A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2020; you can also visit the original URL.
The file type is application/pdf.
Filters
Non-canonical RNA-DNA differences and other human genomic features are enriched within very short tandem repeats
2020
PLoS Computational Biology
Preserved Fulltext
Very short tandem repeats bear substantial genetic, evolutional, and pathological significance in genome analyses. ...
Non-canonical and C-to-U RNA-editing events are enriched inside and/or adjacent to MNRs, while all categories of RNA-editing events are under-represented in DNRs. ...
Acknowledgments We thank Luis Nassar and Matthew Speir from UCSC Genomics Institute for assistance in compilation of the tract data hub. ...
doi:10.1371/journal.pcbi.1007968
pmid:32511223
fatcat:f75dvytjlrfjzjd2rh3vao3y7a
Tools and databases for solving problems in detection and identification of repetitive DNA sequences
2020
Periodicum biologorum
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2021; you can also visit the original URL.
The file type is application/pdf.
Some of the described assets are focused on detection of a wide range of repeats while the others are focused on a specific type of repetitive DNA sequences, generated as an answer to specific research ...
Genome compartments known to carry out very important biological functions (e.g. centromeres and telomeres) are mostly constituted of repetitive sequences. ...
Tools and databases aiming at the detection of tandem repeats While many tools are focused on detection of different types of repetitive DNA sequences, there are those specialized for a specific type of ...
doi:10.18054/pb.v121-122i1-2.10571
fatcat:2fw5aqnninadjefffnajqc3dqy
Tandem repeats modify the structure of human genes hosted in segmental duplications
2009
Genome Biology
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2010; you can also visit the original URL.
The file type is application/pdf.
It can be downloaded, printed and distributed freely for any purposes (see copyright notice below). Articles in Genome Biology are listed in PubMed and archived at PubMed Central. ...
For information about publishing your research in Genome Biology go to http://genomebiology.com/info/instructions/ Genome Biology ...
Acknowledgements This work was supported by AIRC Start-Up grant and by the Italian Ministry of Health to FDC. ...
doi:10.1186/gb-2009-10-12-r137
pmid:19954527
pmcid:PMC2812944
fatcat:fozqpvqjobhkla4wjrkmuwvo34
Global Mapping of DNA Conformational Flexibility on Saccharomyces cerevisiae
2015
PLoS Computational Biology
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2017; you can also visit the original URL.
The file type is application/pdf.
Author Summary High DNA helix torsional flexibility characterizes sequences which are enriched in fragile sites, loci of peculiar chromosome instability inside human genome often associated with cancer ...
(TA) n repeats of different extension shape the central structure of peaks and co-localize with polyadenylation efficiency element (EE) signals. ORFs with flexible peaks share common features. ...
The notion that enriched tandem repeats in S. cerevisiae could guide transcriptional modulation has been established for genes carrying very variable tracts of repeats in promoter; the involved genes have ...
doi:10.1371/journal.pcbi.1004136
pmid:25860149
pmcid:PMC4393290
fatcat:7ijn5pmdwzcnfdiqtias3acu3e
Variation in human chromosome 21 ribosomal RNA genes characterized by TAR cloning and long-read sequencing
2018
Nucleic Acids Research
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2019; you can also visit the original URL.
The file type is application/pdf.
Accurate long-read sequencing of 13 isolates covering ∼0.82 Mb of the chromosome 21 rDNA complement revealed substantial variation among tandem repeat rDNA copies, several palindromic structures and potential ...
Despite the key role of the human ribosome in protein biosynthesis, little is known about the extent of sequence variation in ribosomal DNA (rDNA) or its pre-rRNA and rRNA products. ...
ACKNOWLEDGEMENTS The authors thank Alice Young and the NIH Intramural Sequencing Center (NISC) for assistance with PacBio sequencing. ...
doi:10.1093/nar/gky442
pmid:29788454
pmcid:PMC6061828
fatcat:jxu2gcgrwfcffflt4233tq3xfi
Centromere identity from the DNA point of view
2014
Chromosoma
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2017; you can also visit the original URL.
The file type is application/pdf.
However, some evolutionary preferences seem to exist, and long-term established centromeres are frequently formed on long arrays of satellite DNAs and/or transposable elements. ...
Here, we comprehensively review the current state of knowledge on the composition and functionality of DNA sequences underlying active centromeres and discuss their contribution to the functioning of different ...
and the source are credited. ...
doi:10.1007/s00412-014-0462-0
pmid:24763964
pmcid:PMC4107277
fatcat:w4mna5l7kbgqjif34zauvt75uu
Strong epigenetic similarity between maize centromeric and pericentromeric regions at the level of small RNAs, DNA methylation and H3 chromatin modifications
2011
Nucleic Acids Research
Preserved Fulltext
The Internet Archive has a preservation copy of this work in our general collections.
The file type is application/pdf.
We applied genome-wide sequencing approaches to quantify RNA expression, DNA methylation and histone modification distributions in maize (Zea mays), focusing on two maize chromosomes with nearly fully ...
RNA expression and chromatin modification frequencies were broadly associated with distance from centromeres, gradually peaking or dipping toward arms. ...
Ellis for expert advice and helpful discussions; Yeching Huang, Tao Zhang and Yufeng Wu for technical help with bioinformatic software; and Sarah Wolf, Rashin Ghaffari and Kathryn S. ...
doi:10.1093/nar/gkr862
pmid:22058126
pmcid:PMC3287186
fatcat:kvcscdk24fgcbgui4kzyuwalz4
Repetitive DNA loci and their modulation by the non-canonical nucleic acid structures R-loops and G-quadruplexes
2017
Nucleus
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2019; you can also visit the original URL.
The file type is application/pdf.
