Differential GC content between exons and introns establishes distinct strategies of splice-site recognition.

PubWeight™: 1.41‹?› | Rank: Top 5%

🔗 View Article (PMID 22832277)

Published in Cell Rep on May 03, 2012

Authors

Maayan Amit1, Maya Donyo, Dror Hollander, Amir Goren, Eddo Kim, Sahar Gelfman, Galit Lev-Maor, David Burstein, Schraga Schwartz, Benny Postolsky, Tal Pupko, Gil Ast

Author Affiliations

1: Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine, Tel-Aviv University, Ramat Aviv 69978, Israel.

Articles citing this

Complexity of the alternative splicing landscape in plants. Plant Cell (2013) 2.62

Dynamic integration of splicing within gene regulatory pathways. Cell (2013) 2.25

Getting up to speed with transcription elongation by RNA polymerase II. Nat Rev Mol Cell Biol (2015) 1.97

Genome-wide dynamics of Pol II elongation and its interplay with promoter proximal pausing, chromatin, and exons. Elife (2014) 1.82

Widespread intron retention in mammals functionally tunes transcriptomes. Genome Res (2014) 1.65

DNA-methylation effect on cotranscriptional splicing is dependent on GC architecture of the exon-intron structure. Genome Res (2013) 1.44

SON connects the splicing-regulatory network with pluripotency in human embryonic stem cells. Nat Cell Biol (2013) 1.18

Chromatin and epigenetic regulation of pre-mRNA processing. Hum Mol Genet (2012) 1.10

Genome-wide discovery of human splicing branchpoints. Genome Res (2015) 1.08

Unexpected selection to retain high GC content and splicing enhancers within exons of multiexonic lncRNA loci. RNA (2015) 0.97

Intron retention is a widespread mechanism of tumor-suppressor inactivation. Nat Genet (2015) 0.95

RBFOX and PTBP1 proteins regulate the alternative splicing of micro-exons in human brain transcripts. Genome Res (2015) 0.95

Coupling of RNA Polymerase II Transcription Elongation with Pre-mRNA Splicing. J Mol Biol (2016) 0.92

The role of Dichaete in transcriptional regulation during Drosophila embryonic development. BMC Genomics (2013) 0.91

Evidence for GC-biased gene conversion as a driver of between-lineage differences in avian base composition. Genome Biol (2014) 0.86

In silico screening based on predictive algorithms as a design tool for exon skipping oligonucleotides in Duchenne muscular dystrophy. PLoS One (2015) 0.83

The nucleosome landscape of Plasmodium falciparum reveals chromatin architecture and dynamics of regulatory sequences. Nucleic Acids Res (2015) 0.83

A simple model to explain evolutionary trends of eukaryotic gene architecture and expression: how competition between splicing and cleavage/polyadenylation factors may affect gene expression and splice-site recognition in eukaryotes. Bioessays (2013) 0.83

Intron retention in the alternatively spliced region of RON results from weak 3' splice site recognition. PLoS One (2013) 0.83

RNA-Seq SSRs of Moth Orchid and Screening for Molecular Markers across Genus Phalaenopsis (Orchidaceae). PLoS One (2015) 0.83

Nucleotide sequence composition adjacent to intronic splice sites improves splicing efficiency via its effect on pre-mRNA local folding in fungi. RNA (2015) 0.82

A dynamic intron retention program in the mammalian megakaryocyte and erythrocyte lineages. Blood (2016) 0.82

Accurate, model-based tuning of synthetic gene expression using introns in S. cerevisiae. PLoS Genet (2014) 0.82

Widespread differences in cortex DNA methylation of the "language gene" CNTNAP2 between humans and chimpanzees. Epigenetics (2014) 0.81

Impact of human pathogenic micro-insertions and micro-deletions on post-transcriptional regulation. Hum Mol Genet (2014) 0.81

Global analysis of physical and functional RNA targets of hnRNP L reveals distinct sequence and epigenetic features of repressed and enhanced exons. RNA (2015) 0.81

Unraveling patterns of site-to-site synonymous rates variation and associated gene properties of protein domains and families. PLoS One (2014) 0.81

