Comparative genomics of muskmelon reveals a potential role for retrotransposons in the modification of gene expression

R Yano, T Ariizumi, S Nonaka, Y Kawazu… - Communications …, 2020 - nature.com
Melon exhibits substantial natural variation especially in fruit ripening physiology, including
both climacteric (ethylene-producing) and non-climacteric types. However, genomic …

Non-coding RNAs and transposable elements in plant genomes: emergence, regulatory mechanisms and roles in plant development and stress responses

J Hou, D Lu, AS Mason, B Li, M Xiao, S An, D Fu - Planta, 2019 - Springer
Main conclusion This review will provide evidence for the indispensable function of these
elements in regulating plant development and resistance to biotic and abiotic stresses, as …

Exaptation of transposable element coding sequences

Z Joly-Lopez, TE Bureau - Current opinion in genetics & development, 2018 - Elsevier
Transposable elements (TEs) are mobile genetic elements that were once perceived as
merely selfish, but are now recognized as potent agents of adaptation. One way TEs …

Epigenetic mechanisms of abiotic stress response and memory in plants

I Mozgova, P Mikulski, A Pecinka, S Farrona - Epigenetics in plants of …, 2019 - Springer
Being sessile organisms, plants are exposed to multiple stimuli without possibility for
escape. Therefore, plants have evolved to be able to adapt their developmental and …

Measuring performance metrics of machine learning algorithms for detecting and classifying transposable elements

S Orozco-Arias, JS Piña, R Tabares-Soto… - Processes, 2020 - mdpi.com
Because of the promising results obtained by machine learning (ML) approaches in several
fields, every day is more common, the utilization of ML to solve problems in bioinformatics. In …

Long-lasting defence priming by β-aminobutyric acid in tomato is marked by genome-wide changes in DNA methylation

M Catoni, R Alvarez-Venegas, D Worrall… - Frontiers in Plant …, 2022 - frontiersin.org
Exposure of plants to stress conditions or to certain chemical elicitors can establish a primed
state, whereby responses to future stress encounters are enhanced. Stress priming can be …

Nearby transposable elements impact plant stress gene regulatory networks: a meta-analysis in A. thaliana and S. lycopersicum

J Deneweth, Y Van de Peer, V Vermeirssen - BMC genomics, 2022 - Springer
Background Transposable elements (TE) make up a large portion of many plant genomes
and are playing innovative roles in genome evolution. Several TEs can contribute to gene …

The evolutionary volte-face of transposable elements: from harmful jumping genes to major drivers of genetic innovation

M Nicolau, N Picault, G Moissiard - Cells, 2021 - mdpi.com
Transposable elements (TEs) are self-replicating DNA elements that constitute major
fractions of eukaryote genomes. Their ability to transpose can modify the genome structure …

The CERV protein of Cer1, a C. elegans LTR retrotransposon, is required for nuclear export of viral genomic RNA and can form giant nuclear rods

B Sun, H Kim, CC Mello, JR Priess - PLoS Genetics, 2023 - journals.plos.org
Retroviruses and closely related LTR retrotransposons export full-length, unspliced genomic
RNA (gRNA) for packaging into virions and to serve as the mRNA encoding GAG and POL …

Emerging roles of chromatin in the maintenance of genome organization and function in plants

Z Vergara, C Gutierrez - Genome Biology, 2017 - Springer
Chromatin is not a uniform macromolecular entity; it contains different domains
characterized by complex signatures of DNA and histone modifications. Such domains are …