuticular wax accumulation in plants contributes to drought tolerance. Here, we compared the drought levels on two varieties with different genotypes in turnip (Brassica rapa var. rapa) and found that the drought tolerance was higher in the waxy KTRG-B48a than in the wax-free KTRG-B48b. A combination of PacBio and Illumina sequencing analyses revealed that differential transcripts were mainly enriched in the wax synthesis pathway, and a splice variant (BrrWSD1-X2) was identified in the waxy KTRG-B48a. BrrWSD1-X2 had a stronger ability to synthesize wax esters than BrrWSD1-X1 using heterologous expression in yeast (Saccharomyces cerevisiae) mutant H1246a. Then, we speculated that the T to C transversion of the third intron and the higher number of TA repeats in the third intron of BrrWSD1 DNA in the waxy KTRG-B48a may result in a lower efficiency of splicing recognition of the third intron, resulting in the emergence of BrrWSD1-X2 in waxy varieties.


Assuntos
Brassica rapa/fisiologia , Ésteres/metabolismo , Proteínas de Plantas/genética , Proteínas de Plantas/metabolismo , Ceras/metabolismo , Brassica rapa/genética , Secas , Processamento de RNA , Água/análise , Água/metabolismo
3.
BMC Evol Biol ; 19(1): 162, 2019 08 02.
Artigo em Inglês | MEDLINE | ID: mdl-31375061

RESUMO

BACKGROUND: Two spliceosomal intron types co-exist in eukaryotic precursor mRNAs and are excised by distinct U2-dependent and U12-dependent spliceosomes. In the diplomonad Giardia lamblia, small nuclear (sn) RNAs show hybrid characteristics of U2- and U12-dependent spliceosomal snRNAs and 5 of 11 identified remaining spliceosomal introns are trans-spliced. It is unknown whether unusual intron and spliceosome features are conserved in other diplomonads. RESULTS: We have identified spliceosomal introns, snRNAs and proteins from two additional diplomonads for which genome information is currently available, Spironucleus vortens and Spironucleus salmonicida, as well as relatives, including 6 verified cis-spliceosomal introns in S. vortens. Intron splicing signals are mostly conserved between the Spironucleus species and G. lamblia. Similar to 'long' G. lamblia introns, RNA secondary structural potential is evident for 'long' (> 50 nt) Spironucleus introns as well as introns identified in the parabasalid Trichomonas vaginalis. Base pairing within these introns is predicted to constrain spatial distances between splice junctions to similar distances seen in the shorter and uniformly-sized introns in these organisms. We find that several remaining Spironucleus spliceosomal introns are ancient. We identified a candidate U2 snRNA from S. vortens, and U2 and U5 snRNAs in S. salmonicida; cumulatively, illustrating significant snRNA differences within some diplomonads. Finally, we studied spliceosomal protein complements and find protein sets in Giardia, Spironucleus and Trepomonas sp. PC1 highly- reduced but well conserved across the clade, with between 44 and 62 out of 174 studied spliceosomal proteins detectable. Comparison with more distant relatives revealed a highly nested pattern, with the more intron-rich fornicate Kipferlia bialata retaining 87 total proteins including nearly all those observed in the diplomonad representatives, and the oxymonad Monocercomonoides retaining 115 total proteins including nearly all those observed in K. bialata. CONCLUSIONS: Comparisons in diplomonad representatives and species of other closely-related metamonad groups indicates similar patterns of intron structural conservation and spliceosomal protein composition but significant divergence of snRNA structure in genomically-reduced species. Relative to other eukaryotes, loss of evolutionarily-conserved snRNA domains and common sets of spliceosomal proteins point to a more streamlined splicing mechanism, where intron sequences and structures may be functionally compensating for the minimalization of spliceosome components.