Comparative Analysis of AGPase Genes and Encoded Proteins in Eight Monocots and Three Dicots with Emphasis on Wheat. Front Plant Sci (2017) 0.80

Orthogonal matrix factorization enables integrative analysis of multiple RNA binding proteins. Bioinformatics (2016) 0.79

Cosplicing network analysis of mammalian brain RNA-Seq data utilizing WGCNA and Mantel correlations. Front Genet (2015) 0.79

How and why overcome the impediments to resolution: lessons from rhinolophid and hipposiderid bats. Mol Biol Evol (2014) 0.78

Whole genome DNA methylation: beyond genes silencing. Oncotarget (2016) 0.78

Intron evolution in Neurospora: the role of mutational bias and selection. Genome Res (2014) 0.77

Purifying Selection on Exonic Splice Enhancers in Intronless Genes. Mol Biol Evol (2016) 0.77

Regulation of constitutive and alternative mRNA splicing across the human transcriptome by PRPF8 is determined by 5' splice site strength. Genome Biol (2015) 0.77

The histone variant H2A.Z promotes efficient cotranscriptional splicing in S. cerevisiae. Genes Dev (2017) 0.77

Do Intron and Coding Sequences of Some Human-Mouse Orthologs Evolve as a Single Unit? J Mol Evol (2016) 0.77

Involvement of PARP1 in the regulation of alternative splicing. Cell Discov (2016) 0.76

Introns Structure Patterns of Variation in Nucleotide Composition in Arabidopsis thaliana and Rice Protein-Coding Genes. Genome Biol Evol (2015) 0.76

Differences in codon bias and GC content contribute to the balanced expression of TLR7 and TLR9. Proc Natl Acad Sci U S A (2016) 0.76

Alternative splicing as a regulator of development and tissue identity. Nat Rev Mol Cell Biol (2017) 0.75

Non-coding RNAs match the deleted genomic regions in humans. Sci Rep (2016) 0.75

Intron gain by tandem genomic duplication: a novel case in a potato gene encoding RNA-dependent RNA polymerase. PeerJ (2016) 0.75

RAG Recombinase as a Selective Pressure for Genome Evolution. Genome Biol Evol (2016) 0.75

DNA-Encoded Chromatin Structural Intron Boundary Signals Identify Conserved Genes with Common Function. Int J Genomics (2015) 0.75

The nonsense-mediated RNA decay pathway is disrupted in inflammatory myofibroblastic tumors. J Clin Invest (2016) 0.75

Splicing repression allows the gradual emergence of new Alu-exons in primate evolution. Elife (2016) 0.75

Mechanical Stress and Single Nucleotide Variants Regulate Alternative Splicing of the MYLK Gene. Am J Respir Cell Mol Biol (2017) 0.75

Pathogenic variants that alter protein code often disrupt splicing. Nat Genet (2017) 0.75

Selection on Position of Nonsense Codons in Introns. Genetics (2016) 0.75

Estimating the prevalence of functional exonic splice regulatory information. Hum Genet (2017) 0.75

Intron retention as a component of regulated gene expression programs. Hum Genet (2017) 0.75

Transcriptional Elongation Regulator 1 Affects Transcription and Splicing of Genes Associated with Cellular Morphology and Cytoskeleton Dynamics and Is Required for Neurite Outgrowth in Neuroblastoma Cells and Primary Neuronal Cultures. Mol Neurobiol (2016) 0.75

Articles by these authors

ConSurf 2005: the projection of evolutionary conservation scores of residues on protein structures. Nucleic Acids Res (2005) 10.60

ConSurf 2010: calculating evolutionary conservation in sequence and structure of proteins and nucleic acids. Nucleic Acids Res (2010) 9.68

ConSurf: identification of functional regions in proteins by surface-mapping of phylogenetic information. Bioinformatics (2003) 7.83

Topology of the human and mouse m6A RNA methylomes revealed by m6A-seq. Nature (2012) 7.00

Site-specific evolutionary rate inference: taking phylogenetic uncertainty into account. J Mol Evol (2005) 7.00

