Identical sequence patterns in the ends of exons and introns of human protein-coding genes

Intron splicing is one of the most important steps involved in the maturation process of a pre-mRNA. Although the sequence profiles around the splice sites have been studied extensively, the levels of sequence identity between the exonic sequences preceding the donor sites and the intronic sequences preceding the acceptor sites has not been examined as thoroughly. In this study we investigated identity patterns between the last 15 nucleotides of the exonic sequence preceding the 5' splice site and the intronic sequence preceding the 3' splice site in a set of human protein-coding genes that do not exhibit intron retention. We found that almost 60% of consecutive exons and introns in human protein-coding genes share at least two identical nucleotides at their 3' ends and, on average, the sequence identity length is 2.47 nucleotides. Based on our findings we conclude that the 3' ends of exons and introns tend to have longer identical sequences within a gene than when being taken from different genes. Our results hold even if the pairs are non-consecutive in the transcription order. (C) 2012 Elsevier Ltd. All rights reserved.

Expression of Mitochondrial Non-coding RNAs (ncRNAs) Is Modulated by High Risk Human Papillomavirus (HPV) Oncogenes

The study of RNA and DNA oncogenic viruses has proved invaluable in the discovery of key cellular pathways that are rendered dysfunctional during cancer progression. An example is high risk human papillomavirus (HPV), the etiological agent of cervical cancer. The role of HPV oncogenes in cellular immortalization and transformation has been extensively investigated. We reported the differential expression of a family of human mitochondrial non-coding RNAs (ncRNAs) between normal and cancer cells. Normal cells express a sense mitochondrial ncRNA (SncmtRNA) that seems to be required for cell proliferation and two antisense transcripts (ASncmtRNAs). In contrast, the ASncmtRNAs are down-regulated in cancer cells. To shed some light on the mechanisms that trigger down-regulation of the ASncmtRNAs, we studied human keratinocytes (HFK) immortalized with HPV. Here we show that immortalization of HFK with HPV-16 or 18 causes down-regulation of the ASncmtRNAs and induces the expression of a new sense transcript named SncmtRNA-2. Transduction of HFK with both E6 and E7 is sufficient to induce expression of SncmtRNA-2. Moreover, E2 oncogene is involved in down-regulation of the ASncmtRNAs. Knockdown of E2 in immortalized cells reestablishes in a reversible manner the expression of the ASncmtRNAs, suggesting that endogenous cellular factors(s) could play functions analogous to E2 during non-HPV-induced oncogenesis.

Analysis of Hepatitis C Virus Intrahost Diversity across the Coding Region by Ultradeep Pyrosequencing

Hepatitis C virus (HCV) is the leading cause of liver disease worldwide. In this study, we analyzed four treatment-naive patients infected with subtype 1a and performed Roche/454 pyrosequencing across the coding region. We report the presence of low-level drug resistance mutations that would most likely have been missed using conventional sequencing methods. The approach described here is broadly applicable to studies of viral diversity and could help to improve the efficacy of direct-acting antiviral agents (DAA) in the treatment of HCV-infected patients.

Trypanosoma cruzi mitochondrial maxicircles display species- and strain-specific variation and a conserved element in the non-coding region

Abstract Background The mitochondrial DNA of kinetoplastid flagellates is distinctive in the eukaryotic world due to its massive size, complex form and large sequence content. Comprised of catenated maxicircles that contain rRNA and protein-coding genes and thousands of heterogeneous minicircles encoding small guide RNAs, the kinetoplast network has evolved along with an extreme form of mRNA processing in the form of uridine insertion and deletion RNA editing. Many maxicircle-encoded mRNAs cannot be translated without this post-transcriptional sequence modification. Results We present the complete sequence and annotation of the Trypanosoma cruzi maxicircles for the CL Brener and Esmeraldo strains. Gene order is syntenic with Trypanosoma brucei and Leishmania tarentolae maxicircles. The non-coding components have strain-specific repetitive regions and a variable region that is unique for each strain with the exception of a conserved sequence element that may serve as an origin of replication, but shows no sequence identity with L. tarentolae or T. brucei. Alternative assemblies of the variable region demonstrate intra-strain heterogeneity of the maxicircle population. The extent of mRNA editing required for particular genes approximates that seen in T. brucei. Extensively edited genes were more divergent among the genera than non-edited and rRNA genes. Esmeraldo contains a unique 236-bp deletion that removes the 5'-ends of ND4 and CR4 and the intergenic region. Esmeraldo shows additional insertions and deletions outside of areas edited in other species in ND5, MURF1, and MURF2, while CL Brener has a distinct insertion in MURF2. Conclusion The CL Brener and Esmeraldo maxicircles represent two of three previously defined maxicircle clades and promise utility as taxonomic markers. Restoration of the disrupted reading frames might be accomplished by strain-specific RNA editing. Elements in the non-coding region may be important for replication, transcription, and anchoring of the maxicircle within the kinetoplast network.