Assuntos
Sequência Conservada , Diplomonadida/genética , Íntrons/genética , Parabasalídeos/genética , Filogenia , Spliceossomos/genética , Regiões 5' não Traduzidas/genética , Pareamento de Bases/genética , Sequência de Bases , Genoma , Conformação de Ácido Nucleico , Processamento de RNA/genética , RNA Mensageiro/genética , RNA Mensageiro/metabolismo , RNA Nuclear Pequeno/química , RNA Nuclear Pequeno/genética , Proteínas Ribossômicas/genética
4.
Cancer Sci ; 110(10): 3132-3144, 2019 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-31390121

RESUMO

Alternative splicing, regulated by DEAD-Box Helicase (DDX) families, plays an important role in cancer. However, the relationship between the DDX family and cancer has not been fully elucidated. In the present study, we identified a candidate oncogene DDX56 on Ch.7p by a bioinformatics approach using The Cancer Genome Atlas (TCGA) dataset of colorectal cancer (CRC). DDX56 expression was measured by RT-qPCR and immunochemical staining in 108 CRC patients. Clinicopathological and survival analyses were carried out using three CRC datasets. Biological roles of DDX56 were explored by gene set enrichment analysis (GSEA), and cell proliferation in vitro and in vivo, cell cycle assays, and using DDX56-knockdown or overexpressed CRC cells. RNA sequencing was carried out to elucidate the effect of DDX56 on mRNA splicing. We found that DDX56 expression was positively correlated with the amplification of DDX56 and was upregulated in CRC cells. High DDX56 expression was associated with lymphatic invasion and distant metastasis and was an independent poor prognostic factor. In vitro analysis, in vivo analysis and GSEA showed that DDX56 promoted proliferation ability through regulating the cell cycle. DDX56 knockdown reduced intron retention and tumor suppressor WEE1 expression, which functions as a G2-M DNA damage checkpoint. We have identified DDX56 as a novel oncogene and prognostic biomarker of CRC that promotes alternative splicing of WEE1.


Assuntos
Proteínas de Ciclo Celular/genética , Neoplasias Colorretais/patologia , RNA Helicases DEAD-box/genética , RNA Helicases DEAD-box/metabolismo , Amplificação de Genes , Proteínas Nucleares/genética , Proteínas Tirosina Quinases/genética , Regulação para Cima , Idoso , Animais , Ciclo Celular , Linhagem Celular Tumoral , Cromossomos Humanos Par 7/genética , Neoplasias Colorretais/genética , Neoplasias Colorretais/metabolismo , Feminino , Regulação Neoplásica da Expressão Gênica , Células HCT116 , Humanos , Masculino , Camundongos , Pessoa de Meia-Idade , Invasividade Neoplásica , Estadiamento de Neoplasias , Transplante de Neoplasias , Prognóstico , Processamento de RNA , Análise de Sequência de RNA , Análise de Sobrevida
5.
Cell Host Microbe ; 26(2): 154-155, 2019 08 14.
Artigo em Inglês | MEDLINE | ID: mdl-31415745

RESUMO

In this issue of Cell Host & Microbe, Courtney et al. (2019a) find that HIV-1 genomic RNA has much more m5C than cellular mRNA. Deleting the m5C "writer" NSUN2 decreases HIV-1 m5C levels, promotes translation of the HIV-1 5' gag gene, and alters splicing at the A2 site.


Assuntos
HIV-1/genética , RNA Viral , Animais , Vírus da Leucemia Murina , Metilação , Camundongos , Processamento de RNA
6.
Rinsho Ketsueki ; 60(7): 810-817, 2019.
Artigo em Japonês | MEDLINE | ID: mdl-31391371

RESUMO

Acute myeloid leukemia (AML) remains a devasting disease. Progress has been made to define molecular mechanisms underlying disease pathogenesis due, in part, to the near-complete understanding of AML genome. Nonetheless, functional studies are necessary to assess the significance of AML-associated mutations and devise urgently needed therapies. Genome-wide knockout screening, employing CRISPR-Cas9 genome editing, is a powerful tool in functional genomics. In this study, genome-wide CRISPR screening was performed using mouse leukemia cell lines developed in our Center, followed by in vivo screening. Among 20,611 genes, 130 AML essential genes were identified, including clinically actionable candidates. It was shown that mRNA decapping enzyme scavenger (DCPS), an enzyme implicated in mRNA decay pathway, is essential for AML survival. ShRNA-mediated gene knockdown and DCPS inhibitor (RG3039) were employed to validate findings. RG3039 induced cell-cycle arrest and apoptosis in vitro. Furthermore, mass spectrometry analysis revealed an association between DCPS and RNA metabolic pathways, and RNA-Seq showed that RG3039 treatment induced aberrant mRNA splicing in AML cells. Importantly, RG3039 exhibited anti-leukemia effects in PDX models. These findings identify DCPS as a novel therapeutic target for AML, shedding new light on the nuclear RNA metabolic pathway in leukemogenesis.


