Universal NicE-seq for high-resolution accessible chromatin profiling for formaldehyde-fixed and FFPE tissues

Hang Gyeong Chin,George Spracklin,Pengying Hao,Zhiyi Sun,Pierre-Olivier Estève,Udayakumar S Vishnu,Paloma Cejas,Sriharsa Pradhan,Henry W Long,Shuang-Yong Xu

doi:10.1186/s13148-020-00921-6

Abstract

Accessible chromatin plays a central role in gene expression and chromatin architecture. Current accessible chromatin approaches depend on limited digestion/cutting and pasting adaptors at the accessible DNA, thus requiring additional materials and time for optimization. Universal NicE-seq (UniNicE-seq) is an improved accessible chromatin profiling method that negates the optimization step and is suited to a variety of mammalian cells and tissues. Addition of 5-methyldeoxycytidine triphosphate during accessible chromatin labeling and an on-bead library making step substantially improved the signal to noise ratio while protecting the accessible regions from repeated nicking in cell lines, mouse T cells, mouse kidney, and human frozen tissue sections. We also demonstrate one tube UniNicE-seq for the FFPE tissue section for direct NGS library preparation without sonication and DNA purification steps. These refinements allowed reliable mapping of accessible chromatin for high-resolution genomic feature studies.

Highlights

The eukaryotic nuclear genome is packaged into chromatin, consisting primarily of DNA, proteins, and RNA, which is further condensed into larger folded chromosome structures during cell division
Universal NicE-seq protects labeled accessible chromatin against enzymatic degradation During the previously published NicE-seq labeling reaction, the nucleotide mixture contained Deoxynucleoside triphosphate (dNTP) supplemented with biotin-14-Deoxyadenosine triphosphate (dATP) and biotin-14-Deoxycytidine triphosphate (dCTP) [6]
To prevent repeated nicking at the same site, we substituted the dCTP in the labeling reaction with of 5-methyldeoxycytidine triphosphate (5mdCTP)

Summary

Introduction

The eukaryotic nuclear genome is packaged into chromatin, consisting primarily of DNA, proteins, and RNA, which is further condensed into larger folded chromosome structures during cell division. In the refinement to the previous NicE-seq protocol, nuclei are incubated with Nt.CviPII, which nicks human genomic DNA with sequence specificity CCD (D = A/G/T) followed by labeling reaction with 5-methyldeoxycytidine triphosphate (5-mdCTP) and biotin-14-dCTP in the dNTPs mixture to label all available deoxycytidine triphosphates at the nicking sites. This will render these sites in the newly labeled accessible chromatin DNA resistant to further nicking. 5mC-incorporated accessible chromatin remains resistant to further degradation eliminating time-consuming titration and would allow automation on a variety of biological samples

Methods

Results

Conclusion