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1.
Nat Commun ; 12(1): 847, 2021 02 08.
Artículo en Inglés | MEDLINE | ID: mdl-33558503

RESUMEN

A large G4C2-repeat expansion in C9orf72 is the most common genetic cause of amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). Neuronal degeneration associated with this expansion arises from a loss of C9orf72 protein, the accumulation of RNA foci, the expression of dipeptide repeat (DPR) proteins, or all these factors. We report the discovery of a new targeting sequence that is common to all C9orf72 transcripts but enables preferential knockdown of repeat-containing transcripts in multiple cellular models and C9BAC transgenic mice. We optimize stereopure oligonucleotides that act through this site, and we demonstrate that their preferential activity depends on both backbone stereochemistry and asymmetric wing design. In mice, stereopure oligonucleotides produce durable depletion of pathogenic signatures without disrupting protein expression. These oligonucleotides selectively protect motor neurons harboring C9orf72-expansion mutation from glutamate-induced toxicity. We hypothesize that targeting C9orf72 with stereopure oligonucleotides may be a viable therapeutic approach for the treatment of C9orf72-associated neurodegenerative disorders.


Asunto(s)
Proteína C9orf72/genética , Expansión de las Repeticiones de ADN/genética , Mutación/genética , Oligonucleótidos/química , Oligonucleótidos/genética , Esclerosis Amiotrófica Lateral/genética , Esclerosis Amiotrófica Lateral/patología , Animales , Proteína C9orf72/química , Exones/genética , Glutamatos/toxicidad , Intrones/genética , Ratones , Neuronas Motoras/efectos de los fármacos , Neuronas Motoras/patología , Empalme del ARN/genética , ARN Mensajero/genética , ARN Mensajero/metabolismo , Estereoisomerismo
2.
Medicine (Baltimore) ; 100(6): e24301, 2021 Feb 12.
Artículo en Inglés | MEDLINE | ID: mdl-33578525

RESUMEN

RATIONALE: Marfan syndrome (MFS) has been defined as a genetic disorder that affects various systems such as the musculoskeletal, orbital, and cardiovascular systems. Neonatal MFS is considered rare and the most severe form of MFS is characterized by rapidly progressive atrioventricular valve dysfunction, often leading to death during early childhood due to congestive heart failure. PATIENT CONCERNS: A newborn with neonatal MFS and severe cardiac involvement. He presented various severe clinical features such as arachnodactyly, camptodactyly, elbow and knee joint contracture, senile facial appearance, and deep settling with down-slanting palpebral fissure, hypoplastic ear cartilage, sagging mouth, brachycephaly, and ectopia lentis. DIAGNOSIS: Genetic analysis revealed a novel mutation at nucleotide 3964 (c.3964 + 1 G > T) in intron 32 of the fibrillin-1 gene. This mutation is identified to be in the so-called neonatal region of fibrillin-1 exon 24 to 32, as reported previously. INTERVENTIONS: The patient was managed medically for improving the low cardiac output according to severe mitral regurgitation and aortic regurgitation. Afterload reduction, full sedation, and use of diuretic were attempted to improve the oliguria and heart failure. OUTCOMES: Despite the medical management, aortic regurgitation, mitral regurgitation, pulmonary hypertension, and cardiac contractility got worse. Surgical treatment is essential to prolong the patient's life, however, considerations for the grave progression of the disease make families decide to continue palliative care instead of surgical treatment. A few months after birth, he presented with rapidly progressive aortic regurgitation, mitral regurgitation, and congestive heart failure leading to death. CONCLUSIONS: This review demonstrated the prominent characteristics of neonatal MFS mutations, it would be helpful for the recognition of novel neonatal MFS variants and valuable for the understanding of the genotype-phenotype correlations and using the plans for managements and counseling in neonatal MFS.


Asunto(s)
Anomalías Congénitas/genética , Fibrilina-1/genética , Intrones/genética , Síndrome de Marfan/genética , Anomalías Cardiovasculares/complicaciones , Sistema Cardiovascular/patología , Anomalías Congénitas/etiología , Exones/genética , Resultado Fatal , Fibrilinas/genética , Insuficiencia Cardíaca/tratamiento farmacológico , Humanos , Recién Nacido , Masculino , Mutación , Oliguria/tratamiento farmacológico
3.
Zhonghua Yi Xue Yi Chuan Xue Za Zhi ; 38(1): 20-22, 2021 Jan 10.
Artículo en Chino | MEDLINE | ID: mdl-33423251

RESUMEN

OBJECTIVE: To explore the molecular basis for an individual suspected as AwB subtype through DNA sequencing. METHODS: ABO serology was carried out with the standard tube method. To identify the ABO gene haplotype, the amplicons of exon 7 were cloned and sequenced. RESULTS: Serological results showed that the forward typing was AwB and the reverse typing was B. Sequencing analysis revealed that the sample has contained an O01 allele in addition with c.297A>G, c.657C>T, c.796C>A, c.803G>C, c.930G>A variants as compared with the A101 allele. CONCLUSION: Through sequencing analysis, the sample with an AwB subtype by serological testing was identified as a novel B(A) phenotype, which was unreported previously.


