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Non-canonical RNA-DNA differences and other human genomic features are enriched within very short tandem repeats

Hui Yu, Shilin Zhao, Scott Ness, Huining Kang, Quanhu Sheng, David C. Samuels, Olufunmilola Oyebamiji, Ying-yong Zhao, Yan Guo, Lilia M. Iakoucheva
2020 PLoS Computational Biology  
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

Eva Satovic
2020 Periodicum biologorum  
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

Anna De Grassi, Francesca D Ciccarelli
2009 Genome Biology  
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

Giulia Menconi, Andrea Bedini, Roberto Barale, Isabella Sbrana, Christos A. Ouzounis
2015 PLoS Computational Biology  
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

Jung-Hyun Kim, Alexander T Dilthey, Ramaiah Nagaraja, Hee-Sheung Lee, Sergey Koren, Dawood Dudekula, William H Wood III, Yulan Piao, Aleksey Y Ogurtsov, Koichi Utani, Vladimir N Noskov, Svetlana A Shabalina (+3 others)
2018 Nucleic Acids Research  
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

Miroslav Plohl, Nevenka Meštrović, Brankica Mravinac
2014 Chromosoma  
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

Jonathan I. Gent, Yuzhu Dong, Jiming Jiang, R. Kelly Dawe
2011 Nucleic Acids Research  
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

Amanda C. Hall, Lauren A. Ostrowski, Violena Pietrobon, Karim Mekhail
2017 Nucleus  
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

Elena M. Pugacheva, Evgeny Teplyakov, Qiongfang Wu, Jingjing Li, Cheng Chen, Chengcheng Meng, Jian Liu, Susan Robinson, Dmitry Loukinov, Abdelhalim Boukaba, Andrew Paul Hutchins, Victor Lobanenkov (+1 others)
2016 Epigenetics & Chromatin  
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

Aleksei S. Shatskikh, Alexei A. Kotov, Vladimir E. Adashev, Sergei S. Bazylev, Ludmila V. Olenina
2020 Frontiers in Cell and Developmental Biology  
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]

Tor Erik Jørgensen, Steinar Daae Johansen
2018 Mitochondrial DNA - New Insights  
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

Vladimir A Kuznetsov, Vladyslav Bondarenko, Thidathip Wongsurawat, Surya P Yenamandra, Piroon Jenjaroenpun
2018 Nucleic Acids Research  
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

Pasquale Termolino, Gaetana Cremona, Maria Federica Consiglio, Clara Conicella
2016 Chromosoma  
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

Stéphane Boissinot, Akash Sookdeo
2016 Genome Biology and Evolution  
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

Katherine A Bolton, Jason P Ross, Desma M Grice, Nikola A Bowden, Elizabeth G Holliday, Kelly A Avery-Kiejda, Rodney J Scott
2013 BMC Genomics  
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
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