Fig. 1.

Escherichia coli type I-E CRISPR-Cas system spacer retrieval from K12 strain and a palaeo DNA sample. (a) A Logo of the E. coli type I-E CRISPR repeat is shown at the top. The arrows above and below the Logo indicate primers used in PCR amplification. A scheme showing expected products of PCR amplification from an E. coli type I-E CRISPR array using repeat-specific primers is presented below. Repeats are dark grey, and spacers are light grey. Expected amplification products are shown below as black lines with their sizes indicated. (b) The procedure outlined in (a) was applied to E. coli K12 strain containing two CRISPR arrays (CRISPR1 and CRISPR2, schematically shown at the bottom, with repeats indicated in grey, and spacers are in colour). Rightward horizontal arrows indicate promoters in the leader of each array. Leader-proximal spacers are coloured with lighter shades of blue, while leader-distant spacers are shown in progressively darker colours. The number of Illumina reads corresponding to each spacer is shown on the histograms above. (c, d) Results of E. coli type I-E CRISPR spacer amplification from K12 strain (c) and mammoth intestinal (‘Int’) and stomach (‘St’) content samples (d). Lanes marked as ‘−’ show results obtained with mock-purified DNA.