Asunto(s)
Sistema del Grupo Sanguíneo ABO , Alelos , Mutación Missense , Sistema del Grupo Sanguíneo ABO/sangre , Sistema del Grupo Sanguíneo ABO/genética , Secuencia de Bases , Exones/genética , Humanos , Fenotipo
4.
Zhonghua Yi Xue Yi Chuan Xue Za Zhi ; 38(1): 78-82, 2021 Jan 10.
Artículo en Chino | MEDLINE | ID: mdl-33423265

RESUMEN

OBJECTIVE: To detect variant of the CD40L gene and infection of Jamestown Canyon virus (JCV) in a 7-year-and-9-month-old boy with co-commitment progressive multifocal leukoencephalopathy (PML) and X-linked hyper IgM syndrome (XHIGM). METHODS: Peripheral blood samples of the child and his parents were collected for the extraction of genomic DNA. The 5 exons and exon/intronic boundaries of the CD40L gene were subjected to PCR amplification and sequencing. Suspected variants were analyzed by using bioinformatic software. The JCV gene was amplified from genomic DNA by nested PCR and sequenced. RESULTS: The child was found to harbor a hemizygous c.506 A>C (p.Y169S) missense variant in exon 5 of the CD40L gene. The variant may affect the TNFH domain of the CD40L protein and result in structural instability and loss of hydrophobic interaction between CD40L and CD40. As predicted by PolyPhen2 and SIFT software, the variant was probably damaging (score = 1.00) and deleterious (score= -8.868). His mother was found to be a heterozygous carrier, while the same variant was not found in his father. Gel electrophoresis of the nested PCR product revealed presence of target JCV band, which was confirmed to be 99% identical with the JCV gene by sequencing. CONCLUSION: The patient was diagnosed with co-commitment XHIGM and PML based on the testing of the CD40L gene and JCV infection.


Asunto(s)
Ligando de CD40 , Síndrome de Inmunodeficiencia con Hiper-IgM Tipo 1 , Leucoencefalopatía Multifocal Progresiva , Adulto , Ligando de CD40/genética , Niño , Exones/genética , Femenino , Humanos , Síndrome de Inmunodeficiencia con Hiper-IgM Tipo 1/genética , Leucoencefalopatía Multifocal Progresiva/genética , Masculino , Mutación Missense , Reacción en Cadena de la Polimerasa
5.
Nat Commun ; 12(1): 286, 2021 01 12.
Artículo en Inglés | MEDLINE | ID: mdl-33436599

RESUMEN

High-throughput sequencing protocols such as RNA-seq have made it possible to interrogate the sequence, structure and abundance of RNA transcripts at higher resolution than previous microarray and other molecular techniques. While many computational tools have been proposed for identifying mRNA variation through differential splicing/alternative exon usage, challenges in its analysis remain. Here, we propose a framework for unbiased and robust discovery of aberrant RNA transcript structures using short read sequencing data based on shape changes in an RNA-seq coverage profile. Shape changes in selecting sample outliers in RNA-seq, SCISSOR, is a series of procedures for transforming and normalizing base-level RNA sequencing coverage data in a transcript independent manner, followed by a statistical framework for its analysis ( https://github.com/hyochoi/SCISSOR ). The resulting high dimensional object is amenable to unsupervised screening of structural alterations across RNA-seq cohorts with nearly no assumption on the mutational mechanisms underlying abnormalities. This enables SCISSOR to independently recapture known variants such as splice site mutations in tumor suppressor genes as well as novel variants that are previously unrecognized or difficult to identify by any existing methods including recurrent alternate transcription start sites and recurrent complex deletions in 3' UTRs.


