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Nucleosome formation potential of exons, introns, and Alu repeats

V. G. Levitsky, O. A. Podkolodnaya, N. A. Kolchanov, N. L. Podkolodny
2001 Bioinformatics  
A program for constructing nucleosome formation potential profile was applied for investigation of exons, introns, and repetitive sequences.  ...  We have demonstrated that introns and repetitive sequences exhibit higher nucleosome formation potentials than exons.  ...  The authors thank A.V.Katokhin for useful discussions and to G.B.Chirikova for paper translating.  ... 
doi:10.1093/bioinformatics/17.11.1062 pmid:11724736 fatcat:vwfddnhs2bedpe3xn3ghmpy2ym

"Genome design" model: Evidence from conserved intronic sequence in human-mouse comparison

A. E. Vinogradov
2006 Genome Research  
sequence in human-mouse comparison "Genome design" model: Evidence from conserved intronic data Supplementary http://www.genome.org/cgi/content/full/gr.4318206/DC1 "Supplementary Research Data"  ...  Tchernajenko, and two anonymous reviewers for helpful comments. This work was supported by the Russian Foundation for Basic Research (RFBR) and by the Programme of the Presidium  ...  The higher nucleosome formation potential was found in vertebrate noncoding DNA (including introns) compared to exons, and in human tissuespecific genes compared to housekeeping genes (Levitsky et al.  ... 
doi:10.1101/gr.4318206 pmid:16461636 pmcid:PMC1415212 fatcat:7qsdixoyqbeonhyxz6hfgsis5q

RECON: a program for prediction of nucleosome formation potential

V. G. Levitsky
2004 Nucleic Acids Research  
The program RECON has been designed for constructing profiles of nucleosome potential, characterizing the probability of nucleosome formation along DNA sequences.  ...  The program used for recognition of nucleosome formation sites in genomic DNA sequences.  ...  Lavryushev for interface design, and to Drs D. P. Furman and A.V. Katokhin for useful discussions. The work was supported by the Russian  ... 
doi:10.1093/nar/gkh482 pmid:15215408 pmcid:PMC441620 fatcat:vtrv35a7bvfnfjgcm4ogpqqdaq

Secondary structure of pre-mRNA introns for genes of 15q11-12 locus. Mapping of functionally significant motives of RNA binding proteins and f nucleosome positioning signals [article]

Viya Borisovna Fedoseyeva, Irina Alexandrovna Zharinova, Alexander Anatolyevich Alexandrov
2018 bioRxiv   pre-print
Mapping of the nucleosome potential reveals alternation of strong and weak signals at the 3'-end portion of GABRB3 and clusters of nucleosome positioning signal in the vicinity of the Alu cluster.  ...  A model of potential intron RNA influence on splicing has been suggested based on its interaction with Py-tract-binding RNP, serine-arginine SRSF proteins, ncRNA Malat1, as well as the action of Alu cluster  ...  which would probably 614 hamper the formation of a nucleosome cluster and complicate transcriptional elongation.  ... 
doi:10.1101/409243 fatcat:o7opkuudjbdzviuhvagmw3fo5i

Multilayered control of exon acquisition permits the emergence of novel forms of regulatory control

Nesli Avgan, Juli I. Wang, Javier Fernandez-Chamorro, Robert J. Weatheritt
2019 Genome Biology  
The long introns of mammals are pools of evolutionary potential due to the multiplicity of sequences that permit the acquisition of novel exons.  ...  However, the permissibility of genes to this type of acquisition and its influence on the evolution of cell regulation is poorly understood.  ...  Chavali, and S. Gueroussov for helpful discussions and critical review of the manuscript. Review history The review history is available as Additional file 7.  ... 
doi:10.1186/s13059-019-1757-5 pmid:31315652 pmcid:PMC6637531 fatcat:corigkozyjes5hg63utx5tkucu

High-resolution characterization of CPD hotspot formation in human fibroblasts

A. G. Zavala, R. T. Morris, J. J. Wyrick, M. J. Smerdon
2013 Nucleic Acids Research  
These results indicate that nucleosomes associated with hotspots of CPD formation are readily rearranged, potentially making them accessible to DNA repair machinery.  ...  CPD hotspots occur almost equally in genic and intergenic regions. However, these hotspots are significantly more prevalent adjacent to repeat elements, especially Alu repeats.  ...  Genic CPD hotspots were defined as intronic if the maximum MA intensity ratio of the peak did not fall within the exon sequence of a gene.  ... 
doi:10.1093/nar/gkt912 pmid:24137003 pmcid:PMC3902913 fatcat:whxoml63afdv3kq36j4ykfz3ee

DNA hypermethylation of alternatively spliced and repeat sequences in humans

Andigoni Malousi, Sofia Kouidou
2012 Molecular Genetics and Genomics  
cassette exons which are occasionally spliced and have weaker average splicing potential, relative to constitutive exons (p \ 0.0001).  ...  introns or bleeding exons, (p = 0.706 and p = 0.313, respectively).  ...  Splicing potential in cassette and constitutive exons The flanking 5 0 and 3 0 intron ends of the analyzed cassette and constitutive exons were then evaluated for their compliance with the canonical forms  ... 
doi:10.1007/s00438-012-0703-y pmid:22740315 pmcid:PMC3407362 fatcat:b4dxj6roafcgngipftsqttshum