Assuntos
Sistemas CRISPR-Cas , Leucemia Mieloide Aguda/genética , Processamento de RNA , Estabilidade de RNA , Animais , Linhagem Celular Tumoral , Repetições Palindrômicas Curtas Agrupadas e Regularmente Espaçadas , Edição de Genes , Camundongos , RNA Interferente Pequeno
7.
Adv Exp Med Biol ; 1157: 29-39, 2019.
Artigo em Inglês | MEDLINE | ID: mdl-31342436

RESUMO

Post-transcriptional regulation of gene expression is fundamental for all forms of life, as it critically contributes to the composition and quantity of a cell's proteome. These processes encompass splicing, polyadenylation, mRNA decay, mRNA editing and modification and translation and are modulated by a variety of RNA-binding proteins (RBPs). Alterations affecting RBP expression and activity contribute to the development of different types of cancer. In this chapter, we discuss current research shedding light on the role of different RBPs in gliomas. These studies place RBPs as modulators of critical signaling pathways, establish their relevance as prognostic markers and open doors for new therapeutic strategies.


Assuntos
Glioma , Proteínas de Ligação a RNA , Glioma/fisiopatologia , Humanos , Poliadenilação , Processamento de RNA , Estabilidade de RNA , Proteínas de Ligação a RNA/metabolismo
8.
Adv Exp Med Biol ; 1157: 133-177, 2019.
Artigo em Inglês | MEDLINE | ID: mdl-31342441

RESUMO

In recent years, the RNA molecule became one of the most promising targets for therapeutic intervention. Currently, a large number of RNA-based therapeutics are being investigated both at the basic research level and in late-stage clinical trials. Some of them are even already approved for treatment. RNA-based approaches can act at pre-mRNA level (by splicing modulation/correction using antisense oligonucleotides or U1snRNA vectors), at mRNA level (inhibiting gene expression by siRNAs and antisense oligonucleotides) or at DNA level (by editing mutated sequences through the use of CRISPR/Cas). Other RNA approaches include the delivery of in vitro transcribed (IVT) mRNA or the use of oligonucleotides aptamers. Here we review these approaches and their translation into clinics trying to give a brief overview also on the difficulties to its application as well as the research that is being done to overcome them.


Assuntos
Terapia Genética , Oligonucleotídeos Antissenso , Oligonucleotídeos , Terapia Genética/tendências , Humanos , Processamento de RNA , RNA Mensageiro , RNA Interferente Pequeno
9.
Zhonghua Yi Xue Yi Chuan Xue Za Zhi ; 36(7): 666-671, 2019 Jul 10.
Artigo em Chinês | MEDLINE | ID: mdl-31302907