Androgen responsive intronic non-coding RNAs

Abstract Background Transcription of large numbers of non-coding RNAs originating from intronic regions of human genes has been recently reported, but mechanisms governing their biosynthesis and biological functions are largely unknown. In this work, we evaluated the existence of a common mechanism of transcription regulation shared by protein-coding mRNAs and intronic RNAs by measuring the effect of androgen on the transcriptional profile of a prostate cancer cell line. Results Using a custom-built cDNA microarray enriched in intronic transcribed sequences, we found 39 intronic non-coding RNAs for which levels were significantly regulated by androgen exposure. Orientation-specific reverse transcription-PCR indicated that 10 of the 13 were transcribed in the antisense direction. These transcripts are long (0.5–5 kb), unspliced and apparently do not code for proteins. Interestingly, we found that the relative levels of androgen-regulated intronic transcripts could be correlated with the levels of the corresponding protein-coding gene (asGAS6 and asDNAJC3) or with the alternative usage of exons (asKDELR2 and asITGA6) in the corresponding protein-coding transcripts. Binding of the androgen receptor to a putative regulatory region upstream from asMYO5A, an androgen-regulated antisense intronic transcript, was confirmed by chromatin immunoprecipitation. Conclusion Altogether, these results indicate that at least a fraction of naturally transcribed intronic non-coding RNAs may be regulated by common physiological signals such as hormones, and further corroborate the notion that the intronic complement of the transcriptome play functional roles in the human gene-expression program.

Identification of protein-coding and non-coding RNA expression profiles in CD34+ and in stromal cells in refractory anemia with ringed sideroblasts

Abstract Background Myelodysplastic syndromes (MDS) are a group of clonal hematological disorders characterized by ineffective hematopoiesis with morphological evidence of marrow cell dysplasia resulting in peripheral blood cytopenia. Microarray technology has permitted a refined high-throughput mapping of the transcriptional activity in the human genome. Non-coding RNAs (ncRNAs) transcribed from intronic regions of genes are involved in a number of processes related to post-transcriptional control of gene expression, and in the regulation of exon-skipping and intron retention. Characterization of ncRNAs in progenitor cells and stromal cells of MDS patients could be strategic for understanding gene expression regulation in this disease. Methods In this study, gene expression profiles of CD34+ cells of 4 patients with MDS of refractory anemia with ringed sideroblasts (RARS) subgroup and stromal cells of 3 patients with MDS-RARS were compared with healthy individuals using 44 k combined intron-exon oligoarrays, which included probes for exons of protein-coding genes, and for non-coding RNAs transcribed from intronic regions in either the sense or antisense strands. Real-time RT-PCR was performed to confirm the expression levels of selected transcripts. Results In CD34+ cells of MDS-RARS patients, 216 genes were significantly differentially expressed (q-value ≤ 0.01) in comparison to healthy individuals, of which 65 (30%) were non-coding transcripts. In stromal cells of MDS-RARS, 12 genes were significantly differentially expressed (q-value ≤ 0.05) in comparison to healthy individuals, of which 3 (25%) were non-coding transcripts. Conclusions These results demonstrated, for the first time, the differential ncRNA expression profile between MDS-RARS and healthy individuals, in CD34+ cells and stromal cells, suggesting that ncRNAs may play an important role during the development of myelodysplastic syndromes.