Asunto(s)
ARN Mensajero/química , Análisis de Secuencia de ARN , Programas Informáticos , Islas de CpG/genética , Exones/genética , Sitios Genéticos , Genoma Humano , Humanos , Reproducibilidad de los Resultados , Proteína p53 Supresora de Tumor/genética
6.
Nat Commun ; 12(1): 2, 2021 01 04.
Artículo en Inglés | MEDLINE | ID: mdl-33397972

RESUMEN

Oxford Nanopore (ONT) is a leading long-read technology which has been revolutionizing transcriptome analysis through its capacity to sequence the majority of transcripts from end-to-end. This has greatly increased our ability to study the diversity of transcription mechanisms such as transcription initiation, termination, and alternative splicing. However, ONT still suffers from high error rates which have thus far limited its scope to reference-based analyses. When a reference is not available or is not a viable option due to reference-bias, error correction is a crucial step towards the reconstruction of the sequenced transcripts and downstream sequence analysis of transcripts. In this paper, we present a novel computational method to error correct ONT cDNA sequencing data, called isONcorrect. IsONcorrect is able to jointly use all isoforms from a gene during error correction, thereby allowing it to correct reads at low sequencing depths. We are able to obtain a median accuracy of 98.9-99.6%, demonstrating the feasibility of applying cost-effective cDNA full transcript length sequencing for reference-free transcriptome analysis.


Asunto(s)
Perfilación de la Expresión Génica , Nanoporos , Nanotecnología/métodos , Algoritmos , Alelos , Animales , Drosophila melanogaster/genética , Exones/genética , Regulación de la Expresión Génica , Heurística , Polimorfismo de Nucleótido Simple/genética , Isoformas de Proteínas/metabolismo , Sitios de Empalme de ARN/genética , ARN Mensajero/genética , ARN Mensajero/metabolismo
7.
Nat Commun ; 12(1): 682, 2021 01 29.
Artículo en Inglés | MEDLINE | ID: mdl-33514745

RESUMEN

Alternative splicing relies on the combinatorial recruitment of splicing regulators to specific RNA binding sites. Chromatin has been shown to impact this recruitment. However, a limited number of histone marks have been studied at a global level. In this work, a machine learning approach, applied to extensive epigenomics datasets in human H1 embryonic stem cells and IMR90 foetal fibroblasts, has identified eleven chromatin modifications that differentially mark alternatively spliced exons depending on the level of exon inclusion. These marks act in a combinatorial and position-dependent way, creating characteristic splicing-associated chromatin signatures (SACS). In support of a functional role for SACS in coordinating splicing regulation, changes in the alternative splicing of SACS-marked exons between ten different cell lines correlate with changes in SACS enrichment levels and recruitment of the splicing regulators predicted by RNA motif search analysis. We propose the dynamic nature of chromatin modifications as a mechanism to rapidly fine-tune alternative splicing when necessary.


Asunto(s)
Empalme Alternativo/genética , Cromatina/genética , Código de Histonas/genética , Línea Celular , Conjuntos de Datos como Asunto , Epigenómica/métodos , Exones/genética , Fibroblastos , Histonas/genética , Histonas/metabolismo , Células Madre Embrionarias Humanas , Humanos , Aprendizaje Automático , Motivos de Nucleótidos/genética , RNA-Seq
8.
Nat Commun ; 12(1): 73, 2021 01 04.
Artículo en Inglés | MEDLINE | ID: mdl-33397987

RESUMEN

In the male germ cells of placental mammals, 26-30-nt-long PIWI-interacting RNAs (piRNAs) emerge when spermatocytes enter the pachytene phase of meiosis. In mice, pachytene piRNAs derive from ~100 discrete autosomal loci that produce canonical RNA polymerase II transcripts. These piRNA clusters bear 5' caps and 3' poly(A) tails, and often contain introns that are removed before nuclear export and processing into piRNAs. What marks pachytene piRNA clusters to produce piRNAs, and what confines their expression to the germline? We report that an unusually long first exon (≥ 10 kb) or a long, unspliced transcript correlates with germline-specific transcription and piRNA production. Our integrative analysis of transcriptome, piRNA, and epigenome datasets across multiple species reveals that a long first exon is an evolutionarily conserved feature of pachytene piRNA clusters. Furthermore, a highly methylated promoter, often containing a low or intermediate level of CG dinucleotides, correlates with germline expression and somatic silencing of pachytene piRNA clusters. Pachytene piRNA precursor transcripts bind THOC1 and THOC2, THO complex subunits known to promote transcriptional elongation and mRNA nuclear export. Together, these features may explain why the major sources of pachytene piRNA clusters specifically generate these unique small RNAs in the male germline of placental mammals.


