Association analysis of repetitive elements and R-loop formation across species

2020 ◽  
Author(s):  
Sree Rama Chaitanya Sridhara
Keyword(s):  
Association Analysis ◽  
Repetitive Elements ◽  
Loop Formation

scholarly journals Association analysis of repetitive elements and R-loop formation across species

2020 ◽  
Author(s):  
Chao Zeng ◽  
Masahiro Onoguchi ◽  
Michiaki Hamada
Keyword(s):  
Fruit Fly ◽  
Low Complexity ◽  
Repetitive Elements ◽  
S2 Cells ◽  
Loop Formation ◽  
Long Terminal Repeats ◽  
Long Interspersed Nuclear Elements ◽  
Regulatory Effects ◽  
Species Specific ◽  
Simple Repeats

ABSTRACTGenomes are known to have a large number of repetitive elements. Emerging evidence suggests that these non-coding elements may play an important regulatory role. However, few studies have investigated the effect of repetitive elements on R-loop formation. In this study, we found different repetitive elements related to R-loop formation in various species. By controlling length and genomic distributions, we observed that satellites, long interspersed nuclear elements (LINEs), and DNAs were each specifically enriched for R-loops in humans, fruit flies, and Arabidopsis thaliana, respectively. R-loops also tended to arise in regions of low-complexity or simple repeats across species. We also found that the repetitive elements associated with R-loop formation differ according to developmental stage. For instance, LINEs and long terminal repeats (LTRs) are more likely to contain R-loops in embryos (fruit fly) and then turn out to be low-complexity and simple repeats in post-developmental S2 cells. Our results indicate that repetitive elements may have species-specific or development-specific regulatory effects on R-loop formation. This work advances our understanding of repetitive elements and R-loop biology.

scholarly journals Sequence and Structure Characteristics of 22 Deletion Breakpoints in Intron 44 of the DMD Gene Based on Long-Read Sequencing

2021 ◽  
Vol 12 ◽  
Author(s):  
Chang Geng ◽  
Yuanren Tong ◽  
Siwen Zhang ◽  
Chao Ling ◽  
Xin Wu ◽  
...  
Keyword(s):  
Becker Muscular Dystrophy ◽  
Repetitive Elements ◽  
Loop Formation ◽  
End Joining ◽  
Origin Firing ◽  
Large Deletions ◽  
Long Read ◽  
Non Homologous End Joining ◽  
Dmd Gene ◽  
Palindromic Sequences

Purpose: Exon deletions make up to 80% of mutations in the DMD gene, which cause Duchenne and Becker muscular dystrophy. Exon 45-55 regions were reported as deletion hotspots and intron 44 harbored more than 25% of deletion start points. We aimed to investigate the fine structures of breakpoints in intron 44 to find potential mechanisms of large deletions in intron 44.Methods: Twenty-two dystrophinopathy patients whose deletion started in intron 44 were sequenced using long-read sequencing of a DMD gene capture panel. Sequence homology, palindromic sequences, and polypyrimidine sequences were searched at the breakpoint junctions. RepeatMasker was used to analyze repetitive elements and Mfold was applied to predict secondary DNA structure.Results: With a designed DMD capture panel, 22 samples achieved 2.25 gigabases and 1.28 million reads on average. Average depth was 308× and 99.98% bases were covered at least 1×. The deletion breakpoints in intron 44 were scattered and no breakpoints clustered in any region less than 500 bp. A total of 72.7% of breakpoints located in distal 100 kb of intron 44 and more repetitive elements were found in this region. Microhomologies of 0–1 bp were found in 36.4% (8/22) of patients, which corresponded with non-homologous end-joining. Microhomologies of 2–20 bp were found in 59.1% (13/22) of patients, which corresponded with microhomology-mediated end-joining. Moreover, a 7 bp insertion was found in one patient, which might be evidence of aberrant replication origin firing. Palindromic sequences, polypyrimidine sequences, and small hairpin loops were found near several breakpoint junctions. No evidence of large hairpin loop formation in deletion root sequences was observed.Conclusion: This study was the first to explore possible mechanisms underlying exon deletions starting from intron 44 of the DMD gene based on long-read sequencing. Diverse mechanisms might be associated with deletions in the DMD gene.

