Faculty Opinions recommendation of Genome-wide detection of tandem DNA repeats that are expanded in autism.

2020 ◽  
Author(s):  
Branko Aleksic
Keyword(s):  
Dna Repeats ◽  
Genome Wide

scholarly journals Super-resolution microscopy of chromatin fibers and quantitative DNA methylation analysis of DNA fiber preparations

2021 ◽  
Author(s):  
Michal Franek ◽  
Agata Kilar ◽  
Petr Fojtík ◽  
Marie Olšinová ◽  
Aleš Benda ◽  
...  
Keyword(s):  
Single Cell Analysis ◽  
Super Resolution ◽  
Single Copy ◽  
Histone Variants ◽  
Dna Repeats ◽  
Genome Wide ◽  
Custom Script ◽  
Chromatin Immunoprecipitation Sequencing ◽  
Super Resolution Microscopy ◽  
Dna Methylation Analysis

Analysis of histone variants and epigenetic marks is dominated by genome-wide approaches in the form of chromatin immunoprecipitation-sequencing (ChIP-seq) and related methods. While uncontested in their value for single-copy genes, mapping the chromatin of DNA repeats is problematic for biochemical techniques based on averaging cell populations or high number of repeats in a single cell analysis. Extending chromatin and DNA fibers allows us to study the epigenetics of individual repeats in their specific chromosomal context and thus constitutes an important tool for a wholesome understanding of the epigenetic organization of genomes. We present that using an optimized fiber extension protocol is essential to obtain more reproducible data, where the clustering of fibers is minimized. We also demonstrate that applying super-resolution microscopy is important to reliably evaluate the distribution of histone modifications on individual fibers. Furthermore, we introduce a custom script to analyse methylation levels on DNA fibers and apply it to map the methylation of telomeres, ribosomal genes and centromeres.

scholarly journals Genome-Wide Stochastic Adaptive DNA Amplification at Direct and Inverted DNA Repeats in the Parasite Leishmania

PLoS Biology ◽  
2014 ◽  
Vol 12 (5) ◽  
pp. e1001868 ◽  
Author(s):  
Jean-Michel Ubeda ◽  
Frédéric Raymond ◽  
Angana Mukherjee ◽  
Marie Plourde ◽  
Hélène Gingras ◽  
...  
Keyword(s):  
Dna Amplification ◽  
Dna Repeats ◽  
Genome Wide ◽  
Parasite Leishmania

scholarly journals PRAP: an ab initio software package for automated genome-wide analysis of DNA repeats for prokaryotes

2013 ◽  
Vol 29 (21) ◽  
pp. 2683-2689 ◽  
Author(s):  
Gwo-Liang Chen ◽  
Yun-Juan Chang ◽  
Chun-Hway Hsueh
Keyword(s):  
Ab Initio ◽  
Software Package ◽  
Dna Repeats ◽  
Genome Wide Analysis ◽  
Genome Wide

Genome-wide detection of tandem DNA repeats that are expanded in autism

Nature ◽  
2020 ◽  
Vol 586 (7827) ◽  
pp. 80-86 ◽  
Author(s):  
Brett Trost ◽  
Worrawat Engchuan ◽  
Charlotte M. Nguyen ◽  
Bhooma Thiruvahindrapuram ◽  
Egor Dolzhenko ◽  
...  
Keyword(s):  
Dna Repeats ◽  
Genome Wide

Genome-wide analysis of long, exact DNA repeats in rhizobia

2013 ◽  
Vol 35 (4) ◽  
pp. 441-449 ◽  
Author(s):  
Julie E. Hernández-Salmerón ◽  
Eduardo Valencia-Cantero ◽  
Gustavo Santoyo
Keyword(s):  
Dna Repeats ◽  
Genome Wide Analysis ◽  
Genome Wide

scholarly journals Expansion of LINEs and species-specific DNA repeats drives genome expansion in Asian Gypsy Moths

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Francois Olivier Hebert ◽  
Luca Freschi ◽  
Gwylim Blackburn ◽  
Catherine Béliveau ◽  
Ken Dewar ◽  
...  
Keyword(s):  
Molecular Mechanisms ◽  
Phenotypic Traits ◽  
Dna Repeats ◽  
Genome Sequences ◽  
Genomic Signatures ◽  
Metabolic Functions ◽  
Genome Wide ◽  
Gypsy Moths ◽  
Asian Gypsy Moth ◽  
Species Specific

