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Modeling splicing sites with pairwise correlations

M. Arita, K. Tsuda, K. Asai
2002 Bioinformatics  
The method suits to model splicing sites in human DNA, which are reported to have higher-order dependencies.  ...  It approximates the multiple correlations among residuals with pair-wise correlations, with the learning cost Ç´Ñ ¾ Òµ where Ò is the number of training sequences, each of length Ñ.  ...  Two types of splicing junctions are commonly called an acceptor (3' splice site) and a donor (5' splice site).  ... 
doi:10.1093/bioinformatics/18.suppl_2.s27 pmid:12385980 fatcat:fa3brrsb2bayxjkhezqzexutli

Non-parametric Bayesian density estimation for biological sequence space with applications to pre-mRNA splicing and the karyotypic diversity of human cancer [article]

Wei-Chia Chen, Juannan Zhou, Jason Meyer Sheltzer, Justin Block Kinney, David Martin McCandlish
2020 bioRxiv   pre-print
To demonstrate the power of this method, we use it to explore the high-dimensional geometry of the distribution of 5' splice sites found in the human genome and to understand the accumulation of chromosomal  ...  In particular, we define a family of priors for probability distributions over sequence space with a single hyper-parameter that controls the expected magnitude of higher-order correlations.  ...  In addition, modeling and identification of splice sites was one of the early successes of maximum entropy models with pairwise interactions and remains a common method for scoring splice sites [9] .  ... 
doi:10.1101/2020.11.25.399253 fatcat:pzxkhidgi5dx3i7pm572uz2tdy

Mining divergent and conserved signals in 5′ splicing site sequences [article]

Maximiliano Beckel, Bruno Kaufman, Marcelo Yanovsky, Ariel Chernomoretz
2021 bioRxiv   pre-print
We considered a regularized maximum entropy modeling framework to mine for non-trivial two-site correlations in donor sequences of 14 different eukaryote organisms.  ...  Noticeably, we could also identify specific two-site coupling patterns for plants and for animals and argue that these differences, in association with taxon-specific features involving U6 snRNP, could  ...  Inset: relationship between model-estimated, σ model ij , and observed, σ nat ij two-site correlations.  ... 
doi:10.1101/2021.07.14.452117 fatcat:qs7t5kralnhfhmx6dtl5tjta5m

Coevolutionary networks of splicing cis-regulatory elements

X. Xiao, Z. Wang, M. Jang, C. B. Burge
2007 Proceedings of the National Academy of Sciences of the United States of America  
Here, we developed a generalized Bayesian network to model the coevolution of splicing cis elements in diverse eukaryotic taxa.  ...  Cross-exon but not cross-intron compensatory interactions between the 5 splice site (5ss) and 3 splice site (3ss) were observed in human/mouse, indicating that the exon is the primary evolutionary unit  ...  In both the fishes and the flies, splice site strength changed in a correlated fashion with intron length, suggesting that shorter intron lengths increase splicing efficiency in both of these systems  ... 
doi:10.1073/pnas.0707349104 pmid:17998536 pmcid:PMC2141820 fatcat:xquybahgw5e2pnm5knsoplnaui

Quantitative Activity Profile and Context Dependence of All Human 5′ Splice Sites

Mandy S. Wong, Justin B. Kinney, Adrian R. Krainer
2018 Molecular Cell  
Mutations at the 5′ splice site (5′ss) frequently cause defective splicing and disease, due to interference with the initial recognition of the exon-intron boundary by U1 small nuclear ribonucleoprotein  ...  Pre-mRNA splicing is an essential step in the expression of most human genes.  ...  Note that pairwise models were inferred only for GU splice sites. Analyses for each separate library are shown in Figure S7C. (B) Same as A, but for SMN1. See also Figure S7D. .  ... 
doi:10.1016/j.molcel.2018.07.033 pmid:30174293 pmcid:PMC6179149 fatcat:ijcu54hsofgkfnhk5lhjq7v4ba