RESUMO

OBJECTIVE: To study the correlation of splicing mutations at the 5' end of the DMD gene with their phenotypes. METHODS: DMD gene mutations were analyzed using Multiplex Ligation Probe Amplification (MLPA) and Sanger sequencing. Co-segregation analysis was performed for the pedigrees of the probands. Influence of mutations on protein function was predicted by bioinformatic analysis. RESULTS: Three novel splicing mutations were identified in three patients with different phenotypes. Patient 1 carried a c.31+3insT mutation and presented primarily with dilated cardiomyopathy (XLDC). There was no clinical signs of skeletal myopathy. Bioinformatic analysis predicted that the mutation may inactivate the splicing donor of intron 1 and lead to premature termination of protein translation. Patient 2 carried a c.264_264+4delTGTAA mutation, which led to loss of splicing donor site for intron 4, and manifested Becker muscular dystrophy (BMD). The mutation was predicted to result in skipping of exon 4. The defective protein may still retain most of its function. Patient 3 had Duchenne muscular dystrophy (DMD) and carried a c.832-3C>T mutation which was predicted to decrease the activity of splicing acceptor of intron 8, resulting in usage of alternative acceptor site or retain of intron 8. All related transcripts may cause premature termination of protein translation and complete loss of protein function. The three mutations were all inherited from the mothers of the patients. CONCLUSION: Three novel splicing mutations were discovered at the 5' end of DMD gene in three patients with different disease phenotypes. Our study may facilitate understanding of the influence of splicing mutations at the 5' end of the DMD gene on dystrophin function and the correlation between genotypes and phenotypes.


Assuntos
Distrofina/genética , Distrofia Muscular de Duchenne/genética , Mutação , Processamento de RNA , Humanos , Fenótipo
10.
BMC Biol ; 17(1): 56, 2019 07 16.
Artigo em Inglês | MEDLINE | ID: mdl-31311534

RESUMO

BACKGROUND: Adaptive responses to stress are essential for cell and organismal survival. In metazoans, little is known about the impact of environmental stress on RNA homeostasis. RESULTS: By studying the regulation of a cadmium-induced gene named numr-1 in Caenorhabditis elegans, we discovered that disruption of RNA processing acts as a signal for environmental stress. We find that NUMR-1 contains motifs common to RNA splicing factors and influences RNA splicing in vivo. A genome-wide screen reveals that numr-1 is strongly and specifically induced by silencing of genes that function in basal RNA metabolism including subunits of the metazoan integrator complex. Human integrator processes snRNAs for functioning with splicing factors, and we find that silencing of C. elegans integrator subunits disrupts snRNA processing, causes aberrant pre-mRNA splicing, and induces the heat shock response. Cadmium, which also strongly induces numr-1, has similar effects on RNA and the heat shock response. Lastly, we find that heat shock factor-1 is required for full numr-1 induction by cadmium. CONCLUSION: Our results are consistent with a model in which disruption of integrator processing of RNA acts as a molecular damage signal initiating an adaptive stress response mediated by heat shock factor-1. When numr-1 is induced via this pathway in C. elegans, its function in RNA metabolism may allow it to mitigate further damage and thereby promote tolerance to cadmium.


Assuntos
Cádmio/toxicidade , Caenorhabditis elegans/fisiologia , Regulação da Expressão Gênica , Resposta ao Choque Térmico/fisiologia , Processamento Pós-Transcricional do RNA/fisiologia , Processamento de RNA , Animais , Caenorhabditis elegans/genética , Proteínas de Caenorhabditis elegans/genética , Proteínas de Caenorhabditis elegans/metabolismo , Resposta ao Choque Térmico/genética , Proteínas Nucleares/genética , Proteínas Nucleares/metabolismo , Fatores de Processamento de RNA/genética , Fatores de Processamento de RNA/metabolismo , RNA Nuclear Pequeno/genética , RNA Nuclear Pequeno/metabolismo , Estresse Fisiológico
11.
Nat Commun ; 10(1): 2983, 2019 07 05.
Artigo em Inglês | MEDLINE | ID: mdl-31278301

RESUMO

Ttriple-negative breast cancer (TNBC) is an aggressive and highly metastatic breast cancer subtype. Enhanced TNBC cell motility is a prerequisite of TNBC cell dissemination. Here, we apply an imaging-based RNAi phenotypic cell migration screen using two highly motile TNBC cell lines (Hs578T and MDA-MB-231) to provide a repository of signaling determinants that functionally drive TNBC cell motility. We have screened ~4,200 target genes individually and discovered 133 and 113 migratory modulators of Hs578T and MDA-MB-231, respectively, which are linked to signaling networks predictive for breast cancer progression. The splicing factors PRPF4B and BUD31 and the transcription factor BPTF are essential for cancer cell migration, amplified in human primary breast tumors and associated with metastasis-free survival. Depletion of PRPF4B, BUD31 and BPTF causes primarily down regulation of genes involved in focal adhesion and ECM-interaction pathways. PRPF4B is essential for TNBC metastasis formation in vivo, making PRPF4B a candidate for further drug development.


