TY - JOUR T1 - Quantitative multiplexed imaging of chromatin ultrastructure with Decode-PAINT JF - bioRxiv DO - 10.1101/2022.08.01.502089 SP - 2022.08.01.502089 AU - Hiroshi M. Sasaki AU - Jocelyn Y. Kishi AU - Chao-ting Wu AU - Brian J. Beliveau AU - Peng Yin Y1 - 2022/01/01 UR - http://biorxiv.org/content/early/2022/08/03/2022.08.01.502089.abstract N2 - Super-resolution chromatin imaging techniques are emerging as powerful tools for spatial genomics. However, it remains challenging to visualize the genome on the order of tens of nanometers, a scale that can reveal rich structural detail about the nuclear organization. Here we introduce Decode-PAINT, a multiplexed in situ method, which leverages rapid diffraction-limited pre-decoding and DNA-PAINT (DNA points accumulation for imaging nanoscale topography). Decode-PAINT visualizes multiple discrete genomic regions at a resolution close to the nucleosome scale with a simple and easy-to-implement optical setup, reduces total imaging time by omitting multiple rounds of single-molecule recording, and enables the interrogation of the ultrastructure of the targets with <12 nm lateral and <20 nm axial resolution. We showcase the ability of our approach to perform multiplexed, high-resolution profiling of chromatin structure by performing targeted imaging of nine regions of active and inactive X chromosomes in individual cells. In short, Decode-PAINT accelerates in situ structural genomics.Competing Interest StatementP.Y. is a cofounder of Ultivue, Inc., NuProbe Global, and Torus Biosystems, Inc. P.Y. holds patents on DNA-PAINT and SABER and related technologies, and is a co-founder and director of Ultivue, Inc., NuProbe Global, Torus Biosystems, Inc., 3EO Health, Spear Bio Inc, and Digital Biology Inc. J.Y.K. and B.J.B. hold patents on SABER. ER -