Neural coding tools, based on Information Theory, applied to discrete time series: from electrophysiology to neuroethology

This work is supported by Brazilian agencies Fapesp, CAPES and CNPq

Audição e linguagem em crianças deficientes auditivas implantadas inseridas em ambiente bilíngue: um estudo de casos

O implante coclear (IC) tem sido indicado para crianças deficientes auditivas de grau severo e/ou profundo que não tem benefício com o aparelho de amplificação sonora individual (AASI), e que apresentem família adequada e motivada para o uso do dispositivo, bem como condições adequadas de reabilitação na cidade de origem. Atualmente, a procura pelo IC também ocorre por pais surdos, fluentes na Língua Brasileira de Sinais (LIBRAS), que recorrem a este tratamento para oferecer outra realidade para seus filhos. O ambiente destas crianças é bilíngue, dado pela LIBRAS dos pais e pela linguagem oral dos familiares próximos, do fonoaudiólogo e da escola. Neste sentido, o presente estudo visou acompanhar quatro crianças deficientes auditivas implantadas, sendo duas crianças filhas de pais deficientes auditivos fluentes na LIBRAS (expostas a ambiente bilíngue) e duas crianças filhas de pais sem alterações auditivas (expostas a ambiente oral). Para tanto, as habilidades de audição e de aquisição da linguagem oral foram comparadas nas quatro crianças implantadas. Foi possível observar que as quatro crianças apresentaram habilidades auditivas e de linguagem semelhantes ao longo do primeiro ano de uso do IC. Contudo, a partir disto, as crianças inseridas em ambiente bilíngue apresentaram melhor desempenho auditivo e linguístico, comparado ao desenvolvimento das outras crianças. As crianças inseridas em ambiente bilíngue podem se beneficiar do IC, desenvolvendo habilidades auditivas e de linguagem similares às das crianças inseridas em ambiente oral. Ressalta-se que os benefícios do dispositivo são obtidos a partir de aspectos multifatoriais, e estudos mais aprofundados são necessários.

Ablefaro macrostomia - síndrome e audição: relato de dois casos familiares

Introdução: Síndrome de Ablefaro MAcrostomia (AMS) é uma condição rara que compreende pálpebras ausentes ou curto, orelhas anormais, macrostomia, genitália anômalo, pele redundante e cabelos ausente. Brancati et al (2004) relataram uma ocorrência estimada de perda auditiva em 70% desta população. Estudos específicos sobre a audição em AMS não estavam presentes nos jornais que compilados. Relato dos casos: Paciente 1 é o primeiro filho de um ano de idade, a mãe 23 anos e pai de 25 anos de idade, não consangüíneos. Suas características clínicas são pouco cabelo no couro cabeludo, orelhas em forma de taça, raiz nasal larga, narinas antevertidas, macrostomia, os dedos com membranas, pele redundante e hipoplasia mamilos e lábios. Ela não tem atraso no desenvolvimento neuropsicomotor e a fala é normal. A audição foi avaliada aos 15 anos com uma perda auditiva em 6 kHz. Paciente 2 é o terceiro filho do mesmo casal. Ela tem falta grave das pálpebras, uma ponte nasal baixa com narinas hipoplásica e anteversão, macrostomia, orelhas anormalmente modelados, a ausência de mamilos, um de 6 cm onfalocele, ânus anteriormente localizado, hipoplasia dos grandes lábios, unhas hipoplasia, atenuação distal de falanges e pele redundante. Ela está se desenvolvendo com atraso no desenvolvimento neuropsicomotor, fala normal e perda auditiva condutiva leve bilateral. A avaliação audiológica incluiu quatro procedimentos: história clínica audiológica, inspeção otológica, imitanciometria, audiometria tonal e discurso. Conclusões: Os pacientes estudados com AMS apresentaram perda auditiva leve e esta perda de audição pode ser considerado como uma parte do fenótipo AMS sendo compatível os achados com a literatura.

Acceda y BuStreaming: integración de audio y vídeo en el proceso de autoarchivo del Repositorio de la ULPGC en acceso abierto

Comunicación presentada en 4 Jornadas "Os Repositorios" celebradas en la Universidad de Barcelona entre los días 3 al 5 de marzo del 2010. Estas Jornadas están organizadas conjuntamente por el CBUC, UB, UAB, UPC y UOC y el eje central de esta edición son las políticas de promoción del acceso abierto.Se recoge en la comunicación las últimas actuaciones que la Biblioteca Universitaria ha llevado a cabo para sumarse al movimiento Open Access y se presentan: Acceda, Documentación científica de la ULPGC en abierto y BUStreaming canal universitario de audio y video digital.

Dynamically reconfigurable architectures for video coding and hyperspectral imaging systems

Programa de Doctorado: Ingeniería de Telecomunicación Avanzada.