Assuntos
Movimento Celular/genética , Regulação Neoplásica da Expressão Gênica , Proteínas Serina-Treonina Quinases/metabolismo , Ribonucleoproteína Nuclear Pequena U4-U6/metabolismo , Neoplasias de Mama Triplo Negativas/patologia , Antígenos Nucleares/genética , Antígenos Nucleares/metabolismo , Linhagem Celular Tumoral , Estudos de Coortes , Conjuntos de Dados como Assunto , Intervalo Livre de Doença , Matriz Extracelular/metabolismo , Feminino , Adesões Focais/genética , Humanos , Microscopia Intravital , Proteínas do Tecido Nervoso/genética , Proteínas do Tecido Nervoso/metabolismo , Proteínas Nucleares/genética , Proteínas Nucleares/metabolismo , Proteínas Serina-Treonina Quinases/genética , Interferência de RNA , Processamento de RNA/genética , RNA Interferente Pequeno/metabolismo , Ribonucleoproteína Nuclear Pequena U4-U6/genética , Transdução de Sinais/genética , Análise de Sobrevida , Fatores de Transcrição/genética , Fatores de Transcrição/metabolismo , Neoplasias de Mama Triplo Negativas/genética , Neoplasias de Mama Triplo Negativas/mortalidade
12.
Cell Mol Life Sci ; 76(15): 2899-2916, 2019 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-31147750

RESUMO

Methylation of histone H3 lysine 36 (H3K36) plays crucial roles in the partitioning of chromatin to distinctive domains and the regulation of a wide range of biological processes. Trimethylation of H3K36 (H3K36me3) demarcates body regions of the actively transcribed genes, providing signals for modulating transcription fidelity, mRNA splicing and DNA damage repair; and di-methylation of H3K36 (H3K36me2) spreads out within large intragenic regions, regulating distribution of histone H3 lysine 27 trimethylation (H3K27me3) and possibly DNA methylation. These H3K36 methylation-mediated events are biologically crucial and controlled by different classes of proteins responsible for either 'writing', 'reading' or 'erasing' of H3K36 methylation marks. Deregulation of H3K36 methylation and related regulatory factors leads to pathogenesis of disease such as developmental syndrome and cancer. Additionally, recurrent mutations of H3K36 and surrounding histone residues are detected in human tumors, further highlighting the importance of H3K36 in biology and medicine. This review will elaborate on current advances in understanding H3K36 methylation and related molecular players during various chromatin-templated cellular processes, their crosstalks with other chromatin factors, as well as their deregulations in the diseased contexts.


Assuntos
Histonas/metabolismo , Neoplasias/patologia , Transtornos do Neurodesenvolvimento/patologia , Metilases de Modificação do DNA/metabolismo , Reparo do DNA , Histona Desmetilases/metabolismo , Histona-Lisina N-Metiltransferase/metabolismo , Humanos , Metilação , Neoplasias/metabolismo , Transtornos do Neurodesenvolvimento/metabolismo , Processamento de RNA
13.
Mol Biol (Mosk) ; 53(3): 524-528, 2019.
Artigo em Russo | MEDLINE | ID: mdl-31184618

RESUMO

Proteins with homo-repeats of more than 4 amino acid residues in length were examined to understand whether some splicing sites in pre-mRNA may be attributed to homo-repeats in human proteins. The human proteome was found to contain a total of 404 proteins with homo-repeats that account for at least one splicing site in pre-mRNA. Pre-mRNA splicing sites were more often found in the C-terminal part (67%) than in the middle orN-terminal part of a homo-repeat. Ten homo-repeats were identified to have two splicing sites per repeat. The repeats were lysine homo-repeats in all but one case.


