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 be...
| Main Authors: | , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
MDPI AG
2021-12-01
|
| Series: | International Journal of Molecular Sciences |
| Subjects: | |
| Online Access: | https://www.mdpi.com/1422-0067/22/24/13623 |
| _version_ | 1797503692891488256 |
|---|---|
| author | Braulio Valdebenito-Maturana Cristina Guatimosim Mónica Alejandra Carrasco Juan Carlos Tapia |
| author_facet | Braulio Valdebenito-Maturana Cristina Guatimosim Mónica Alejandra Carrasco Juan Carlos Tapia |
| author_sort | Braulio Valdebenito-Maturana |
| collection | DOAJ |
| description | 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. |
| first_indexed | 2024-03-10T03:54:22Z |
| format | Article |
| id | doaj.art-23b7f521f19740e98544034de6674eb2 |
| institution | Directory Open Access Journal |
| issn | 1661-6596 1422-0067 |
| language | English |
| last_indexed | 2024-03-10T03:54:22Z |
| publishDate | 2021-12-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | International Journal of Molecular Sciences |
| spelling | doaj.art-23b7f521f19740e98544034de6674eb22023-11-23T08:49:08ZengMDPI AGInternational Journal of Molecular Sciences1661-65961422-00672021-12-0122241362310.3390/ijms222413623Spatially Resolved Expression of Transposable Elements in Disease and Somatic Tissue with SpatialTEBraulio Valdebenito-Maturana0Cristina Guatimosim1Mónica Alejandra Carrasco2Juan Carlos Tapia3Núcleo Científico Multidisciplinario, School of Medicine, Universidad de Talca, Campus Talca, Talca 3460000, ChileDepartamento de Morfologia, ICB, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, BrazilSchool of Medicine, Universidad de Talca, Campus Talca, Talca 3460000, ChileSchool of Medicine, Universidad de Talca, Campus Talca, Talca 3460000, ChileSpatial 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.https://www.mdpi.com/1422-0067/22/24/13623spatial transcriptomicstransposable elementsgene regulationspinal cord & brainkidneyamyotrophic lateral sclerosis disease |
| spellingShingle | Braulio Valdebenito-Maturana Cristina Guatimosim Mónica Alejandra Carrasco Juan Carlos Tapia Spatially Resolved Expression of Transposable Elements in Disease and Somatic Tissue with SpatialTE International Journal of Molecular Sciences spatial transcriptomics transposable elements gene regulation spinal cord & brain kidney amyotrophic lateral sclerosis disease |
| title | Spatially Resolved Expression of Transposable Elements in Disease and Somatic Tissue with SpatialTE |
| title_full | Spatially Resolved Expression of Transposable Elements in Disease and Somatic Tissue with SpatialTE |
| title_fullStr | Spatially Resolved Expression of Transposable Elements in Disease and Somatic Tissue with SpatialTE |
| title_full_unstemmed | Spatially Resolved Expression of Transposable Elements in Disease and Somatic Tissue with SpatialTE |
| title_short | Spatially Resolved Expression of Transposable Elements in Disease and Somatic Tissue with SpatialTE |
| title_sort | spatially resolved expression of transposable elements in disease and somatic tissue with spatialte |
| topic | spatial transcriptomics transposable elements gene regulation spinal cord & brain kidney amyotrophic lateral sclerosis disease |
| url | https://www.mdpi.com/1422-0067/22/24/13623 |
| work_keys_str_mv | AT brauliovaldebenitomaturana spatiallyresolvedexpressionoftransposableelementsindiseaseandsomatictissuewithspatialte AT cristinaguatimosim spatiallyresolvedexpressionoftransposableelementsindiseaseandsomatictissuewithspatialte AT monicaalejandracarrasco spatiallyresolvedexpressionoftransposableelementsindiseaseandsomatictissuewithspatialte AT juancarlostapia spatiallyresolvedexpressionoftransposableelementsindiseaseandsomatictissuewithspatialte |