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Genome-wide characterization of long terminal repeat retrotransposons provides insights into trait evolution of four cucurbit species
Cucurbits are a diverse plant family that includes economically important crops, such as cucumber, watermelon, melon, and pumpkin. Knowledge of the...
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Large-scale long terminal repeat insertions produced a significant set of novel transcripts in cotton
Genomic analysis has revealed that the 1,637-Mb Gossypium arboreum genome contains approximately 81% transposable elements (TEs), while only 57% of...
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Repeat DNA Sequences in Flax Genomes
Transposable elements (TE) are important components in plant genomes. They are abundant, not only in flax but also in a wide range of species,...
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High-fidelity (repeat) consensus sequences from short reads using combined read clustering and assembly
BackgroundDespite the many cheap and fast ways to generate genomic data, good and exact genome assembly is still a problem, with especially the...
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Hallucination of closed repeat proteins containing central pockets
In pseudocyclic proteins, such as TIM barrels, β barrels, and some helical transmembrane channels, a single subunit is repeated in a cyclic pattern,...
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Identification of high-copy number long terminal repeat retrotransposons and their expansion in Phalaenopsis orchids
BackgroundTransposable elements (TEs) are fragments of DNA that can insert into new chromosomal locations. They represent a great proportion of...
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SMCHD1 and LRIF1 converge at the FSHD-associated D4Z4 repeat and LRIF1 promoter yet display different modes of action
Facioscapulohumeral muscular dystrophy (FSHD) is caused by the epigenetic derepression of the 4q-linked D4Z4 macrosatellite repeat resulting in...
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SUMO protease FUG1, histone reader AL3 and chromodomain protein LHP1 are integral to repeat expansion-induced gene silencing in Arabidopsis thaliana
Epigenetic gene silencing induced by expanded repeats can cause diverse phenotypes ranging from severe growth defects in plants to genetic diseases...
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High-Throughput Profiling of Extrachromosomal Linear DNAs of Long Terminal Repeat Retrotransposons by ALE-seq
Extrachromosomal linear DNA (eclDNA) is the reverse-transcribed cDNA intermediate derived from long terminal repeat (LTR) transposable elements (TEs)...
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Measuring Repeat-Associated Non-AUG (RAN) Translation
Expansions of short nucleotide repeats account for more than 50 neurological or neuromuscular diseases. Many repeat expansion-containing RNAs can...
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Structural and biochemical investigations of a HEAT-repeat protein involved in the cytosolic iron-sulfur cluster assembly pathway
Iron-sulfur clusters are essential for life and defects in their biosynthesis lead to human diseases. The mechanism of cluster assembly and delivery...
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Telomere sequence variability in genotypes from natural plant populations: unusual block-organized double-monomer terminal telomeric arrays
BackgroundTelomeres are the nucleoprotein complexes that physically cap the ends of eukaryotic chromosomes. Most plants possess Arabidopsis -type...
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Design of functionalised circular tandem repeat proteins with longer repeat topologies and enhanced subunit contact surfaces
Circular tandem repeat proteins (‘cTRPs’) are de novo designed protein scaffolds (in this and prior studies, based on antiparallel two-helix bundles)...
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Genome wide annotation and characterization of young, intact long terminal repeat retrotransposons (In-LTR-RTs) of seven legume species
Availability of genome sequence of different legume species has provided an opportunity to characterize the abundance, distribution, and divergence...
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Identifying and correcting repeat-calling errors in nanopore sequencing of telomeres
Nanopore long-read sequencing is an emerging approach for studying genomes, including long repetitive elements like telomeres. Here, we report...
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Armadillo repeat-containing kinesin represents the versatile plus-end-directed transporter in Physcomitrella
Kinesin-1, also known as conventional kinesin, is widely used for microtubule plus-end-directed (anterograde) transport of various cargos in animal...
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Multi-method computational evaluation of the inhibitors against leucine-rich repeat kinase 2 G2019S mutant for Parkinson's disease
Leucine-rich repeat kinase 2 G2019S mutant (LRRK2 G2019S) is a potential target for Parkinson's disease therapy. In this work, the computational...
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Furin extracellularly cleaves secreted PTENα/β to generate C-terminal fragment with a tumor-suppressive role
PTENα and PTENβ (PTENα/β), two long translational variants of phosphatase and tensin homolog on chromosome 10 (PTEN), exert distinct roles from...
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TAR30, a homolog of the canonical plant TTTAGGG telomeric repeat, is enriched in the proximal chromosome regions of peanut (Arachis hypogaea L.)
Telomeres are the physical ends of eukaryotic linear chromosomes that play critical roles in cell division, chromosome maintenance, and genome...
