Splooce

Kroll, José Eduardo; Galante, Pedro A. F.; O’Hara, Daniel T.; Navarro, Fábio C. P.; Ohno-Machado, Lucila; Souza, Sandro J. de

doi:10.4161/rna.22182

Cited by 8 publications

(12 citation statements)

References 39 publications

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“…The numbers of ASEs corresponding to each type in both saline and METH-treated groups were identified and calculated. As observed previously, the most frequent event type in both groups was exon skipping, followed by A3′SS, A5′SS and intron retention22. However, the numbers of ASEs in METH-treated group were about 10–40% less than those in saline-treated group (Fig.…”

Section: Resultssupporting

confidence: 77%

mRNA changes in nucleus accumbens related to methamphetamine addiction in mice

Zhu

Dong

et al. 2016

Sci Rep

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Methamphetamine (METH) is a highly addictive psychostimulant that elicits aberrant changes in the expression of microRNAs (miRNAs) and long non-coding RNAs (lncRNAs) in the nucleus accumbens of mice, indicating a potential role of METH in post-transcriptional regulations. To decipher the potential consequences of these post-transcriptional regulations in response to METH, we performed strand-specific RNA sequencing (ssRNA-Seq) to identify alterations in mRNA expression and their alternative splicing in the nucleus accumbens of mice following exposure to METH. METH-mediated changes in mRNAs were analyzed and correlated with previously reported changes in non-coding RNAs (miRNAs and lncRNAs) to determine the potential functions of these mRNA changes observed here and how non-coding RNAs are involved. A total of 2171 mRNAs were differentially expressed in response to METH with functions involved in synaptic plasticity, mitochondrial energy metabolism and immune response. 309 and 589 of these mRNAs are potential targets of miRNAs and lncRNAs respectively. In addition, METH treatment decreases mRNA alternative splicing, and there are 818 METH-specific events not observed in saline-treated mice. Our results suggest that METH-mediated addiction could be attributed by changes in miRNAs and lncRNAs and consequently, changes in mRNA alternative splicing and expression. In conclusion, our study reported a methamphetamine-modified nucleus accumbens transcriptome and provided non-coding RNA-mRNA interaction networks possibly involved in METH addiction.

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Section: Resultssupporting

confidence: 77%

mRNA changes in nucleus accumbens related to methamphetamine addiction in mice

Zhu

Dong

et al. 2016

Sci Rep

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“…Additionally, several comprehensive databases for alternative splicing have been developed such as HOLLYWOOD [113], ASD [114], BIPASS [117], ECgene [118], ASPicDB [121], AspAlt [125], H-DBAS [128], SPLOOCE [129], and APPRIS [130]. For example, the ECgene provides EST and serial analysis of gene expression (SAGE) data-based annotation and visualization for alternative splicing (AS).…”

Section: Alternative Splicing-related Bioinformatics Resourcesmentioning

confidence: 99%

Alternative Splicing for Diseases, Cancers, Drugs, and Databases

Tang

Lee

Hou

et al. 2013

The Scientific World Journal

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Alternative splicing is a major diversification mechanism in the human transcriptome and proteome. Several diseases, including cancers, have been associated with dysregulation of alternative splicing. Thus, correcting alternative splicing may restore normal cell physiology in patients with these diseases. This paper summarizes several alternative splicing-related diseases, including cancers and their target genes. Since new cancer drugs often target spliceosomes, several clinical drugs and natural products or their synthesized derivatives were analyzed to determine their effects on alternative splicing. Other agents known to have modulating effects on alternative splicing during therapeutic treatment of cancer are also discussed. Several commonly used bioinformatics resources are also summarized.

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“…O SPLICING ALTERNATIVO 5 (Kroll et al, 2012). Esses eventos existem devido à complexa regulação do splicing e à alta frequência de eventos simples de splicing alternativo.…”

Section: 3unclassified

“…Padrões anormais e complexos de splicing alternativo tem sido diretamente relacionados com o câncer (Venables, 2006). Por exemplo, aproximadamente 46% e 12% de todas as sequências variantes expressas em tecidos normais e patológicos humanos apresentam mais de 1 e 2 eventos, respectivamente (Kroll et al, 2012). Um dos eventos complexos mais conhecidos são os éxons mutualmente excludentes, no qual a presença de um éxon promove o skipping de um éxon adjacente, e vice-versa (figura 2.3).…”

Section: 3unclassified

“…Por exemplo, em 2004 existiam aproximadamente 7,7 milhões de sequências expressas humanas disponíveis no GenBank e, atualmente, existem mais de 20 milhões (Benson et al, 2012). Esses números não incluem as sequências obtidas a partir de sequenciamentos de próxima geração (NGS), os quais estão sendo exaustivamente explorados e podem ser uma excelente fonte para a descoberta de novos ASEs (Kroll et al, 2012;Roberts et al, 2011;Trapnell et al, 2009;Wheeler et al, 2007).…”

Section: Introductionunclassified

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Explorando a complexidade do transcriptoma humano

Kroll¹

Self Cite

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O splicing alternativo é um processo no qual moléculas idênticas de pré-mRNA são processadas de diferentes formas. Ele é fundamental em organismos complexos, pois é responsável por criar uma ampla diversidade de proteínas a partir de um número relativamente pequeno de genes. Contudo, poucas proteínas advindas do splicing alternativo já foram identificadas, visto que a maioria dos espectros de espectrometria de massa em tandem (MS/MS) não encontra sequências correspondentes nos diversos bancos de dados de proteínas disponíveis. Entre diversos fatores, isso ocorre porque um número reduzido de eventos de splicing alternativo (ASEs) são conhecidos e devidamente estudados. Nesse trabalho, o espectro de eventos observáveis foi ampliado por meio da análise de eventos complexos de splicing alternativo (CASEs), que consideram múltiplos ASEs em um ou diferentes transcritos. Foi desenvolvido um novo método de análise utilizando expressões regulares (regexes) associada a uma sintaxe baseada em caracteres intuitivos. O método de análise e a sintaxe foram implementados em uma ferramenta web denominada de SPLOOCE (http://www.bioinformatics-brazil.org/splooce) que também apresenta ferramentas extras de análise. Adicionalmente, os subestimados eventos do tipo retenção de íntron (IR) foram explorados em busca de evidências funcionais por meio de análises de MS/MS. Como resultado, eventos bastante incomuns foram observados no proteoma humano, sugerindo que muito pouco ainda é conhecido sobre a complexidade transcriptômica e proteômica humana. Portanto, com base nesses dados, esse trabalho representa um grande avanço no estudo de fenômenos de splicing alternativo ainda pouco explorados.

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Splooce

Cited by 8 publications

References 39 publications

mRNA changes in nucleus accumbens related to methamphetamine addiction in mice

mRNA changes in nucleus accumbens related to methamphetamine addiction in mice

Alternative Splicing for Diseases, Cancers, Drugs, and Databases

Explorando a complexidade do transcriptoma humano

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