Abstract Two subspecies of Asian gypsy moth (AGM), Lymantria dispar asiatica and L. dispar japonica, pose a serious alien invasive threat to North American forests. Despite decades of research on the ecology and biology of this pest, limited AGM-specific genomic resources are currently available. Here, we report on the genome sequences and functional content of these AGM subspecies. The genomes of L.d. asiatica and L.d. japonica are the largest lepidopteran genomes sequenced to date, totaling 921 and 999 megabases, respectively. Large genome size in these subspecies is driven by the accumulation of specific classes of repeats. Genome-wide metabolic pathway reconstructions suggest strong genomic signatures of energy-related pathways in both subspecies, dominated by metabolic functions related to thermogenesis. The genome sequences reported here will provide tools for probing the molecular mechanisms underlying phenotypic traits that are thought to enhance AGM invasiveness.

scholarly journals Comparative analysis of DNA repeats and identification of a Fesreba centromeric element in fescues and ryegrasses

2020 ◽  
Author(s):  
Jana Zwyrtková ◽  
Alžběta Němečková ◽  
Jana Čížková ◽  
Kateřina Holušová ◽  
Veronika Kapustová ◽  
...  
Keyword(s):  
Comparative Analysis ◽  
Dna Sequences ◽  
Sequence Data ◽  
Grass Species ◽  
Striking Difference ◽  
Dna Repeats ◽  
Copy Numbers ◽  
Genome Wide ◽  
Speed Up

Abstract Background Cultivated grasses are an important source of food for domestic animals worldwide. Better knowledge of their genomes can speed up development of cultivars with better quality and resistance to biotic and abiotic stresses. The most widely grown grasses are tetraploid ryegrass ( Lolium ) species and diploid and hexaploid fescues ( Festuca ) species. In this work we characterized repetitive DNA sequences and their contribution to genome size in seven fescue and ryegrass species. Results Partial genome sequences were produced by Illumina technology and used for genome-wide comparative analyses using RepeatExplorer pipeline. Retrotransposons were found to be the most abundant repeat types in all seven grass species. Athila element of Ty3/gypsy family showed most striking difference in copy numbers in nuclear genomes between fescues and ryegrasses. The sequence data enabled the assembly of an LTR element Fesreba, which is highly enriched in centromeric and (peri)centromeric regions in all species. A combination of FISH with a probe specific to Fesreba element and immunostaining with CENH3 antibody showed their colocalization and indicated a possible role of Fesreba in centromere function. Conclusions Comparative analysis of repeatome in a set of fescues and ryegrasses provided new insights into their genome organization and divergence, including the assembly of LTR element Fesreba. The element was abundant in centromeric regions of the fescues and ryegrasses and may have a role in function of their centromeres.

scholarly journals Comparative analysis of DNA repeats and identification of novel Fesreba centromeric element in fescues and ryegrasses

2020 ◽  
Author(s):  
Jana Zwyrtková ◽  
Alžběta Němečková ◽  
Jana Čížková ◽  
Kateřina Holušová ◽  
Veronika Kapustová ◽  
...  
Keyword(s):  
Dna Sequences ◽  
Sequence Data ◽  
Grass Species ◽  
Dna Repeats ◽  
Biotic And Abiotic Stresses ◽  
Centromere Function ◽  
Genome Wide ◽  
Speed Up ◽  
Partial Genome

Abstract Background Cultivated grasses are an important source of food for domestic animals worldwide. Better knowledge of their genomes can speed up the development of new cultivars with better quality and resistance to biotic and abiotic stresses. The most widely grown grasses are tetraploid ryegrass species ( Lolium spp.) and diploid and hexaploid fescue species ( Festuca spp.). In this work we characterized repetitive DNA sequences and their contribution to genome size in five fescue and two ryegrass species, as well as one fescue and two ryegrass cultivars. Results Partial genome sequences produced by Illumina technology were used for genome-wide comparative analyses using RepeatExplorer pipeline. Retrotransposons were found to be the most abundant repeat types in all seven grass species. Athila element of Ty3/gypsy family showed the most striking differences in copy number between fescues and ryegrasses. The sequence data enabled the assembly of an LTR element Fesreba, which is highly enriched in centromeric and (peri)centromeric regions in all species. A combination of FISH with a probe specific to Fesreba element and immunostaining with CENH3 antibody showed their colocalization and indicated a possible role of Fesreba in centromere function. Conclusions Comparative repeatome analysis in a set of fescues and ryegrasses provided new insights into their genome organization and divergence, including the assembly of LTR element Fesreba. A new LTR element Fesreba was identified and found abundant in centromeric regions of the fescues and ryegrasses. It may have a role in the function of their centromeres.

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