From 'JUNK' to Just Unexplored Noncoding Knowledge: the case of transcribed Alus

R. Pandey, M. Mukerji
2011 Briefings in Functional Genomics  
Alu exonization and as probable miRNA targets.  ...  Dynamic and functional Alu repeats seem to be centrally placed to modulate the transcriptional landscape of human genome.  ...  Within genes, Alus occupy 12.8% intronic and 1.6% exonic regions.  ... 
doi:10.1093/bfgp/elr044 fatcat:zowglfgntjavxatee6ctrjdgwq

From 'JUNK' to Just Unexplored Noncoding Knowledge: the case of transcribed Alus

R. Pandey, M. Mukerji
2011 Briefings in Functional Genomics  
Alu exonization and as probable miRNA targets.  ...  Dynamic and functional Alu repeats seem to be centrally placed to modulate the transcriptional landscape of human genome.  ...  Within genes, Alus occupy 12.8% intronic and 1.6% exonic regions.  ... 
doi:10.1093/bfgp/elr029 pmid:21987713 fatcat:7yx2ytqaebgi3kkghrgbhqwkqa

Alpha-galactosidase A gene rearrangements causing Fabry disease. Identification of short direct repeats at breakpoints in an Alu-rich gene

R Kornreich, D F Bishop, R J Desnick
1990 Journal of Biological Chemistry  
These studies indicate that short direct repeats are important in the formation of gene rearrangements, even in human genes like alpha-galactosidase A that are rich in Alu repetitive elements.  ...  Six alpha-galactosidase A gene rearrangements that cause Fabry disease were investigated to assess the role of Alu repetitive elements and short direct and/or inverted repeats in the generation of these  ...  As shown in Fig. 2 , the 5' breakpoint was in intron 2 and the 3' breakpoint was in exon 7. The 4519-bp deletion eliminated 533 bp of intron 2, all of exons and introns 3 to 6, and 277 bp of exon 7.  ... 
pmid:2160973 fatcat:kgp36zdxrnc6bk3quvz5t4nkli

Evolutionary dynamics of circular RNAs in primates [article]

Gabriela Santos-Rodriguez, Irina Voineagu, Robert J Weatheritt
2021 bioRxiv   pre-print
These circRNAs are defined by an extended downstream intron that has shown dramatic lengthening during evolution due to the insertion of novel retrotransposons.  ...  However, our analysis also revealed a subset of circRNAs with conserved neural expression across tens of millions of years of evolution.  ...  For example, the formation of Alu exons is suppressed by the nuclear ribonucleo-217 protein HNRNPC (Zarnack et al., 2013) and the nuclear helicase DHX9 binds to inverted repeat Alu these inclusions can  ... 
doi:10.1101/2021.05.01.442284 fatcat:dz4dxfnecnfvdeutq5d4cytnru

Uneven Distribution of Potential Triplex Sequences in the Human Genome - In Silico Study using the R/Bioconductor Package Triplex
english

Matej Lexa, Tomás Martínek, Marie Brázdová
2014 Proceedings of the International Conference on Bioinformatics Models, Methods and Algorithms  
(microsatellites), Alu and combined elements, such as SVA.  ...  Using the R/Bioconductor package triplex, we found these sequences to be excluded from exons, while present mostly in a small number of repetitive sequence classes, especially short sequence tandem repeats  ...  For example, triplex DNA has been found to be incompatible with nucleosome formation and may act as a nucleosome barrier (Westin et al., 1995) .  ... 
doi:10.5220/0004824100800088 dblp:conf/biostec/LexaMB14 fatcat:hjnjt753yjbhfcvkxgcsazvjhu

Lessons from non-canonical splicing

Christopher R. Sibley, Lorea Blazquez, Jernej Ule
2016 Nature reviews genetics  
They are therefore under precise regulation and quality control, which minimises their potential to disrupt gene 10 expression.  ...  This includes cryptic events located far from the currently annotated exons, and 5 unconventional splicing mechanisms that have important roles in regulating gene expression.  ...  As inverted Alu repeats are known to be a target for RNA editing, it is thus possible that formation of circRNAs could be regulated by editing.  ... 
doi:10.1038/nrg.2016.46 pmid:27240813 pmcid:PMC5154377 fatcat:dht7op2v4nehthniwwrvksasta

Non-LTR retrotransposons and microsatellites

Fiorella C. Grandi, Wenfeng An
2013 Mobile Genetic Elements  
among exonic, intronic and intergenic regions (note "exonic regions" herein include not only protein-coding sequences but also 5' and 3' untranslated regions); (2) Di-, tetra-and pentanucleotide microsatellites  ...  amount of microsatellite variation as compared with intergenic and intronic sequences, reflecting increased selective constraints on exonic sequences. 14 Polymorphism incidence increases with repeat number  ... 
doi:10.4161/mge.25674 pmid:24195012 pmcid:PMC3812793 fatcat:qwzm4wtw7na4ldsesw43i7szry

cis regulation of the keratin 18 gene in transgenic mice

N S Neznanov, R G Oshima
1993 Molecular and Cellular Biology  
In addition, exon 6 and the intron 1 regulatory region were distinguished from the remainder of K18 by differential DNA methylation in expressing and nonexpressing tissues.  ...  These results suggest that DNA methylation is not the primary mechanism of control of the gene. An Alu RNA polymerase III transcription unit and exon 6 are implicated in regulation of K18.  ...  This work was supported by a grant from the DHHS, NCI, CA42302, and Cancer Center grant CA30199.  ... 
doi:10.1128/mcb.13.3.1815 pmid:7680099 pmcid:PMC359494 fatcat:bmzuk6disvg77c6zd7cvs4j4qy
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