Assuntos
Proteínas/análise , Proteínas/química , Precursores de RNA/genética , Sítios de Splice de RNA/genética , Sequências Repetitivas de Aminoácidos/genética , Humanos , Lisina/genética , Lisina/metabolismo , Proteínas/genética , Proteoma/análise , Proteoma/química , Proteoma/genética , Processamento de RNA/genética
14.
RNA ; 25(9): 1130-1149, 2019 09.
Artigo em Inglês | MEDLINE | ID: mdl-31175170

RESUMO

Minor intron splicing plays a central role in human embryonic development and survival. Indeed, biallelic mutations in RNU4ATAC, transcribed into the minor spliceosomal U4atac snRNA, are responsible for three rare autosomal recessive multimalformation disorders named Taybi-Linder (TALS/MOPD1), Roifman (RFMN), and Lowry-Wood (LWS) syndromes, which associate numerous overlapping signs of varying severity. Although RNA-seq experiments have been conducted on a few RFMN patient cells, none have been performed in TALS, and more generally no in-depth transcriptomic analysis of the ∼700 human genes containing a minor (U12-type) intron had been published as yet. We thus sequenced RNA from cells derived from five skin, three amniotic fluid, and one blood biosamples obtained from seven unrelated TALS cases and from age- and sex-matched controls. This allowed us to describe for the first time the mRNA expression and splicing profile of genes containing U12-type introns, in the context of a functional minor spliceosome. Concerning RNU4ATAC-mutated patients, we show that as expected, they display distinct U12-type intron splicing profiles compared to controls, but that rather unexpectedly mRNA expression levels are mostly unchanged. Furthermore, although U12-type intron missplicing concerns most of the expressed U12 genes, the level of U12-type intron retention is surprisingly low in fibroblasts and amniocytes, and much more pronounced in blood cells. Interestingly, we found several occurrences of introns that can be spliced using either U2, U12, or a combination of both types of splice site consensus sequences, with a shift towards splicing using preferentially U2 sites in TALS patients' cells compared to controls.


Assuntos
Nanismo/genética , Retardo do Crescimento Fetal/genética , Microcefalia/genética , Osteocondrodisplasias/genética , Processamento de RNA/genética , Transcriptoma/genética , Adulto , Idoso , Sequência de Bases/genética , Pré-Escolar , Sequência Consenso/genética , Feminino , Perfilação da Expressão Gênica/métodos , Humanos , Lactente , Íntrons/genética , Masculino , Pessoa de Meia-Idade , RNA/genética , RNA Mensageiro/genética , RNA Nuclear Pequeno/genética , Spliceossomos/genética , Adulto Jovem
15.
Nat Med ; 25(6): 911-919, 2019 06.
Artigo em Inglês | MEDLINE | ID: mdl-31160820

RESUMO

It is estimated that 350 million individuals worldwide suffer from rare diseases, which are predominantly caused by mutation in a single gene1. The current molecular diagnostic rate is estimated at 50%, with whole-exome sequencing (WES) among the most successful approaches2-5. For patients in whom WES is uninformative, RNA sequencing (RNA-seq) has shown diagnostic utility in specific tissues and diseases6-8. This includes muscle biopsies from patients with undiagnosed rare muscle disorders6,9, and cultured fibroblasts from patients with mitochondrial disorders7. However, for many individuals, biopsies are not performed for clinical care, and tissues are difficult to access. We sought to assess the utility of RNA-seq from blood as a diagnostic tool for rare diseases of different pathophysiologies. We generated whole-blood RNA-seq from 94 individuals with undiagnosed rare diseases spanning 16 diverse disease categories. We developed a robust approach to compare data from these individuals with large sets of RNA-seq data for controls (n = 1,594 unrelated controls and n = 49 family members) and demonstrated the impacts of expression, splicing, gene and variant filtering strategies on disease gene identification. Across our cohort, we observed that RNA-seq yields a 7.5% diagnostic rate, and an additional 16.7% with improved candidate gene resolution.


