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| Dou,Tong-Hai; Gao,Yuan; Chen,Cheng-Wen; Xu,Min-Jie; Fu,Mao-Bin; Zhang,Liang; Zhou,Yan. |
| ABSTRACT Background: Alternative splicing (AS), which plays an important role in gene expression and functional regulation, has been analyzed on genome-scale by various bioinformatic approaches based on RNA-seq data. Compared with the huge number of studies on mouse, the AS researches approaching the rat, whose genome is intermedia between mouse and human, were still limited. To enrich the knowledge on AS events in rodents' brain, we perfomed a comprehensive analysis on four transcriptome libraries (mouse cerebrum, mouse cerebellum, rat cerebrum, and rat cerebellum), recruiting high-throughput sequencing technology. An optimized exon-exon junction library approach was introduced to adapt the longer RNA-seq reads and to improve mapping efficiency.... |
| Tipo: Info:eu-repo/semantics/article |
Palavras-chave: RNA-seq; Exon-exon junction; Alternative splicing; Cerebrum; Cerebellum. |
| Ano: 2017 |
URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1516-89132017000100400 |
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| Chen,W.L.; Luo,D.F.; Gao,C.; Ding,Y.; Wang,S.Y.. |
| The familial acute myeloid leukemia related factor gene (FAMLF) was previously identified from a familial AML subtractive cDNA library and shown to undergo alternative splicing. This study used real-time quantitative PCR to investigate the expression of the FAMLF alternative-splicing transcript consensus sequence (FAMLF-CS) in peripheral blood mononuclear cells (PBMCs) from 119 patients with de novo acute leukemia (AL) and 104 healthy controls, as well as in CD34+ cells from 12 AL patients and 10 healthy donors. A 429-bp fragment from a novel splicing variant of FAMLF was obtained, and a 363-bp consensus sequence was targeted to quantify total FAMLF expression. Kruskal-Wallis, Nemenyi, Spearman's correlation, and Mann-Whitney U-tests were used to analyze... |
| Tipo: Info:eu-repo/semantics/article |
Palavras-chave: FAMLF; Gene expression; Leukemia; Real-time polymerase chain reaction; Alternative splicing. |
| Ano: 2015 |
URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S0100-879X2015000700603 |
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| Erdem,Gokce Celikyapi; Erdemir,Sule; Abaci,Irem; Aydin,Asli K. Kirectepe; Everest,Elif; Turanli,Eda Tahir. |
| Abstract The function of gene body DNA methylation in alternative splicing, and its relation to disease pathogenesis is not fully elucidated. The gene for familial Mediterranean fever (MEFV) encodes the pyrin protein and contains a 998 bp CpG island, covering the second exon, which is differentially methylated in FMF patients compared to healthy controls. Our further observation of increased exon 2-spliced MEFV transcript in leukocytes of FMF patients provoked us to test the role of exon methylation in alternative splicing using inflammatory cell culture models. First, in vitro exon methylation triggered an increased level of exon 2 exclusion using a splicing cassette in a promyelocytic leukemia cell line (HL-60). HL-60 cells subjected to methylating and... |
| Tipo: Info:eu-repo/semantics/article |
Palavras-chave: Exon methylation; MEFV; Pyrin; Alternative splicing; Inflammation. |
| Ano: 2017 |
URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1415-47572017000400688 |
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| Botto,Adrian E. Cambindo; Muñoz,Juan C.; Giono,Luciana E.; Nieto-Moreno,Nicolás; Cuenca,Carmen; Kornblihtt,Alberto R.; Muñoz,Manuel J.. |
| Abstract Splicing, the process that catalyzes intron removal and flanking exon ligation, can occur in different ways (alternative splicing) in immature RNAs transcribed from a single gene. In order to adapt to a particular context, cells modulate not only the quantity but also the quality (alternative isoforms) of their transcriptome. Since 95% of the human coding genome is subjected to alternative splicing regulation, it is expected that many cellular pathways are modulated by alternative splicing, as is the case for the DNA damage response. Moreover, recent evidence demonstrates that upon a genotoxic insult, classical DNA damage response kinases such as ATM, ATR and DNA-PK orchestrate the gene expression response therefore modulating alternative splicing... |
| Tipo: Info:eu-repo/semantics/article |
Palavras-chave: DNA damage; Alternative splicing; ATR; ATM; DNA-PK. |
| Ano: 2020 |
URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1415-47572020000200310 |
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| Guevelou, Eric; Huvet, Arnaud; Sussarellu, Rossana; Milan, Massimo; Guo, Xinmei; Li, Li; Zhang, Guofan; Quillien, Virgile; Daniel, Jean-yves; Quere, Claudie; Boudry, Pierre; Corporeau, Charlotte. |
