TeXP

TeXP quantifies autonomous transcription of Long Interspersed Nuclear Element 1 (LINE-1) subfamilies from short-read RNA-seq data to distinguish pervasive versus autonomous transcription signals.

Key Features:

• Deconvolution of transcription signals: Constructs mappability signatures specific to LINE-1 subfamilies to deconvolve short-read RNA-seq reads and separate pervasive transcription from autonomous LINE-1 activity.
• Quantitative analysis across samples: Provides quantitative measures of LINE-1 activity across cell lines, cellular compartments, and healthy tissues and reports that the majority of transcriptome reads overlapping LINE-1 derive from pervasive transcription, with autonomous transcription levels independently validated by digital droplet PCR (ddPCR).
• Assessment in healthy somatic cells: Accounts for pervasive transcription to enable accurate estimation of autonomous LINE-1 activity in healthy somatic cells, revealing activity previously underestimated outside neuroprogenitor cells.
• Correlation with biological processes: Reports correlations between LINE-1 autonomous activity and cell turnover rates, including lower activity in low-turnover tissues such as the adult central nervous system.

Scientific Applications:

• Transposable element activity quantification: Accurate quantification of autonomous LINE-1 transcription to study genetic variation driven by transposable elements.
• Genomic stability and epigenetic regulation: Assessment of LINE-1 autonomous activity to investigate impacts on genomic stability and epigenetic regulation in human tissues.
• Evolutionary and human genetics studies: Evaluation of the evolutionary impact of LINE-1 and its role in human genetics through subfamily-resolved transcription measurements.

Methodology:

Builds mappability signatures from LINE-1 subfamilies and uses those signatures to deconvolve short-read RNA-seq reads into pervasive and autonomous transcription components.