Alternative splicing in human transcriptome: Functional and structural influence on proteins

Yura, Kei; Shionyu, Masafumi; Hagino, Kei; Hijikata, Atsushi; Hirashima, Yoshinori; Nakahara, Taku; Eguchi, Tatsuya; Shinoda, K.; Yamaguchi, Akihiro; Takahashi, Ken; Itoh, Takeshi; Imanishi, Tadashi; Gojobori, Takashi; Gô, Mitiko

doi:10.1016/j.gene.2006.05.015

Cited by 65 publications

(62 citation statements)

References 42 publications

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“…For 87% of these MXEs, at least one of the exon termini is embedded within a secondary structural element, suggesting that these exons are in fact true MXEs and not mis‐classified cassette exons (Fig 2C, yellow and green coloured symbols). This high level of structural conservation also strongly supports the hypothesis that MXEs modulate but do not considerably alter protein functions (Letunic et al , 2002; Yura et al , 2006; Abascal et al , 2015a; Tress et al , 2017a). Of the remaining 13% (Fig 2C, blue coloured symbols), many MXEs would lead to frame shifts if they were spliced as cassette exons (both exons present or absent in the transcript, blue circles), and in multiple cases (e.g.…”

Section: Resultssupporting

confidence: 75%

The landscape of human mutually exclusive splicing

Hatje

Rahman

Vidal

et al. 2017

Molecular Systems Biology

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Mutually exclusive splicing of exons is a mechanism of functional gene and protein diversification with pivotal roles in organismal development and diseases such as Timothy syndrome, cardiomyopathy and cancer in humans. In order to obtain a first genomewide estimate of the extent and biological role of mutually exclusive splicing in humans, we predicted and subsequently validated mutually exclusive exons (MXEs) using 515 publically available RNA‐Seq datasets. Here, we provide evidence for the expression of over 855 MXEs, 42% of which represent novel exons, increasing the annotated human mutually exclusive exome more than fivefold. The data provide strong evidence for the existence of large and multi‐cluster MXEs in higher vertebrates and offer new insights into MXE evolution. More than 82% of the MXE clusters are conserved in mammals, and five clusters have homologous clusters in Drosophila. Finally, MXEs are significantly enriched in pathogenic mutations and their spatio‐temporal expression might predict human disease pathology.

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Section: Resultssupporting

confidence: 75%

The landscape of human mutually exclusive splicing

Hatje

Rahman

Vidal

et al. 2017

Molecular Systems Biology

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“…The encoding of multiple proteins by single genes is required to generate the complexity observed in higher eukaryotes (Yura et al, 2006). Genes whose pre-messenger RNAs have multiple alternative splicing locations can produce proteins differing in allosteric regulation, protein localization, and enzymatic activity (Black, 2003).…”

Section: Discussionmentioning

confidence: 99%

Analysis of biochemical compounds and differentially expressed genes of the anthocyanin biosynthetic pathway in variegated peach flowers

et al. 2015

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ABSTRACT. Variegated plants are highly valuable in the floriculturalmarket, yet the genetic mechanism underlying this attractive phenomenon has not been completely elucidated. In this study, we identified and measured different compounds in pink and white flower petals of peach (Prunus persica) by high-performance liquid chromatography and liquid chromatography/mass spectrometry analyses. No cyanidin-based or pelargonidin-based compounds were detected in white petals, but high levels of these compounds were found in pink petals. Additionally, we sequenced and analyzed the expression of six key structural genes in the anthocyanin biosynthesis pathway (CHI, CHS, DFR, F3'H, ANS, and UFGT) in both white and pink petals. Quantitative real-time polymerase chain reaction revealed all six genes to be expressed at greatly reduced levels in white flower petals, relative to pink. No allelic variations were found in the transcribed sequences. However, alignment of transcribed and genomic sequences of the ANS gene detected alternative splicing, resulting in transcripts (2015) of 1.071 and 942 bp. Only the longer transcript was observed in white flower petals. Since ANS is the key intermediate enzyme catalyzing the colorless leucopelargonidin and leucocyanidin to substrates required for completion of anthocyanin biosynthesis, the ANS gene is implicated in flower color variegation and should be explored in future studies. This article, together with a previous transcriptome study, elucidates the mechanism underlying peach flower color variegation in terms of the key structural genes involved in anthocyanin biosynthesis.

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“…By using the EST mapping technique, we find that nearly half the ion channel genes identified in both the human cochlear and mouse organ of Corti cDNA libraries have previously unannotated variants. It is reasonable to expect that alternative transcripts differ in their expression patterns (Yura et al 2006). …”

Section: Discussionmentioning

confidence: 99%

Ion Channel Gene Expression in the Inner Ear

Gabashvili

Sokolowski

Morton

et al. 2007

JARO

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The ion channel genome is still being defined despite numerous publications on the subject. The ion channel transcriptome is even more difficult to assess. Using high-throughput computational tools, we surveyed all available inner ear cDNA libraries to identify genes coding for ion channels. We mapped over 100,000 expressed sequence tags (ESTs) derived from human cochlea, mouse organ of Corti, mouse and zebrafish inner ear, and rat vestibular end organs to Homo sapiens, Mus musculus, Danio rerio, and Rattus norvegicus genomes. A survey of EST data alone reveals that at least a third of the ion channel genome is expressed in the inner ear, with highest expression occurring in hair cell-enriched mouse organ of Corti and rat vestibule. Our data and comparisons with other experimental techniques that measure gene expression show that every method has its limitations and does not per se provide a complete coverage of the inner ear ion channelome. In addition, the data show that most genes produce alternative transcripts with the same spectrum across multiple organisms, no ion channel gene variants are unique to the inner ear, and many splice variants have yet to be annotated. Our high-throughput approach offers a qualitative computational and experimental analysis of ion channel genes in inner ear cDNA collections. A lack of data and incomplete gene annotations prevent both rigorous statistical analyses and comparisons of entire ion channelomes derived from different tissues and organisms.

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Alternative splicing in human transcriptome: Functional and structural influence on proteins

Cited by 65 publications

References 42 publications

The landscape of human mutually exclusive splicing

The landscape of human mutually exclusive splicing

Analysis of biochemical compounds and differentially expressed genes of the anthocyanin biosynthetic pathway in variegated peach flowers

Ion Channel Gene Expression in the Inner Ear

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