splice ≈ splice
View article: The diversity of splicing modifiers acting on A -1 bulged 5 -splice sites reveals rules for rational drug design
The diversity of splicing modifiers acting on A -1 bulged 5 -splice sites reveals rules for rational drug design Open
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Diverse alternative back-splicing and alternative splicing landscape of circular RNAs Open
Circular RNAs (circRNAs) derived from back-spliced exons have been widely identified as being co-expressed with their linear counterparts. A single gene locus can produce multiple circRNAs through alternative back-splice site selection and…
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A survey of the sorghum transcriptome using single-molecule long reads Open
Alternative splicing and alternative polyadenylation (APA) of pre-mRNAs greatly contribute to transcriptome diversity, coding capacity of a genome and gene regulatory mechanisms in eukaryotes. Second-generation sequencing technologies have…
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CADD-Splice—improving genome-wide variant effect prediction using deep learning-derived splice scores Open
Background Splicing of genomic exons into mRNAs is a critical prerequisite for the accurate synthesis of human proteins. Genetic variants impacting splicing underlie a substantial proportion of genetic disease, but are challenging to ident…
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GeneMark-EP+: eukaryotic gene prediction with self-training in the space of genes and proteins Open
We have made several steps toward creating a fast and accurate algorithm for gene prediction in eukaryotic genomes. First, we introduced an automated method for efficient ab initio gene finding, GeneMark-ES, with parameters trained in iter…
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A new view of transcriptome complexity and regulation through the lens of local splicing variations Open
Alternative splicing (AS) can critically affect gene function and disease, yet mapping splicing variations remains a challenge. Here, we propose a new approach to define and quantify mRNA splicing in units of local splicing variations (LSV…
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Improved transcriptome assembly using a hybrid of long and short reads with StringTie Open
Short-read RNA sequencing and long-read RNA sequencing each have their strengths and weaknesses for transcriptome assembly. While short reads are highly accurate, they are rarely able to span multiple exons. Long-read technology can captur…
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Androgen receptor splice variant-7 expression emerges with castration resistance in prostate cancer Open
Work at the University of Washington and in the Plymate and Nelson laboratories is supported by the Department of Defense Prostate Cancer Research Program (W81XWH-14-2-0183, W81XWH-12-PCRP-TIA, W81XWH-15-1-0430, and W81XWH-13-2-0070), the …
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ggsashimi: Sashimi plot revised for browser- and annotation-independent splicing visualization Open
We present ggsashimi, a command-line tool for the visualization of splicing events across multiple samples. Given a specified genomic region, ggsashimi creates sashimi plots for individual RNA-seq experiments as well as aggregated plots fo…
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The Size of the Human Proteome: The Width and Depth Open
This work discusses bioinformatics and experimental approaches to explore the human proteome, a constellation of proteins expressed in different tissues and organs. As the human proteome is not a static entity, it seems necessary to estima…
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CD44 splice isoform switching determines breast cancer stem cell state Open
Although changes in alternative splicing have been observed in cancer, their functional contributions still remain largely unclear. Here we report that splice isoforms of the cancer stem cell (CSC) marker CD44 exhibit strikingly opposite f…
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Prediction and Quantification of Splice Events from RNA-Seq Data Open
Analysis of splice variants from short read RNA-seq data remains a challenging problem. Here we present a novel method for the genome-guided prediction and quantification of splice events from RNA-seq data, which enables the analysis of un…
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Splice site m6A methylation prevents binding of U2AF35 to inhibit RNA splicing Open
The N6-methyladenosine (m6A) RNA modification is used widely to alter the fate of mRNAs. Here we demonstrate that the C. elegans writer METT-10 (the ortholog of mouse METTL16) deposits an m6A mark on the 3' splice site (AG) of the S-adenos…
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Recurrent Loss of NFE2L2 Exon 2 Is a Mechanism for Nrf2 Pathway Activation in Human Cancers Open
The Nrf2 pathway is frequently activated in human cancers through mutations in Nrf2 or its negative regulator KEAP1. Using a cell-line-derived gene signature for Nrf2 pathway activation, we found that some tumors show high Nrf2 activity in…
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Aberrant RNA Splicing in Cancer and Drug Resistance Open
More than 95% of the 20,000 to 25,000 transcribed human genes undergo alternative RNA splicing, which increases the diversity of the proteome. Isoforms derived from the same gene can have distinct and, in some cases, opposing functions. Ac…