scholarly journals Association analysis of repetitive elements and R-loop formation across species

Mobile DNA ◽  
2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Chao Zeng ◽  
Masahiro Onoguchi ◽  
Michiaki Hamada
Keyword(s):  
Fruit Fly ◽  
Low Complexity ◽  
Wide Distribution ◽  
Long Terminal Repeat Retrotransposons ◽  
Repetitive Elements ◽  
Loop Formation ◽  
Genome Wide ◽  
Regulatory Effects ◽  
Species Specific ◽  
Simple Repeats

Abstract Background Although recent studies have revealed the genome-wide distribution of R-loops, our understanding of R-loop formation is still limited. Genomes are known to have a large number of repetitive elements. Emerging evidence suggests that these sequences may play an important regulatory role. However, few studies have investigated the effect of repetitive elements on R-loop formation. Results We found different repetitive elements related to R-loop formation in various species. By controlling length and genomic distributions, we observed that satellite, long interspersed nuclear elements (LINEs), and DNA transposons were each specifically enriched for R-loops in humans, fruit flies, and Arabidopsis thaliana, respectively. R-loops also tended to arise in regions of low-complexity or simple repeats across species. We also found that the repetitive elements associated with R-loop formation differ according to developmental stage. For instance, LINEs and long terminal repeat retrotransposons (LTRs) are more likely to contain R-loops in embryos (fruit fly) and then turn out to be low-complexity and simple repeats in post-developmental S2 cells. Conclusions Our results indicate that repetitive elements may have species-specific or development-specific regulatory effects on R-loop formation. This work advances our understanding of repetitive elements and R-loop biology.

Point Defect Absorption and Dislocation Loop Formation at Grain Boundaries in Hvem-Irradiated Zr and Its Alloys:1. Influence of Solute Addition

1985 ◽  
Vol 43 ◽  
pp. 350-351
Author(s):  
R.A. Herring ◽  
M. Griffiths ◽  
M.H Loretto ◽  
R.E. Smallman
Keyword(s):  
Grain Boundary ◽  
Grain Boundaries ◽  
Point Defect ◽  
Reactor Core ◽  
Solute Concentration ◽  
Nuclear Industry ◽  
Dislocation Loops ◽  
Loop Formation ◽  
Component Material ◽  
Impurity Interaction

Because Zr is used in the nuclear industry to sheath fuel and as structural component material within the reactor core, it is important to understand Zr's point defect properties. In the present work point defect-impurity interaction has been assessed by measuring the influence of grain boundaries on the width of the zone denuded of dislocation loops in a series of irradiated Zr alloys. Electropolished Zr and its alloys have been irradiated using an AEI EM7 HVEM at 1 MeV, ∼675 K and ∼10-6 torr vacuum pressure. During some HVEM irradiations it has been seen that there is a difference in the loop nucleation and growth behaviour adjacent to the grain boundary as compared with the mid-grain region. The width of the region influenced by the presence of the grain boundary should be a function of the irradiation temperature, dose rate, solute concentration and crystallographic orientation.

ROPO Effect in Gender- Generational Characteristics

2020 ◽  
Vol 11 (1) ◽  
pp. 43-43
Author(s):  
Radovan Bačík ◽  
Mária Oleárová ◽  
Martin Rigelský
Keyword(s):  
Association Analysis ◽  
Search Engines ◽  
Product Information ◽  
Customer Behavior ◽  
Internet Research ◽  
The Internet ◽  
Significant Progress ◽  
Customer Reviews ◽  
Online Purchase ◽  
Brick And Mortar

The development of the Internet and the current technologies have contributed to a significant progress in the consumer shopping process. Today, shopping decisions are more intuitive and much easier to make. E-shops, search engines, customer reviews and other similar tools reduce costs of searching for products or product information, thus boosting the habit of searching for information on the Internet - "Research Shopper Phenomenon" (Verhoef et al. 2007). According to Verhoef et al. (2015), this phenomenon leads to a phenomenon where consumers search for product information using one channel (Internet) and then make a purchase through another channel (brick-and-mortar shop). Heinrich and Thalmair (2013) refer to this effect as the "research online, purchase offline" or "ROPO" effect for short. This phenomenon can also be observed in reverse. Keywords: customer behavior, research online – purchase offline, association analysis

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