Here, we discuss key mechanisms that maintain rDNA repeats, telomeres, and transposons in yeast and human before highlighting emerging roles for non-canonical DNA structures at these repetitive loci. ...
The major source of repetitive DNA sequences and thus the most vulnerable constituents of the genome are the rDNA (rDNA) repeats, telomeres, and transposable elements. ...
Of particular interest, 2 types of non-canonical DNA structures known as R-loops (harbouring RNA-DNA hybrids) and G-quadruplexes (GQ) are especially abundant within repetitive DNA loci. 5 The formation ...
doi:10.1080/19491034.2017.1292193
pmid:28406751
pmcid:PMC5403138
fatcat:iaddok3nkbfxjjbqs7yoa2jdge
The cancer-associated CTCFL/BORIS protein targets multiple classes of genomic repeats, with a distinct binding and functional preference for humanoid-specific SVA transposable elements
2016
Epigenetics & Chromatin
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2017; you can also visit the original URL.
The file type is application/pdf.
in human genome when activated. ...
The CTCF-only enrichment is characteristic for evolutionary old and inactive repeat classes, while BORIS and CTCF co-binding predominately occurs at uncharacterized tandem repeats. ...
tandem repeat of two different Alu (shown in the schematic). ...
doi:10.1186/s13072-016-0084-2
pmid:27588042
pmcid:PMC5007689
fatcat:4jhanhmetfgvtcznhpqyqu7fyi
Functional Significance of Satellite DNAs: Insights From Drosophila
2020
Frontiers in Cell and Developmental Biology
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2020; you can also visit the original URL.
The file type is application/pdf.
Many satellites are transcribed with the generation of long or small non-coding RNAs. ...
Since their discovery more than 60 years ago, satellite repeats are still one of the most enigmatic parts of eukaryotic genomes. ...
Gvozdev and A. D. Stolyarenko for discussions and valuable comments on this manuscript. ...
doi:10.3389/fcell.2020.00312
pmid:32432114
pmcid:PMC7214746
fatcat:4u6tersmnbfozo7ba6kxtgzvua
Expanding the Coding Potential of Vertebrate Mitochondrial Genomes: Lesson Learned from the Atlantic Cod
[chapter]
2018
Mitochondrial DNA - New Insights
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2019; you can also visit the original URL.
The file type is application/pdf.
Vertebrate mitochondrial genomes are highly conserved in structure, gene content, and function. ...
In addition to the well-characterized 37 canonical gene products encoded by vertebrate mitochondrial genomes, new classes of gene products representing peptides and noncoding RNAs have been discovered. ...
Acknowledgements We thank the current and former members of the mitochondrial DNA research team at the Genomics Group, Nord University, for the discussion and support. ...
doi:10.5772/intechopen.75883
fatcat:rvzprgxp2zdgvoll4odfdmkb5i
Toward predictive R-loop computational biology: genome-scale prediction of R-loops reveals their association with complex promoter structures, G-quadruplexes and transcriptionally active enhancers
2018
Nucleic Acids Research
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2019; you can also visit the original URL.
The file type is application/pdf.
regions, G-rich regions and disease-associated genomic loci in the human genome. ...
We introduced and characterized an abundant class of reverse-forward RLFS clusters highly enriched in non-B DNA structures, which localized to promoters, gene ends and enhancers. ...
T.W. and P.J. generated RLFS data and together with V.A.K. and V.B. integrated these data with other datasets. V.A.K. wrote the final version of the manuscript. ...
doi:10.1093/nar/gky554
pmid:29945198
fatcat:c3ov6umaqncvjihwjaf2q5cz7e
Insights into epigenetic landscape of recombination-free regions
2016
Chromosoma
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2017; you can also visit the original URL.
The file type is application/pdf.
Under normal conditions, the repeat-containing regions undergo little or no meiotic crossover (CO) recombination. COs within repeats are risky for the genome integrity. ...
Indeed, they can promote non-allelic homologous recombination (NAHR) resulting in deleterious genomic rearrangements associated with diseases in humans. ...
In a wide range of organisms, telomeres consist of short tandem repeats. ...
doi:10.1007/s00412-016-0574-9
pmid:26801812
pmcid:PMC4830869
fatcat:we325y7j2jesxn2irwwkse6ftq
The Evolution of Line-1 in Vertebrates
2016
Genome Biology and Evolution
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2019; you can also visit the original URL.
The file type is application/pdf.
In contrast, non-mammalian genomes (fish, amphibians, reptiles) harbor a large diversity of concurrently transposing families, which are all represented by very small number of recently inserted copies ...
The highly divergent L1 families of lizard, frog, and fish share species-specific features suggesting that they are subjected to the same functional constraints imposed by their host. ...
Acknowledgments We thank Robert Ruggiero and three anonymous reviewers for their helpful comments on the manuscript. ...
doi:10.1093/gbe/evw247
pmid:28175298
pmcid:PMC5381506
fatcat:wozhcw22lvek7e3jhz64mcosuy
STaRRRT: a table of short tandem repeats in regulatory regions of the human genome
2013
BMC Genomics
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2021; you can also visit the original URL.
The file type is application/pdf.
Tandem repeats (TRs) are unstable regions commonly found within genomes that have consequences for evolution and disease. ...
The most common TRs are short tandem repeats (STRs), or microsatellites. Promoter located STRs are considerably more polymorphic than coding region STRs. ...
Background Tandem repeats (TRs) are stretches of DNA that contain nucleotide patterns repeated adjacent to one another and are common throughout the human genome [1] . ...
doi:10.1186/1471-2164-14-795
pmid:24228761
pmcid:PMC3840602
fatcat:jyav5uv5sffmrijcpeq2dmwi6e
« Previous
Showing results 1 — 15 out of 4,033 results