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FDA Approval of Nusinersen for Spinal Muscular Atrophy Makes 2016 the Year of Splice Modulating Oligonucleotides Open
With the Food and Drug Administration (FDA) approval of nusinersen (tradename Spinraza) for treatment of spinal muscular atrophy patients on December 23 [1], 2016 brought us not one, but two approved splice modulating oligonucleotides to t…
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<i>ABCA4</i>midigenes reveal the full splice spectrum of all reported noncanonical splice site variants in Stargardt disease Open
Stargardt disease is caused by variants in the ABCA4 gene, a significant part of which are noncanonical splice site (NCSS) variants. In case a gene of interest is not expressed in available somatic cells, small genomic fragments carrying p…
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Efficient and accurate detection of splice junctions from RNA-seq with Portcullis Open
Next-generation sequencing technologies enable rapid and cheap genome-wide transcriptome analysis, providing vital information about gene structure, transcript expression, and alternative splicing. Key to this is the accurate identificatio…
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APPRIS 2017: principal isoforms for multiple gene sets Open
The APPRIS database (http://appris-tools.org) uses protein structural and functional features and information from cross-species conservation to annotate splice isoforms in protein-coding genes. APPRIS selects a single protein isoform, the…
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Detection of aberrant splicing events in RNA-seq data using FRASER Open
Aberrant splicing is a major cause of rare diseases. However, its prediction from genome sequence alone remains in most cases inconclusive. Recently, RNA sequencing has proven to be an effective complementary avenue to detect aberrant spli…
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Improving genetic diagnosis in Mendelian disease with transcriptome sequencing Open
Exome and whole-genome sequencing are becoming increasingly routine approaches in Mendelian disease diagnosis. Despite their success, the current diagnostic rate for genomic analyses across a variety of rare diseases is approximately 25-50…
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SpliceRover: interpretable convolutional neural networks for improved splice site prediction Open
Motivation During the last decade, improvements in high-throughput sequencing have generated a wealth of genomic data. Functionally interpreting these sequences and finding the biological signals that are hallmarks of gene function and reg…
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Detection and visualization of differential splicing in RNA-Seq data with JunctionSeq Open
Although RNA-Seq data provide unprecedented isoform-level expression information, detection of alternative isoform regulation (AIR) remains difficult, particularly when working with an incomplete transcript annotation. We introduce Junctio…
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Circular RNAs: An emerging type of RNA in cancer Open
Circular RNAs (circRNAs), a novel type of widespread and diverse endogenous non-coding RNAs (ncRNAs), which are different from the linear RNAs, form a covalently closed continuous loop without 5’ or 3’ polarities. The majority of circRNAs …
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Regulation of BK Channels by Beta and Gamma Subunits Open
Ca 2+ - and voltage-gated K + channels of large conductance (BK channels) are expressed in a diverse variety of both excitable and inexcitable cells, with functional properties presumably uniquely calibrated for the cells in which they are…
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Postcatalytic spliceosome structure reveals mechanism of 3′–splice site selection Open
Understanding splicing from the 3′ end The spliceosome removes introns from eukaryotic mRNA precursors and yields mature transcripts by joining exons. Despite decades of functional studies and recent progress in understanding the spliceoso…
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The time-resolved transcriptome of <i>C. elegans</i> Open
We generated detailed RNA-seq data for the nematode Caenorhabditis elegans with high temporal resolution in the embryo as well as representative samples from post-embryonic stages across the life cycle. The data reveal that early and late …
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A framework for individualized splice-switching oligonucleotide therapy Open
Splice-switching antisense oligonucleotides (ASOs) could be used to treat a subset of individuals with genetic diseases 1 , but the systematic identification of such individuals remains a challenge. Here we performed whole-genome sequencin…
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Large-scale analysis of branchpoint usage across species and cell lines Open
The coding sequence of each human pre-mRNA is interrupted, on average, by 11 introns that must be spliced out for proper gene expression. Each intron contains three obligate signals: a 5′ splice site, a branch site, and a 3′ splice site. S…
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Androgen receptor splice variants and prostate cancer: From bench to bedside Open
Therapeutic interventions for advanced prostate cancer (PCa) center on inhibiting androgen receptor (AR) and downstream signaling pathways. Resistance to androgen deprivation therapy and/or AR antagonists is inevitable and molecular mechan…