Cellular Taxonomy of the Mouse Striatum as Revealed by Single-Cell RNA-Seq

Ozgun Gokce, Geoffrey M. Stanley, Barbara Treutlein, Norma F. Neff, J. Gray Camp, Robert C. Malenka, Patrick E. Rothwell, Marc V. Fuccillo, Thomas C. Südhof, Stephen R. Quake
2016 Cell Reports  
Description of previously unknown medium spiny neuron subtypes d Discrete cell types that exist in a continuous spectrum of transcriptional states d Neurons that have the largest transcriptome and more complex splicing  ...  No splicing factors were found with high correlation to any other cell types.  ...  Here, we performed a global analysis to quantify and compare genes with compound splice sites by cell type (Figure 7B ).  ... 
doi:10.1016/j.celrep.2016.06.059 pmid:27425622 pmcid:PMC5004635 fatcat:5itzzteq75hnpdub2d6nlcoedq

Genome-wide expression changes mediated by A-to-I RNA editing correlate with hepatic oncogenesis

Jian Li, Qun Li, Chun-Peng Yu, Shuai Chang, Ling-Ling Xie, Song Wang
2021 Translational Cancer Research  
Two intronic self-editing sites in ADAR mRNAs controlled its splicing pattern and may regulate its translation efficiency (TE).  ...  Moreover, the expression of oncogenes was generally upregulated in tumors, whereas tumor suppressor genes (TSG) were downregulated, possibly due to alterations to microRNA binding sites or RNA splicing  ...  samples exhibited lower pairwise correlations with each other; (III) the correlation between normal and tumor samples was lowest.  ... 
doi:10.21037/tcr-21-236 pmid:35116583 pmcid:PMC8798912 fatcat:7q7uy627avgu5gxtjrt3xq3anq

Empirical variance component regression for sequence-function relationships [article]

Juannan Zhou, Mandy S Wong, Wei-Chia Chen, Adrian R Krainer, Justin B Kinney, David M McCandlish
2020 biorxiv/medrxiv   pre-print
efficiency of human pre-mRNA 5′ splice sites for which we also validate our model predictions via additional low-throughput experiments.  ...  of phenotypic variance due to each order of genetic interaction (additive, pairwise, three-way, etc.).  ...  Gray dots represent splice sites not present as functional splice sites (65.9% of all possible splice sites). (D) Abstracted version of panel C.  ... 
doi:10.1101/2020.10.14.339804 fatcat:56uv2wpyyfgm3knwa2zlkud62y

Transcriptome Sequencing from Diverse Human Populations Reveals Differentiated Regulatory Architecture

Alicia R. Martin, Helio A. Costa, Tuuli Lappalainen, Brenna M. Henn, Jeffrey M. Kidd, Muh-Ching Yee, Fabian Grubert, Howard M. Cann, Michael Snyder, Stephen B. Montgomery, Carlos D. Bustamante, Greg Gibson
2014 PLoS Genetics  
Of this population-specific variation, 75.5% is due to expression rather than splicing variability, and we find few genes with strong evidence for differential splicing across populations.  ...  To better understand the spectrum of gene expression variation, alternative splicing, and the population genetics of regulatory variation in humans, we have sequenced the genomes, exomes, and transcriptomes  ...  We also thank Jean Monlong and Robert Guigó for providing well-documented scripts to decompose expression and splicing variability.  ... 
doi:10.1371/journal.pgen.1004549 pmid:25121757 pmcid:PMC4133153 fatcat:4hieukbdvjf7bgolmqwno6ovoq

Cotranscriptional splicing efficiency differs dramatically between Drosophila and mouse

