Extended Data Fig. 2: Mapping transcriptional start sites in L1 elements activated during cellular senescence. | Nature

Extended Data Fig. 2: Mapping transcriptional start sites in L1 elements activated during cellular senescence.

From: L1 drives IFN in senescent cells and promotes age-associated inflammation

Extended Data Fig. 2

5′ RACE was performed with primers C and D (Fig. 1a, Supplementary Table 1) on late senescent cells (16 weeks, point D in Extended Data Fig. 1a), the products were cloned, and individual clones were Sanger sequenced (Methods). a, A multiple sequence alignment of the 50 mappable clones against the L1HS consensus was generated with MAFFT software. The L1HS consensus is shown. Blue shading of the aligned clones shows their degree of identity with the consensus. Green vertical line marks the start (position 1) of the L1HS consensus. Red vertical lines mark short gaps (1–4 nucleotides) opened in the L1HS consensus by individual clones. The consensus of the 50 clones is shown at the bottom and was generated with Jalview. The initiation of L1 transcription is known to be imprecise, with most start sites occurring ±50 bp of the consensus start site, and a subset as far down as +180 bp68. b, Summary of the mapping data and classification of clones to families of L1 elements. The relative start sites were calculated relative to the L1HS consensus start site. RepEnrich software55 was used to assign the clones to L1 families.

Back to article page