Species-specific EcoRI repetitive elements of at least 16 kb in length are present in Lupinus luteus

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.

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Species-specific amplification of tRNA-derived short interspersed repetitive elements (SINEs) by retroposition: a process of parasitization of entire genomes during the evolution of salmonids.

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.91.21.10153 ◽

1994 ◽

Vol 91 (21) ◽

pp. 10153-10157 ◽

Cited By ~ 30

Author(s):

N. Takasaki ◽

S. Murata ◽

M. Saitoh ◽

T. Kobayashi ◽

L. Park ◽

...

Keyword(s):

Repetitive Elements ◽

Specific Amplification ◽

Species Specific

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

Mobile DNA ◽

10.1186/s13100-021-00231-5 ◽

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.

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Activation of phenylpropanoid pathway in legume plants exposed to heavy metals. Part I. Effects of cadmium and lead on phenylalanine ammonia-lyase gene expression, enzyme activity and lignin content.

Acta Biochimica Polonica ◽

10.18388/abp.2011_2267 ◽

2011 ◽

Vol 58 (2) ◽

Cited By ~ 28

Author(s):

Sylwia Pawlak-Sprada ◽

Magdalena Arasimowicz-Jelonek ◽

Magdalena Podgórska ◽

Joanna Deckert

Keyword(s):

Heavy Metals ◽

Phenylalanine Ammonia Lyase ◽

Lignin Content ◽

Mrna Level ◽

Transcript Level ◽

Phenylpropanoid Pathway ◽

Lupinus Luteus ◽

Pal Activity ◽

Species Specific ◽

Cadmium And Lead

Species-specific changes in expression of phenylalanine ammonia-lyase (PAL) and lignin content were detected in roots of soybean (Glycine max L.) and lupine (Lupinus luteus L.) seedlings treated with different concentrations of cadmium (Cd(2+), 0-25 mg/l) or lead (Pb(2+), 0-350 mg/l). The stimulatory effect of both metals was observed in mRNA coding for PAL in soybean. In the case of lupine, changes of PAL mRNA level were dependent on the metal used: Cd(2+) caused a decrease, whereas Pb(2+) an increase of PAL transcript level. The activity of PAL was enhanced in both plant species at higher metal concentrations (15-25 mg/l of Cd(2+) or 150-350 mg/l of Pb(2+)); however it was not directly correlated with PAL mRNA. This suggests a transcriptional and posttranscriptional control of PAL expression under heavy metals stress. In soybean, Cd(2+) or Pb(2+) treatment increased lignin content, while in lupine the effect was opposite. The decreased lignin accumulation in lupine roots in response to heavy metals, despite an increased PAL activity, suggests that the activated phenylpropanoid pathway was involved in the synthesis of secondary metabolites other than lignin.

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DeepGRP: engineering a software tool for predicting genomic repetitive elements using Recurrent Neural Networks with attention

Algorithms for Molecular Biology ◽

10.1186/s13015-021-00199-0 ◽

2021 ◽

Vol 16 (1) ◽

Author(s):

Fabian Hausmann ◽

Stefan Kurtz

Keyword(s):

Machine Translation ◽

De Novo ◽

Repetitive Sequences ◽

Software Tool ◽

Repetitive Elements ◽

Training Data ◽

Implementation Framework ◽

Neural Machine Translation ◽

Species Specific

Abstract Background Repetitive elements contribute a large part of eukaryotic genomes. For example, about 40 to 50% of human, mouse and rat genomes are repetitive. So identifying and classifying repeats is an important step in genome annotation. This annotation step is traditionally performed using alignment based methods, either in a de novo approach or by aligning the genome sequence to a species specific set of repetitive sequences. Recently, Li (Bioinformatics 35:4408–4410, 2019) developed a novel software tool to annotate repetitive sequences using a recurrent neural network trained on sample annotations of repetitive elements. Results We have developed the methods of further and engineered a new software tool . This combines the basic concepts of Li (Bioinformatics 35:4408–4410, 2019) with current techniques developed for neural machine translation, the attention mechanism, for the task of nucleotide-level annotation of repetitive elements. An evaluation on the human genome shows a 20% improvement of the Matthews correlation coefficient for the predictions delivered by , when compared to . predicts two additional classes of repeats (compared to ) and is able to transfer repeat annotations, using RepeatMasker-based training data to a different species (mouse). Additionally, we could show that predicts repeats annotated in the Dfam database, but not annotated by RepeatMasker. is highly scalable due to its implementation in the TensorFlow framework. For example, the GPU-accelerated version of is approx. 1.8 times faster than , approx. 8.6 times faster than RepeatMasker and over 100 times faster than HMMER searching for models of the Dfam database. Conclusions By incorporating methods from neural machine translation, achieves a consistent improvement of the quality of the predictions compared to . Improved running times are obtained by employing TensorFlow as implementation framework and the use of GPUs. By incorporating two additional classes of repeats, provides more complete annotations, which were evaluated against three state-of-the-art tools for repeat annotation.

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Electron Microscopy in the Study of Natural Phytoplankton Assemblages

Proceedings, annual meeting, Electron Microscopy Society of America ◽

10.1017/s0424820100119831 ◽

1985 ◽

Vol 43 ◽

pp. 620-623

Author(s):

Linda Sicko-Goad

Keyword(s):

Electron Microscopy ◽

Aquatic Environment ◽

Size Range ◽

Physical Parameters ◽

Specific Information ◽

Phytoplankton Assemblages ◽

Phytoplankton Productivity ◽

Ecosystem Effects ◽

Time Of Year ◽

Species Specific

Although the use of electron microscopy and its varied methodologies is not usually associated with ecological studies, the types of species specific information that can be generated by these techniques are often quite useful in predicting long-term ecosystem effects. The utility of these techniques is especially apparent when one considers both the size range of particles found in the aquatic environment and the complexity of the phytoplankton assemblages.The size range and character of organisms found in the aquatic environment are dependent upon a variety of physical parameters that include sampling depth, location, and time of year. In the winter months, all the Laurentian Great Lakes are uniformly mixed and homothermous in the range of 1.1 to 1.7°C. During this time phytoplankton productivity is quite low.

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