Asunto(s)
Epigénesis Genética , Exones/genética , Mamíferos/genética , Fase Paquiteno/genética , ARN Interferente Pequeño/metabolismo , 5-Metilcitosina/análogos & derivados , 5-Metilcitosina/metabolismo , Acetilación , Animales , Metilación de ADN/genética , Proteínas de Unión al ADN/metabolismo , Evolución Molecular , Histonas/metabolismo , Intrones/genética , Masculino , Ratones Endogámicos C57BL , Proteínas Nucleares/metabolismo , Especificidad de Órganos/genética , Regiones Promotoras Genéticas/genética , Empalme del ARN/genética , ARN Mensajero/genética , ARN Mensajero/metabolismo , Proteínas de Unión al ARN/metabolismo , Transducción de Señal/genética , Testículo/metabolismo , Transcripción Genética
9.
Nat Commun ; 12(1): 383, 2021 01 15.
Artículo en Inglés | MEDLINE | ID: mdl-33452256

RESUMEN

The transcription factor p63 mediates distinct cellular responses, primarily regulating epithelial and oocyte biology. In addition to the two amino terminal isoforms, TAp63 and ΔNp63, the 3'-end of p63 mRNA undergoes tissue-specific alternative splicing that leads to several isoforms, including p63α, p63ß and p63γ. To investigate in vivo how the different isoforms fulfil distinct functions at the cellular and developmental levels, we developed a mouse model replacing the p63α with p63ß by deletion of exon 13 in the Trp63 gene. Here, we report that whereas in two organs physiologically expressing p63α, such as thymus and skin, no abnormalities are detected, total infertility is evident in heterozygous female mice. A sharp reduction in the number of primary oocytes during the first week after birth occurs as a consequence of the enhanced expression of the pro-apoptotic transcriptional targets Puma and Noxa by the tetrameric, constitutively active, TAp63ß isoform. Hence, these mice show a condition of ovary dysfunction, resembling human primary ovary insufficiency. Our results show that the p63 C-terminus is essential in TAp63α-expressing primary oocytes to control cell death in vivo, expanding the current understanding of human primary ovarian insufficiency.


Asunto(s)
Infertilidad Femenina/genética , Oocitos/patología , Insuficiencia Ovárica Primaria/genética , Transactivadores/genética , Empalme Alternativo/genética , Animales , Apoptosis/genética , Proteínas Reguladoras de la Apoptosis/genética , Células Cultivadas , Modelos Animales de Enfermedad , Exones/genética , Femenino , Heterocigoto , Humanos , Infertilidad Femenina/patología , Masculino , Ratones , Mutación , Cultivo Primario de Células , Insuficiencia Ovárica Primaria/complicaciones , Insuficiencia Ovárica Primaria/patología , Isoformas de Proteínas/genética , Isoformas de Proteínas/metabolismo , Proteínas Proto-Oncogénicas c-bcl-2/genética , Transactivadores/metabolismo , Activación Transcripcional , Proteínas Supresoras de Tumor/genética
10.
Nat Commun ; 12(1): 428, 2021 01 18.
Artículo en Inglés | MEDLINE | ID: mdl-33462199

RESUMEN

The human prototypical SR protein SRSF1 is an oncoprotein that contains two RRMs and plays a pivotal role in RNA metabolism. We determined the structure of the RRM1 bound to RNA and found that the domain binds preferentially to a CN motif (N is for any nucleotide). Based on this solution structure, we engineered a protein containing a single glutamate to asparagine mutation (E87N), which gains the ability to bind to uridines and thereby activates SMN exon7 inclusion, a strategy that is used to cure spinal muscular atrophy. Finally, we revealed that the flexible inter-RRM linker of SRSF1 allows RRM1 to bind RNA on both sides of RRM2 binding site. Besides revealing an unexpected bimodal mode of interaction of SRSF1 with RNA, which will be of interest to design new therapeutic strategies, this study brings a new perspective on the mode of action of SRSF1 in cells.


Asunto(s)
Motivo de Reconocimiento de ARN/genética , Sitios de Empalme de ARN/genética , Empalme del ARN , Factores de Empalme Serina-Arginina/metabolismo , Proteína 1 para la Supervivencia de la Neurona Motora/genética , Sustitución de Aminoácidos , Asparagina/genética , Biología Computacional , Exones/genética , Ácido Glutámico/genética , Células HEK293 , Humanos , Simulación de Dinámica Molecular , Atrofia Muscular Espinal/genética , Atrofia Muscular Espinal/terapia , Resonancia Magnética Nuclear Biomolecular , Ingeniería de Proteínas , Proteínas Recombinantes/genética , Proteínas Recombinantes/aislamiento & purificación , Proteínas Recombinantes/metabolismo , Proteínas Recombinantes/ultraestructura , Factores de Empalme Serina-Arginina/genética , Factores de Empalme Serina-Arginina/aislamiento & purificación , Factores de Empalme Serina-Arginina/ultraestructura , Uridina/metabolismo
11.
Nucleic Acids Res ; 49(1): 479-490, 2021 01 11.
Artículo en Inglés | MEDLINE | ID: mdl-33330934

