Fig 1.
As pervasive transcription is a major factor leading to reads mapping to L1 instances, TeXP functions as an approach to decouple pervasive transcription from autonomous transcription.
(A) The number of reads mapped to LINE-1 subfamilies is proportional to the number of bases annotated as the subfamily for most RNA sequencing experiments. Point colors represent the subfamily average identity to LINE-1 consensus. (B) Healthy human tissues show varied distributions of the genomic-transcriptomic correlation. (C) Pipeline chart describes the TeXP approach.
Fig 2.
Quantification and validation of L1Hs autonomous transcription in human cell lines.
(A) The proportion of reads emanating from pervasive transcription and L1P1, L1PA2, L1PA3, L1PA4, and L1Hs subfamilies in MCF-7 RNA sequencing experiments are shown from the different cell compartments and transcript fractions prior to (left) and after (right) TeXP processing. (B) The absolute number of reads emanating from pervasive transcription and LINE-1 subfamilies are shown across the distinct cell and transcript fractions of the human-derived cell lines GM12878, K-562, and MCF7. (C-D) The quantification of autonomous and pervasive transcripts of L1Hs in the cell lines is shown using ddPCR. (C) The ratio of L1Hs 5’ and 3’ transcripts shows the enrichment of the 3’ end of L1Hs for all cell lines. (D) The absolute quantification of autonomous and pervasive transcripts reveals higher expression of pervasive compared to autonomous transcripts in all cell lines except MCF-7. All data were run in duplicate. All errors bars are mean ± SEM. These data represent two independent experiments. (E) L1Hs autonomous transcription landscape of human healthy primary tissues. Each point is a RNA sequencing experiment, separated by tissue of origin.