The nanoCUT&RUN technique visualizes telomeric chromatin in Drosophila

<p>Advances in genomic technology lead to a more focused pattern for the distribution of chromosomal proteins and a better understanding of their functions. The recent development of the CUT&amp;RUN technique marks one of the important such advances. Here we develop a modified CUT&amp;RUN technique that we termed nanoCUT&amp;RUN, in which a high affinity nanobody to GFP is used to bring micrococcal nuclease to the binding sites of GFP-tagged chromatin proteins. Subsequent activation of the nuclease cleaves the chromatin, and sequencing of released DNA identifies binding sites. We show that nanoCUT&amp;RUN efficiently produces high quality data for the TRL transcription factor in Drosophila embryos, and distinguishes binding sites specific between two TRL isoforms. We further show that nanoCUT&amp;RUN dissects the distributions of the HipHop and HOAP telomere capping proteins, and uncovers unexpected binding of telomeric proteins at centromeres. nanoCUT&amp;RUN can be readily applied to any system in which a chromatin protein of interest, or its isoforms, carries the GFP tag. </p>