Single-cell transcriptomics reveals bimodality in expression and splicing in immune cells. Nature (2013) 6.50

Chromatin organization marks exon-intron structure. Nat Struct Mol Biol (2009) 5.90

Alu-containing exons are alternatively spliced. Genome Res (2002) 5.45

The birth of an alternatively spliced exon: 3' splice-site selection in Alu exons. Science (2003) 5.04

Intronic sequences flanking alternatively spliced exons are conserved between human and mouse. Genome Res (2003) 5.01

Alternative splicing and evolution: diversification, exon definition and function. Nat Rev Genet (2010) 4.30

Inferences of competence from faces predict election outcomes. Science (2005) 4.23

Comparative analysis identifies exonic splicing regulatory sequences--The complex definition of enhancers and silencers. Mol Cell (2006) 4.11

How prevalent is functional alternative splicing in the human genome? Trends Genet (2004) 3.81

Comparison of site-specific rate-inference methods for protein sequences: empirical Bayesian methods are superior. Mol Biol Evol (2004) 3.62

ConSeq: the identification of functionally and structurally important residues in protein sequences. Bioinformatics (2004) 3.50

Different levels of alternative splicing among eukaryotes. Nucleic Acids Res (2006) 3.07

GUIDANCE: a web server for assessing alignment confidence scores. Nucleic Acids Res (2010) 2.95

A structural EM algorithm for phylogenetic inference. J Comput Biol (2002) 2.67

An alignment confidence score capturing robustness to guide tree uncertainty. Mol Biol Evol (2010) 2.39

Comparative analysis of transposed element insertion within human and mouse genomes reveals Alu's unique role in shaping the human transcriptome. Genome Biol (2007) 2.35

Transcriptome-wide discovery of circular RNAs in Archaea. Nucleic Acids Res (2011) 2.33

Selecton 2007: advanced models for detecting positive and purifying selection using a Bayesian inference approach. Nucleic Acids Res (2007) 2.21

Position-dependent alternative splicing activity revealed by global profiling of alternative splicing events regulated by PTB. Nat Struct Mol Biol (2010) 2.19

A non-EST-based method for exon-skipping prediction. Genome Res (2004) 2.15

Alternative splicing: current perspectives. Bioessays (2008) 1.95

Genome-scale identification of Legionella pneumophila effectors using a machine learning approach. PLoS Pathog (2009) 1.94

Minimal conditions for exonization of intronic sequences: 5' splice site formation in alu exons. Mol Cell (2004) 1.93

Comparative analysis detects dependencies among the 5' splice-site positions. RNA (2004) 1.91

Detection and removal of biases in the analysis of next-generation sequencing reads. PLoS One (2011) 1.91

Large-scale comparative analysis of splicing signals and their corresponding splicing factors in eukaryotes. Genome Res (2007) 1.86

Rodent phylogeny revised: analysis of six nuclear genes from all major rodent clades. BMC Evol Biol (2009) 1.80

The average common substring approach to phylogenomic reconstruction. J Comput Biol (2006) 1.79

Insights into the connection between cancer and alternative splicing. Trends Genet (2007) 1.78

RNA-editing-mediated exon evolution. Genome Biol (2007) 1.77

The ConSurf-HSSP database: the mapping of evolutionary conservation among homologs onto PDB structures. Proteins (2005) 1.72

Human-mouse comparative analysis reveals that branch-site plasticity contributes to splicing regulation. Hum Mol Genet (2005) 1.71

Computational characterization of B-cell epitopes. Mol Immunol (2007) 1.60

A model-based approach for detecting coevolving positions in a molecule. Mol Biol Evol (2005) 1.59

Epitopia: a web-server for predicting B-cell epitopes. BMC Bioinformatics (2009) 1.55

The interface of protein structure, protein biophysics, and molecular evolution. Protein Sci (2012) 1.54

Chromatin density and splicing destiny: on the cross-talk between chromatin structure and splicing. EMBO J (2010) 1.53

