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

Valdebenito-Maturana, Braulio; Guatimosim, Cristina; Carrasco, Mónica Alejandra; Tapia, Juan Carlos

Keywords: kidney, gene regulation, transposable elements, amyotrophic lateral sclerosis disease, spatial transcriptomics, spinal cord & brain


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. We present SpatialTE, a tool to analyze TE expression from ST datasets and show its application in somatic and diseased tissues. The results indicate that TEs have spatially regulated expression patterns and that their expression profiles are spatially altered in ALS disease, indicating that TEs might perform differential regulatory functions within tissue organs. We have made SpatialTE publicly available as open-source software under an MIT license.

Más información

Título de la Revista: INFORMATION
Volumen: 22
Número: 24
Editorial: MDPI
Fecha de publicación: 2021
Página de inicio: 13623
Página final: 13628
Idioma: English
Financiamiento/Sponsor: FONDECYTs 1200951, 1200250, 1160888, 1161014; FONDEQUIP-ANID EQM200122


Notas: ISI