Assuntos
Doenças Raras/genética , Ceramidase Ácida/genética , Estudos de Casos e Controles , Criança , Pré-Escolar , Estudos de Coortes , Feminino , Variação Genética , Humanos , Masculino , Modelos Genéticos , Mutação , Oxirredutases atuantes sobre Doadores de Grupo CH-CH/genética , Canais de Potássio/genética , RNA/sangue , RNA/genética , Processamento de RNA/genética , Doenças Raras/sangue , Análise de Sequência de RNA , Sequenciamento Completo do Exoma
16.
Anim Genet ; 50(4): 395-398, 2019 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-31179574

RESUMO

In recent years, Luchuan pigs in southern China have been used to produce high-quality meat by crossbreeding them with Duroc boars; however, PSE (pale, soft and exudative) meat was frequently reported in the crossbred pigs, and the underlying reason remains unknown. We excluded the possibility of the well-known causative mutations in RYR1 and PRKAG3 but identified the existence of an unfavorable allele of a splicing mutation (g.8283C>A) in PHKG1 in two Duroc boars and three Duroc × Luchuan crossbred pigs with PSE meat. An association analysis with 425 Duroc × Luchuan crossbred pigs revealed that the polymorphism of the splicing site of PHKG1 has significant association with the ultimate meat pH value (P = 0.035) and color score (P = 0.004). In addition, a strong cis-eQTL (expression QTL) signal for the expression of PHKG1 was identified in 189 Duroc × Luchuan crossbred pigs, and the splicing mutation was proven to be significantly associated with the expression of PHKG1 (P = 4.01e-11). Furthermore, RNA-sequencing data analysis confirmed that 131 CC homozygotes had only one transcript (T1), with FPKM (fragments per kilobase of transcript per million) of 35.40 ± 7.28, and 58 CA heterozygotes had two types of transcripts (T1 and T2), with FPKM of 19.63 ± 5.11 and 9.20 ± 2.39 respectively. Based on the association and eQTL analysis results, we concluded that PSE meat in Duroc × Luchuan crossbred pigs is caused by the splicing mutation in PHKG1. Our findings further support the effect of the causative mutation in PHKG1 on meat quality. The GEO accession number for the data is GSE124315.


Assuntos
Locos de Características Quantitativas , Sus scrofa/genética , Animais , Carne , Músculo Esquelético/metabolismo , Mutação , Processamento de RNA
17.
Hum Genet ; 138(7): 771-785, 2019 Jul.
Artigo em Inglês | MEDLINE | ID: mdl-31168774

RESUMO

Modulation of dystrophin pre-mRNA splicing is an attractive strategy to ameliorate the severe phenotype of Duchenne muscular dystrophy (DMD), although this requires a better understanding of the mechanism of splicing regulation. Aberrant splicing caused by gene mutations provides a good model to study splicing regulatory cis-elements and binding proteins. In this study, we identified skipping of in-frame exon 25 induced by a nonsense mutation (NM_004006.2:c.3340A > T;p.Lys1114*) in the DMD gene. Site-directed mutagenesis study in minigenes suggested that c.3340A > T converts an exonic splicing enhancer sequence (ESE) to a silencer element (ESS). Indeed, RNA pull-down and functional study provided evidence that c.3340A > T abolishes the binding of the splicing enhancer protein Tra2ß and promotes interactions with the repressor proteins hnRNP A1, hnRNP A2, and hnRNP H. By carefully analyzing the sequence motif encompassing the mutation site, we concluded that the skipping of exon 25 was due to disruption of a Tra2ß-dependent ESE and the creation of a new ESS associated with hnRNP A1 and hnRNP A2, which in turn increased the recruitment of hnRNP H to a nearby binding site. Finally, we demonstrated that c.3340A > T impairs the splicing of upstream intron 24 in a splicing minigene assay. In addition, we showed that the correct splicing of exon 25 is finely regulated by multiple splicing regulators that function in opposite directions by binding to closely located ESE and ESS. Our results clarify the detailed molecular mechanism of exon skipping induced by the nonsense mutation c.3340A > T and also provide information on exon 25 splicing.