KLF6-SV1 drives breast cancer metastasis and is associated with poor survival. Sci Transl Med (2013) 1.53

FastML: a web server for probabilistic reconstruction of ancestral sequences. Nucleic Acids Res (2012) 1.52

A combined empirical and mechanistic codon model. Mol Biol Evol (2006) 1.52

Selecton: a server for detecting evolutionary forces at a single amino-acid site. Bioinformatics (2005) 1.52

Computational modeling and experimental validation of the Legionella and Coxiella virulence-related type-IVB secretion signal. Proc Natl Acad Sci U S A (2013) 1.51

DNA-methylation effect on cotranscriptional splicing is dependent on GC architecture of the exon-intron structure. Genome Res (2013) 1.44

The complexity hypothesis revisited: connectivity rather than function constitutes a barrier to horizontal gene transfer. Mol Biol Evol (2010) 1.44

Tuberculosis: from prehistory to Robert Koch, as revealed by ancient DNA. Lancet Infect Dis (2004) 1.43

A machine-learning approach for predicting B-cell epitopes. Mol Immunol (2008) 1.40

Intronic Alus influence alternative splicing. PLoS Genet (2008) 1.35

SROOGLE: webserver for integrative, user-friendly visualization of splicing signals. Nucleic Acids Res (2009) 1.32

Stepwise prediction of conformational discontinuous B-cell epitopes using the Mapitope algorithm. Proteins (2007) 1.31

A gamma mixture model better accounts for among site rate heterogeneity. Bioinformatics (2005) 1.30

TranspoGene and microTranspoGene: transposed elements influence on the transcriptome of seven vertebrates and invertebrates. Nucleic Acids Res (2007) 1.30

Epitope mapping using combinatorial phage-display libraries: a graph-based algorithm. Nucleic Acids Res (2006) 1.29

The role of transposable elements in the evolution of non-mammalian vertebrates and invertebrates. Genome Biol (2010) 1.29

The importance of being divisible by three in alternative splicing. Nucleic Acids Res (2005) 1.29

The "alternative" choice of constitutive exons throughout evolution. PLoS Genet (2007) 1.27

Regulation of alternative splicing through coupling with transcription and chromatin structure. Annu Rev Biochem (2015) 1.26

DNA motifs determining the efficiency of adaptation into the Escherichia coli CRISPR array. Proc Natl Acad Sci U S A (2013) 1.25

Inference and characterization of horizontally transferred gene families using stochastic mapping. Mol Biol Evol (2009) 1.23

Transcriptome-wide mapping of 5-methylcytidine RNA modifications in bacteria, archaea, and yeast reveals m5C within archaeal mRNAs. PLoS Genet (2013) 1.22

Alu exonization events reveal features required for precise recognition of exons by the splicing machinery. PLoS Comput Biol (2009) 1.20

AluGene: a database of Alu elements incorporated within protein-coding genes. Nucleic Acids Res (2004) 1.19

In silico identification of functional regions in proteins. Bioinformatics (2005) 1.18

The conserved carboxy terminus of the capsid domain of human immunodeficiency virus type 1 gag protein is important for virion assembly and release. J Virol (2004) 1.18

A likelihood framework to analyse phyletic patterns. Philos Trans R Soc Lond B Biol Sci (2008) 1.16

Pepitope: epitope mapping from affinity-selected peptides. Bioinformatics (2007) 1.16

SR proteins: a foot on the exon before the transition from intron to exon definition. Trends Genet (2006) 1.15

Improving the performance of positive selection inference by filtering unreliable alignment regions. Mol Biol Evol (2011) 1.15

The emergence of alternative 3' and 5' splice site exons from constitutive exons. PLoS Comput Biol (2007) 1.15

Tophi and frequent gout flares are associated with impairments to quality of life, productivity, and increased healthcare resource use: Results from a cross-sectional survey. Health Qual Life Outcomes (2012) 1.13

Multifactorial interplay controls the splicing profile of Alu-derived exons. Mol Cell Biol (2008) 1.12

Alternative splicing of Alu exons--two arms are better than one. Nucleic Acids Res (2008) 1.11