RESUMEN

The mammalian Ate1 gene encodes an arginyl transferase enzyme with tumor suppressor function that depends on the inclusion of one of the two mutually exclusive exons (MXE), exons 7a and 7b. We report that the molecular mechanism underlying MXE splicing in Ate1 involves five conserved regulatory intronic elements R1-R5, of which R1 and R4 compete for base pairing with R3, while R2 and R5 form an ultra-long-range RNA structure spanning 30 Kb. In minigenes, single and double mutations that disrupt base pairings in R1R3 and R3R4 lead to the loss of MXE splicing, while compensatory triple mutations that restore RNA structure revert splicing to that of the wild type. In the endogenous Ate1 pre-mRNA, blocking the competing base pairings by LNA/DNA mixmers complementary to R3 leads to the loss of MXE splicing, while the disruption of R2R5 interaction changes the ratio of MXE. That is, Ate1 splicing is controlled by two independent, dynamically interacting, and functionally distinct RNA structure modules. Exon 7a becomes more included in response to RNA Pol II slowdown, however it fails to do so when the ultra-long-range R2R5 interaction is disrupted, indicating that exon 7a/7b ratio depends on co-transcriptional RNA folding. In sum, these results demonstrate that splicing is coordinated both in time and in space over very long distances, and that the interaction of these components is mediated by RNA structure.


Asunto(s)
Empalme Alternativo/genética , Aminoaciltransferasas/genética , Conformación de Ácido Nucleico , Oligonucleótidos Antisentido/farmacología , Oligonucleótidos/farmacología , Pliegue del ARN , Precursores del ARN/genética , ARN Mensajero/genética , Células A549 , Secuencia de Bases , Línea Celular Tumoral , Secuencia Conservada , Exones/genética , Regulación de la Expresión Génica/efectos de los fármacos , Humanos , Intrones/genética , Mutagénesis Sitio-Dirigida , Proteínas de Neoplasias/genética , Oligonucleótidos/genética , Oligonucleótidos Antisentido/genética , Especificidad de Órganos , ARN Mensajero/metabolismo , Alineación de Secuencia , Homología de Secuencia de Ácido Nucleico , Elongación de la Transcripción Genética
12.
Gene ; 765: 145045, 2021 Jan 10.
Artículo en Inglés | MEDLINE | ID: mdl-32777524

RESUMEN

To find the variant spectrum of the cystic fibrosis transmembrane conductance regulator (CFTR) gene, and evaluate its frequent variants in Chinese congenital absence of vas deferens (CAVD) patients. A total of 276 patients with azoospermia and CAVD (aged from 21 to 44 years old) were investigated from May 2013 to September 2019 in the Third Affiliated Hospital of Sun Yat-sen University. Additionally, 50 healthy, unrelated volunteers were recruited as controls (aged from 21 to 46 years old). The 5'-UTR, exons and their flanking side of the CFTR gene were sequenced by high-throughput sequencing technology. The results were compared with those retrieved from the Ensembl Genome Browser. In addition, all 13 novel variants were further confirmed independently by Sanger sequencing and evaluated in the bioinformatics web servers. A schematic of the variant spectrum of the CFTR gene, including 13 novel variants (12 in CAVD patients, one in the control group), is shown, and the frequent variants in Chinese CAVD patients were 5 T (27.54%), c.-8G > C (7.25%), p.Q1352H (5.98%), and p.I556V (3.08%). 5 T was found to be the most frequent variant. p.Q1352H had a significantly high allelic frequency in CAVD patients (P < 0.05). c.-8G > C and p.I556V had high allelic frequencies but showed no difference between patients and controls (P > 0.05). p.Q1352H is the most common and important missense variant in Chinese patients with CAVD, while the pathological effects of C.-8G > C and p.I556V may be weak after evaluation.


Asunto(s)
Regulador de Conductancia de Transmembrana de Fibrosis Quística/genética , Enfermedades Urogenitales Masculinas/genética , Conducto Deferente/anomalías , Adulto , Alelos , Grupo de Ascendencia Continental Asiática/genética , Azoospermia/genética , Regulador de Conductancia de Transmembrana de Fibrosis Quística/metabolismo , Análisis Mutacional de ADN/métodos , Exones/genética , Frecuencia de los Genes/genética , Humanos , Infertilidad Masculina/genética , Masculino , Enfermedades Urogenitales Masculinas/metabolismo , Mutación/genética , Conducto Deferente/metabolismo
13.
Nat Commun ; 11(1): 6411, 2020 12 18.
Artículo en Inglés | MEDLINE | ID: mdl-33339816

RESUMEN

Over 250 million people suffer from schistosomiasis, a tropical disease caused by parasitic flatworms known as schistosomes. Humans become infected by free-swimming, water-borne larvae, which penetrate the skin. The earliest intra-mammalian stage, called the schistosomulum, undergoes a series of developmental transitions. These changes are critical for the parasite to adapt to its new environment as it navigates through host tissues to reach its niche, where it will grow to reproductive maturity. Unravelling the mechanisms that drive intra-mammalian development requires knowledge of the spatial organisation and transcriptional dynamics of different cell types that comprise the schistomulum body. To fill these important knowledge gaps, we perform single-cell RNA sequencing on two-day old schistosomula of Schistosoma mansoni. We identify likely gene expression profiles for muscle, nervous system, tegument, oesophageal gland, parenchymal/primordial gut cells, and stem cells. In addition, we validate cell markers for all these clusters by in situ hybridisation in schistosomula and adult parasites. Taken together, this study provides a comprehensive cell-type atlas for the early intra-mammalian stage of this devastating metazoan parasite.