Assuntos
Distrofina/genética , Elementos Facilitadores Genéticos , Éxons , Distrofia Muscular de Duchenne/genética , Mutação de Sentido Incorreto , Processamento de RNA , Elementos Silenciadores Transcricionais , Adolescente , Regulação da Expressão Gênica , Humanos , Masculino , Distrofia Muscular de Duchenne/patologia
18.
Nat Commun ; 10(1): 2569, 2019 06 12.
Artigo em Inglês | MEDLINE | ID: mdl-31189880

RESUMO

Synonymous mutations have been viewed as silent mutations, since they only affect the DNA and mRNA, but not the amino acid sequence of the resulting protein. Nonetheless, recent studies suggest their significant impact on splicing, RNA stability, RNA folding, translation or co-translational protein folding. Hence, we compile 659194 synonymous mutations found in human cancer and characterize their properties. We provide the user-friendly, comprehensive resource for synonymous mutations in cancer, SynMICdb ( http://SynMICdb.dkfz.de ), which also contains orthogonal information about gene annotation, recurrence, mutation loads, cancer association, conservation, alternative events, impact on mRNA structure and a SynMICdb score. Notably, synonymous and missense mutations are depleted at the 5'-end of the coding sequence as well as at the ends of internal exons independent of mutational signatures. For patient-derived synonymous mutations in the oncogene KRAS, we indicate that single point mutations can have a relevant impact on expression as well as on mRNA secondary structure.


Assuntos
Bases de Dados de Ácidos Nucleicos , Regulação Neoplásica da Expressão Gênica/genética , Neoplasias/genética , Mutação Silenciosa/genética , Conjuntos de Dados como Assunto , Humanos , Mutação de Sentido Incorreto/genética , Mutação Puntual/genética , Proteínas Proto-Oncogênicas p21(ras)/genética , Dobramento de RNA/genética , Processamento de RNA/genética , RNA Mensageiro/química , RNA Mensageiro/genética
19.
Genome Biol ; 20(1): 83, 2019 04 30.
Artigo em Inglês | MEDLINE | ID: mdl-31036063

RESUMO

A proof-of-concept study has demonstrated the application of CRISPR-Cas9 for directed evolution in rice, engineering crops for desired traits.


Assuntos
Repetições Palindrômicas Curtas Agrupadas e Regularmente Espaçadas , Oryza/genética , Sistemas CRISPR-Cas , Processamento de RNA , Spliceossomos
20.
Biochim Biophys Acta Gene Regul Mech ; 1862(6): 634-642, 2019 06.
Artigo em Inglês | MEDLINE | ID: mdl-31042550

RESUMO

Removal of introns by pre-mRNA splicing is fundamental to gene function in eukaryotes. However, understanding the mechanism by which exon-intron boundaries are defined remains a challenging endeavor. Published reports support that the recruitment of U1 snRNP at the 5'ss marked by GU dinucleotides defines the 5'ss as well as facilitates 3'ss recognition through cross-exon interactions. However, exceptions to this rule exist as U1 snRNP recruited away from the 5'ss retains the capability to define the splice site, where the cleavage takes place. Independent reports employing exon 7 of Survival Motor Neuron (SMN) genes suggest a long-distance effect of U1 snRNP on splice site selection upon U1 snRNP recruitment at target sequences with or without GU dinucleotides. These findings underscore that sequences distinct from the 5'ss may also impact exon definition if U1 snRNP is recruited to them through partial complementarity with the U1 snRNA. In this review we discuss the expanded role of U1 snRNP in splice-site selection due to U1 ability to be recruited at more sites than predicted solely based on GU dinucleotides.


Assuntos
Sítios de Splice de RNA , Processamento de RNA/fisiologia , Ribonucleoproteína Nuclear Pequena U1/fisiologia , Processamento Alternativo , Éxons/genética , Humanos , Íntrons/genética , Mutação , Processamento de RNA/genética , RNA Nuclear Pequeno/genética , RNA Nuclear Pequeno/metabolismo , Ribonucleoproteína Nuclear Pequena U1/genética , Proteínas do Complexo SMN , Proteína 1 de Sobrevivência do Neurônio Motor
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