| AMP-activated protein kinase α (AMPKα) is a key regulator of energy balance in many model species during hypoxia. In a marine bivalve, the Pacific oyster Crassostrea gigas, we analyzed the protein content of adductor muscle in response to hypoxia during 6 h. In both smooth and striated muscles, the amount of full-length AMP-activated protein kinase α (AMPKα) remained unchanged during hypoxia. However, hypoxia induced a rapid and muscle-specific response concerning truncated isoforms of AMPKα. In the smooth muscle, a truncated isoform of AMPKα was increased from 1 to 6 h of hypoxia, and was linked with accumulation of AKT kinase, a key enzyme of the insulin signaling pathway which controls intracellular glucose metabolism. In this muscle, aerobic metabolism... |
| Tipo: Text |
Palavras-chave: Marine bivalve; Crassostrea gigas; Hypoxia; AMP-activated protein kinase; Alternative splicing; Adductor muscle. |
| Ano: 2013 |
URL: http://archimer.ifremer.fr/doc/00119/22998/21397.pdf |
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| Boullot, Floriane; Castrec, Justine; Bidault, Adeline; Dantas, Natanael; Payton, Laura; Perrigault, Mickael; Tran, Damien; Amzil, Zouher; Boudry, Pierre; Soudant, Philippe; Hegaret, Helene; Fabioux, Caroline. |
| Paralytic shellfish toxins (PST) bind to voltage-gated sodium channels (Nav) and block conduction of action potential in excitable cells. This study aimed to (i) characterize Nav sequences in Crassostrea gigas and (ii) investigate a putative relation between Nav and PST-bioaccumulation in oysters. The phylogenetic analysis highlighted two types of Nav in C. gigas: a Nav1 (CgNav1) and a Nav2 (CgNav2) with sequence properties of sodium-selective and sodium/calcium-selective channels, respectively. Three alternative splice transcripts of CgNav1 named A, B and C, were characterized. The expression of CgNav1, analyzed by in situ hybridization, is specific to nervous cells and to structures corresponding to neuromuscular junctions. Real-time PCR analyses showed... |
| Tipo: Text |
Palavras-chave: Crassostrea gigas; Sodium channel; Alternative splicing; Alexandrium minutum; Paralytic shellfish toxins. |
| Ano: 2017 |
URL: https://archimer.ifremer.fr/doc/00368/47877/47892.pdf |
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| Duval, David; Pichon, Rémi; Lassalle, Damien; Laffitte, Maud; Gourbal, Benjamain; Galinier, Richard. |
| Thioester-containing proteins (TEPs) superfamily is known to play important innate immune functions in a wide range of animal phyla. TEPs are involved in recognition, and in the direct or mediated killing of several invading organisms or pathogens. While several TEPs have been identified in many invertebrates, only one TEP (named BgTEP) has been previously characterized in the freshwater snail, Biomphalaria glabrata. As the presence of a single member of that family is particularly intriguing, transcriptomic data and the recently published genome were used to explore the presence of other BgTEP related genes in B. glabrata. Ten other TEP members have been reported and classified into different subfamilies: Three complement-like factors (BgC3-1 to BgC3-3),... |
| Tipo: Text |
Palavras-chave: Biomphalaria glabrata; Thioester-containing protein; Alternative splicing; Immunity; Schistosome. |
| Ano: 2020 |
URL: https://archimer.ifremer.fr/doc/00601/71268/69657.pdf |
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| Castanheira,Letícia Eulalio; Rodrigues,Renata Santos; Boldrini-França,Johara; Fonseca,Fernando PP; Henrique-Silva,Flávio; Homsi-Brandeburgo,Maria I; Rodrigues,Veridiana M. |
| Background Hyaluronate is one of the major components of extracellular matrix from vertebrates whose breakdown is catalyzed by the enzyme hyaluronidase. These enzymes are widely described in snake venoms, in which they facilitate the spreading of the main toxins in the victim’s body during the envenoming. Snake venoms also present some variants (hyaluronidases-like substances) that are probably originated by alternative splicing, even though their relevance in envenomation is still under investigation. Hyaluronidases-like proteins have not yet been purified from any snake venom, but the cDNA that encodes these toxins was already identified in snake venom glands by transcriptomic analysis. Herein, we report the cloning and in silicoanalysis of the first... |
| Tipo: Info:eu-repo/semantics/article |
Palavras-chave: Alternative splicing; Hyaluronidase-like; Snake venom. |
| Ano: 2014 |
URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1678-91992014000200330 |
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