Asunto(s)
Mamíferos/parasitología , Parásitos/citología , Parásitos/crecimiento & desarrollo , Schistosoma mansoni/citología , Schistosoma mansoni/crecimiento & desarrollo , Análisis de la Célula Individual , Animales , Esófago/metabolismo , Exones/genética , Regulación de la Expresión Génica , Humanos , Células Musculares/metabolismo , Sistema Nervioso/citología , Neuronas/citología , Parásitos/genética , Schistosoma mansoni/genética , Células Madre/citología , Células Madre/metabolismo , Transcripción Genética
14.
PLoS Negl Trop Dis ; 14(12): e0008932, 2020 12.
Artículo en Inglés | MEDLINE | ID: mdl-33332357

RESUMEN

BACKGROUND: Chagas disease is a neglected zoonosis of growing concern in the southern US, caused by the parasite Trypanosoma cruzi. We genotyped parasites in a large cohort of PCR positive dogs to shed light on parasite transmission cycles and assess potential relationships between parasite diversity and serological test performance. METHODOLOGY/PRINCIPAL FINDINGS: We used a metabarcoding approach based on deep sequencing of T. cruzi mini-exon marker to assess parasite diversity. Phylogenetic analysis of 178 sequences from 40 dogs confirmed the presence of T. cruzi discrete typing unit (DTU) TcI and TcIV, as well as TcII, TcV and TcVI for the first time in US dogs. Infections with multiple DTUs occurred in 38% of the dogs. These data indicate a greater genetic diversity of T. cruzi than previously detected in the US. Comparison of T. cruzi sequence diversity indicated that highly similar T. cruzi strains from these DTUs circulate in hosts and vectors in Louisiana, indicating that they are involved in a shared T. cruzi parasite transmission cycle. However, TcIV and TcV were sampled more frequently in vectors, while TcII and TcVI were sampled more frequently in dogs. CONCLUSIONS/SIGNIFICANCE: These observations point to ecological host-fitting being a dominant mechanism involved in the diversification of T. cruzi-host associations. Dogs with negative, discordant or confirmed positive T. cruzi serology harbored TcI parasites with different mini-exon sequences, which strongly supports the hypothesis that parasite genetic diversity is a key factor affecting serological test performance. Thus, the identification of conserved parasite antigens should be a high priority for the improvement of current serological tests.


Asunto(s)
Enfermedad de Chagas/veterinaria , Exones/genética , Variación Genética , Trypanosoma cruzi/genética , Animales , Enfermedad de Chagas/epidemiología , Enfermedad de Chagas/parasitología , Enfermedad de Chagas/transmisión , Estudios de Cohortes , Perros , Genotipo , Humanos , Louisiana/epidemiología , Filogenia , Pruebas Serológicas/veterinaria , Trypanosoma cruzi/inmunología , Trypanosoma cruzi/fisiología , Zoonosis
15.
BMC Evol Biol ; 20(1): 164, 2020 12 11.
Artículo en Inglés | MEDLINE | ID: mdl-33308147

RESUMEN

BACKGROUND: Eukaryotic protein-coding genes consist of exons and introns. Exon-intron borders are conserved between species and thus their changes might be observed only on quite long evolutionary distances. One of the rarest types of change, in which intron relocates over a short distance, is called "intron sliding", but the reality of this event has been debated for a long time. The main idea of a search for intron sliding is to use the most accurate genome annotation and genome sequence, as well as high-quality transcriptome data. We applied them in a search for sliding introns in mammals in order to widen knowledge about the presence or absence of such phenomena in this group. RESULTS: We didn't find any significant evidence of intron sliding in the primate group (human, chimpanzee, rhesus macaque, crab-eating macaque, green monkey, marmoset). Only one possible intron sliding event supported by a set of high quality transcriptomes was observed between EIF1AX human and sheep gene orthologs. Also, we checked a list of previously observed intron sliding events in mammals and showed that most likely they are artifacts of genome annotations and are not shown in subsequent annotation versions as well as are not supported by transcriptomic data. CONCLUSIONS: We assume that intron sliding is indeed a very rare evolutionary event if it exists at all. Every case of intron sliding needs a lot of supportive data for detection and confirmation.