Y. L. Khodor, J. S. Menet, M. Tolan, M. Rosbash
2012 RNA: A publication of the RNA Society  
An additional difference between species is that only mouse cotranscriptional splicing is optimal when 59-exon length is between 50 and 500 bp, and intron length does not correlate with splicing efficiency  ...  Additionally, absolute gene length correlates positively with cotranscriptional splicing efficiency independently of intron location and position, in flies as well as in mice.  ...  Our work in Drosophila also established that intron length negatively correlates with cotranscriptional splicing efficiency, which supports a model of the intron as the unit across which splice sites are  ... 
doi:10.1261/rna.034090.112 pmid:23097425 pmcid:PMC3504670 fatcat:vrv54lhppbhlhehpszlmrul26i

Dinoflagellate Gene Structure and Intron Splice Sites in a Genomic Tandem Array

Gregory S. Mendez, Charles F. Delwiche, Kirk E. Apt, J. Casey Lippmeier
2015 Journal of Eukaryotic Microbiology  
Two to nine base pairs around the 3 0 splice site are repeated by an identical two to nine base pairs around the 5 0 splice site.  ...  This study characterizes a splice site consensus sequence for dinoflagellate introns.  ...  Within our data, there is a consistent splicing pattern that is also consistent with most other published splice sites from dinoflagellates.  ... 
doi:10.1111/jeu.12230 pmid:25963315 pmcid:PMC5032977 fatcat:mjqbzcrt6fcitif6ct54otjm7i

Lineage-specific sequence evolution and exon edge conservation partially explain the relationship between evolutionary rate and expression level inA. thaliana

Stephen J. Bush, Paula X. Kover, Araxi O. Urrutia
2015 Molecular Ecology  
In plants, the 'edges' of exons, flanking intron junctions, are known to contain splice enhancers and to have a higher degree of conservation compared to the remainder of the coding region.  ...  We investigate the effects of exon edge conservation on the relationship of dN/dS to various sequence characteristics and gene expression parameters in the model plant Arabidopsis thaliana.  ...  ESEs are enriched in the vicinity of splice sites, particularly downstream of a splice acceptor, with their peak abundance increasing closer to an exon-intron boundary (Wu et al. 2005) .  ... 
doi:10.1111/mec.13221 pmid:25930165 pmcid:PMC4480654 fatcat:wuhitxi4ybd7ldydtl344bqm6a

The Role of Alternative Splicing and Differential Gene Expression in Cichlid Adaptive Radiation

Pooja Singh, Christine Börger, Heather More, Christian Sturmbauer
2017 Genome Biology and Evolution  
Our data reveal a surprisingly high degree of alternative splicing events compared with gene expression differences among species and trophic types.  ...  Specifically, genes undergoing splicing across most species were found to be enriched for pharyngeal jaw gene ontology terms.  ...  , guided by splice-sites.  ... 
doi:10.1093/gbe/evx204 pmid:29036566 pmcid:PMC5737861 fatcat:ywzjlwk7k5df5mifl53rdpjz7a

High Intron Sequence Conservation Across Three Mammalian Orders Suggests Functional Constraints

M. P. Hare
2003 Molecular biology and evolution  
nucleotide sites.  ...  conservation is consistent with neutral divergence.  ...  The heterogeneity among loci was not correlated with either GC content or total intron size in humans (Spearman, P . 0:05; table 1), but was correlated with intron position (P 0.05).  ... 
doi:10.1093/molbev/msg111 pmid:12716984 fatcat:wiil3kizgfdifgduad4wdiao4u

The activity of human enhancers is modulated by the splicing of their associated lncRNAs

Jennifer Yihong Tan, Ana Claudia Marques, Ilya Ioshikhes
2022 PLoS Computational Biology  
from transcription across spurious splice sites.  ...  Recently, splicing of elncRNAs was shown to be associated with elevated enhancer activity.  ...  First, pairwise alignment between human and mouse of the different splicing-associated features (including canonical splice sites, exonic splicing enhancers and canonical U1 sites) were separately concatenated  ... 
doi:10.1371/journal.pcbi.1009722 pmid:35015755 pmcid:PMC8803168 fatcat:mfibt4oo35banobsvh7f4lrni4
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