Fig. 1: Strand-specific repair of a double-strand break by cellular NHEJ.
From: Nonhomologous end-joining uses distinct mechanisms to repair each strand of a double strand break
a Linear substrates were introduced into cells. Substrate head and tail ends have mispairs and damage in the top (green) or bottom (orange) strand after alignment by a complex of NHEJ core factors (blue shaded inset; cartoon derived from structure in ref. 12), and can be repaired by two different paths that generate distinct products. b In NHEJ products (?) the top strand (green) was distinguished from the bottom strand (orange) by sequence differences in a mismatched region embedded in the substrate (strand ID), either i) during qPCR, using strand-specific probes with different fluorescent labels (Top strand, FAM+ probe; bottom, HEX + ) or ii) during analysis of sequences of NHEJ products, after ligation of a double stranded sequencing adapter that contained a unique molecular identifier (UMI) consisting of 10 random nucleotides (N10).