Asunto(s)
Evolución Molecular , Intrones/genética , Mamíferos/genética , Animales , Exones/genética , Humanos , Primates/genética , Reproducibilidad de los Resultados , Ovinos/genética , Incertidumbre
16.
Genes (Basel) ; 12(1)2020 12 25.
Artículo en Inglés | MEDLINE | ID: mdl-33375616

RESUMEN

The human serine protease serine 2 TMPRSS2 is involved in the priming of proteins of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and represents a possible target for COVID-19 therapy. The TMPRSS2 gene may be co-expressed with SARS-CoV-2 cell receptor genes angiotensin-converting enzyme 2 (ACE2) and Basigin (BSG), but only TMPRSS2 demonstrates tissue-specific expression in alveolar cells according to single-cell RNA sequencing data. Our analysis of the structural variability of the TMPRSS2 gene based on genome-wide data from 76 human populations demonstrates that a functionally significant missense mutation in exon 6/7 in the TMPRSS2 gene is found in many human populations at relatively high frequencies, with region-specific distribution patterns. The frequency of the missense mutation encoded by rs12329760, which has previously been found to be associated with prostate cancer, ranged between 10% and 63% and was significantly higher in populations of Asian origin compared with European populations. In addition to single-nucleotide polymorphisms, two copy number variants were detected in the TMPRSS2 gene. A number of microRNAs have been predicted to regulate TMPRSS2 and BSG expression levels, but none of them is enriched in lung or respiratory tract cells. Several well-studied drugs can downregulate the expression of TMPRSS2 in human cells, including acetaminophen (paracetamol) and curcumin. Thus, the interactions of TMPRSS2 with SARS-CoV-2, together with its structural variability, gene-gene interactions, expression regulation profiles, and pharmacogenomic properties, characterize this gene as a potential target for COVID-19 therapy.


Asunto(s)
/tratamiento farmacológico , Regulación Enzimológica de la Expresión Génica/efectos de los fármacos , Terapia Molecular Dirigida , Serina Endopeptidasas/genética , Acetaminofén/farmacología , Acetaminofén/uso terapéutico , /biosíntesis , Asia/epidemiología , Basigina/biosíntesis , Basigina/genética , Basigina/fisiología , /genética , Curcumina/farmacología , Curcumina/uso terapéutico , Europa (Continente)/epidemiología , Exones/genética , Frecuencia de los Genes , Predisposición Genética a la Enfermedad , Variación Genética , Humanos , MicroARNs/genética , Mutación Missense , Pruebas de Farmacogenómica , Mapeo de Interacción de Proteínas , Receptores Virales/antagonistas & inhibidores , Receptores Virales/biosíntesis , Receptores Virales/genética , Serina Endopeptidasas/biosíntesis , Serina Endopeptidasas/fisiología , Análisis de la Célula Individual , Glicoproteína de la Espiga del Coronavirus/metabolismo
17.
Rev Soc Bras Med Trop ; 54: e01452020, 2020.
Artículo en Inglés | MEDLINE | ID: mdl-33338108

RESUMEN

INTRODUCTION: We evaluated the association between genetic polymorphisms in exon 1 (A/O alleles) and promoter regions at positions -550 (H/L variant, rs11003125) and -221 (X/Y variant, rs7096206) MBL2 and periportal fibrosis regression. METHODS: This was a retrospective cohort study involving 114 Brazilians infected with Schistosoma mansoni, who were subjected to follow-up for three years after specific treatment for schistosomiasis to estimate the probability of periportal fibrosis regression. RESULTS: A risk association was observed between polymorphism at the exon 1 MBL2 and periportal fibrosis regression. CONCLUSIONS: This study suggests that the polymorphism of exon 1 MBL2 may potentially be used to predict periportal fibrosis regression in this population.


Asunto(s)
Lectina de Unión a Manosa , Esquistosomiasis , Animales , Brasil , Exones/genética , Predisposición Genética a la Enfermedad , Genotipo , Humanos , Cirrosis Hepática/genética , Lectina de Unión a Manosa/genética , Polimorfismo Genético , Polimorfismo de Nucleótido Simple , Estudios Retrospectivos , Esquistosomiasis/genética
18.
Mol Cell ; 80(1): 156-163.e6, 2020 10 01.
Artículo en Inglés | MEDLINE | ID: mdl-33007255

RESUMEN

The production of alternative RNA variants contributes to the tissue-specific regulation of gene expression. In the animal nervous system, a systematic shift toward distal sites of transcription termination produces transcript signatures that are crucial for neuron development and function. Here, we report that, in Drosophila, the highly conserved protein ELAV globally regulates all sites of neuronal 3' end processing and directly binds to proximal polyadenylation sites of target mRNAs in vivo. We uncover an endogenous strategy of functional gene rescue that safeguards neuronal RNA signatures in an ELAV loss-of-function context. When not directly repressed by ELAV, the transcript encoding the ELAV paralog FNE acquires a mini-exon, generating a new protein able to translocate to the nucleus and rescue ELAV-mediated alternative polyadenylation and alternative splicing. We propose that exon-activated functional rescue is a more widespread mechanism that ensures robustness of processes regulated by a hierarchy, rather than redundancy, of effectors.


