The spatial and cellular portrait of transposable element expression during gastric cancer.

Gastric Cancer (GC) is a lethal malignancy, with urgent need for the discovery of novel biomarkers for its early detection. I previously showed that Transposable Elements (TEs) become activated in early GC (EGC), suggesting a role in gene expression. Here, I follow-up on that evidence using single-cell data from gastritis to EGC, and show that TEs are expressed and follow the disease progression, with 2,430 of them being cell populations markers.

Activation of Transposable Elements in Human Skeletal Muscle Fibers upon Statin Treatment.

High cholesterol levels have been linked to a high risk of cardiovascular diseases, and preventative pharmacological care to lower cholesterol levels is critically important. Statins, which are hydroxymethylglutaryl-coenzyme A (HMG-CoA) reductase inhibitors, are drugs used to reduce the endogenous cholesterol synthesis, thus minimizing its pathophysiological effects. Despite the proven benefits, statins therapy is known to cause a number of skeletal muscle disorders, including myalgia, myopathy and myositis.

Dysregulated Expression of Transposable Elements in TDP-43 Human Motor Neurons That Recapitulate Amyotrophic Lateral Sclerosis In Vitro.

Amyotrophic lateral sclerosis (ALS) is a disease that progressively annihilates spinal cord motor neurons, causing severe motor decline and death. The disease is divided into familial and sporadic ALS. Mutations in the TAR DNA binding protein 43 (TDP-43) have been involved in the pathological emergence and progression of ALS, although the molecular mechanisms eliciting the disease are unknown.

SoloTE for improved analysis of transposable elements in single-cell RNA-Seq data using locus-specific expression.

Transposable Elements (TEs) contribute to the repetitive fraction in almost every eukaryotic genome known to date, and their transcriptional activation can influence the expression of neighboring genes in healthy and disease states. Single cell RNA-Seq (scRNA-Seq) is a technical advance that allows the study of gene expression on a cell-by-cell basis. Although a current computational approach is available for the single cell analysis of TE expression, it omits their genomic location.

Spatially Resolved Expression of Transposable Elements in Disease and Somatic Tissue with SpatialTE.

Spatial transcriptomics (ST) is transforming the way we can study gene expression and its regulation through position-specific resolution within tissues. However, as in bulk RNA-Seq, transposable elements (TEs) are not being studied due to their highly repetitive nature. In recent years, TEs have been recognized as important regulators of gene expression, and thus, TE expression analysis in a spatially resolved manner could further help to understand their role in gene regulation within tissues.

Differential regulation of transposable elements (TEs) during the murine submandibular gland development.

The submandibular gland (SG) is a relatively simple organ formed by three cell types: acinar, myoepithelial, and an intricate network of duct-forming epithelial cells, that together fulfills several physiological functions from assisting food digestion to acting as an immune barrier against pathogens. Successful SG organogenesis is the product of highly controlled and orchestrated genetic and transcriptional programs. Mounting evidence links Transposable Elements (TEs), originally thought to be selfish genetic elements, to different aspects of gene regulation in mammalian development and disease.

Locus-specific analysis of Transposable Elements during the progression of ALS in the SOD1G93A mouse model.

Transposable Elements (TEs) are ubiquitous genetic elements with the ability to move within a genome. TEs contribute to a large fraction of the repetitive elements of a genome, and because of their nature, they are not routinely analyzed in RNA-Seq gene expression studies. Amyotrophic Lateral Sclerosis (ALS) is a lethal neurodegenerative disease, and a well-accepted model for its study is the mouse harboring the human SOD1G93A mutant.

GSER (a Genome Size Estimator using R): a pipeline for quality assessment of sequenced genome libraries through genome size estimation.

The first step in any genome research after obtaining the read data is to perform a due quality control of the sequenced reads. In a genome assembly project, the second step is to estimate two important features, the genome size and 'best -mer', to start the assembly tests with different assembly software and its parameters. However, the quality control of the sequenced genome libraries as a whole, instead of focusing on the reads only, is frequently overlooked and realized to be important only when the assembly tests did not render the expected results.

Plant HKT Channels: An Updated View on Structure, Function and Gene Regulation.

HKT channels are a plant protein family involved in sodium (Na) and potassium (K) uptake and Na-K homeostasis. Some HKTs underlie salt tolerance responses in plants, while others provide a mechanism to cope with short-term K shortage by allowing increased Na uptake under K starvation conditions. HKT channels present a functionally versatile family divided into two classes, mainly based on a sequence polymorphism found in the sequences underlying the selectivity filter of the first pore loop.

TEcandidates: prediction of genomic origin of expressed transposable elements using RNA-seq data.

Motivation: In recent years, Transposable Elements (TEs) have been related to gene regulation. However, estimating the origin of expression of TEs through RNA-seq is complicated by multi-mapping reads coming from their repetitive sequences. Current approaches that address multi-mapping reads are focused in expression quantification and not in finding the origin of expression.

Mutantelec: An In Silico mutation simulation platform for comparative electrostatic potential profiling of proteins.

The electrostatic potential plays a key role in many biological processes like determining the affinity of a ligand to a given protein target, and they are responsible for the catalytic activity of many enzymes. Understanding the effect that amino acid mutations will have on the electrostatic potential of a protein, will allow a thorough understanding of which residues are the most important in a protein. MutantElec, is a friendly web application for in silico generation of site-directed mutagenesis of proteins and the comparison of electrostatic potential between the wild type protein and the mutant(s), based on the three-dimensional structure of the protein.