Asunto(s)
Proteínas de Drosophila/metabolismo , Drosophila melanogaster/genética , Proteínas ELAV/metabolismo , Exones/genética , Proteínas del Tejido Nervioso/metabolismo , Neuronas/metabolismo , Proteínas de Unión al ARN/metabolismo , Animales , Masculino , Unión Proteica , ARN Mensajero/genética , ARN Mensajero/metabolismo , Transcriptoma/genética
19.
Nat Commun ; 11(1): 4940, 2020 10 02.
Artículo en Inglés | MEDLINE | ID: mdl-33009411

RESUMEN

The HUSH complex represses retroviruses, transposons and genes to maintain the integrity of vertebrate genomes. HUSH regulates deposition of the epigenetic mark H3K9me3, but how its three core subunits - TASOR, MPP8 and Periphilin - contribute to assembly and targeting of the complex remains unknown. Here, we define the biochemical basis of HUSH assembly and find that its modular architecture resembles the yeast RNA-induced transcriptional silencing complex. TASOR, the central HUSH subunit, associates with RNA processing components. TASOR is required for H3K9me3 deposition over LINE-1 repeats and repetitive exons in transcribed genes. In the context of previous studies, this suggests that an RNA intermediate is important for HUSH activity. We dissect the TASOR and MPP8 domains necessary for transgene repression. Structure-function analyses reveal TASOR bears a catalytically-inactive PARP domain necessary for targeted H3K9me3 deposition. We conclude that TASOR is a multifunctional pseudo-PARP that directs HUSH assembly and epigenetic regulation of repetitive genomic targets.


Asunto(s)
Elementos Transponibles de ADN/genética , Epigénesis Genética , Complejos Multiproteicos/metabolismo , Proteínas Nucleares/metabolismo , Poli(ADP-Ribosa) Polimerasas/metabolismo , Secuencia de Aminoácidos , Antígenos de Neoplasias/metabolismo , Sitios de Unión , Exones/genética , Genoma , Células HEK293 , Células HeLa , Histonas/metabolismo , Humanos , Lisina/metabolismo , Espectroscopía de Resonancia Magnética , Metilación , NAD/metabolismo , Proteínas Nucleares/química , Fosfoproteínas/metabolismo , Unión Proteica , Dominios Proteicos , ARN/metabolismo , Procesamiento Postranscripcional del ARN , Transcripción Genética
20.
Tokai J Exp Clin Med ; 45(3): 113-116, 2020 Sep 20.
Artículo en Inglés | MEDLINE | ID: mdl-32901897

RESUMEN

Mutations in the gene encoding epidermal growth factor receptor (EGFR) are the most frequent driver mutations in lung adenocarcinoma in Japan. Exon 19 deletion and L858R mutation in exon 21 are the most common EGFR mutations. Uncommon mutations, such as G719X, S768I, and L861Q, and compound mutations, combinations of 2 common or uncommon mutations, have also been reported. EGFR tyrosine kinase inhibitors (TKIs) are effective against cancers harboring common mutations; however, their efficacy against cancers with uncommon or compound mutations remains unclear. We report the case of a 67-year-old man with lung adenocarcinoma (clinical stage IIIA [cT1N2M0]), harboring an uncommon compound mutation, G719X and S768I. The cancer progressed within 2 months of initial chemoradiotherapy. Treatment with afatinib (40 mg/day) produced a partial response, which was maintained for 17 months with continued treatment. A literature review revealed that lung cancer with G719X/S768I compound mutation exhibited good response to EGFR-TKIs, even better than that of lung cancers with single uncommon mutations.


Asunto(s)
Adenocarcinoma/tratamiento farmacológico , Adenocarcinoma/genética , Afatinib/uso terapéutico , Antineoplásicos/uso terapéutico , Neoplasias Pulmonares/tratamiento farmacológico , Neoplasias Pulmonares/genética , Mutación , Inhibidores de Proteínas Quinasas/uso terapéutico , Anciano , Receptores ErbB/genética , Exones/genética , Eliminación de Gen , Humanos , Masculino , Resultado del Tratamiento
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