High Sensitivity Profiling of Chromatin Structure by MNase-SSP.

Cell Reports
Vijay RamaniJay Shendure

Abstract

A complete view of eukaryotic gene regulation requires that we accurately delineate how transcription factors (TFs) and nucleosomes are arranged along linear DNA in a sensitive, unbiased manner. Here we introduce MNase-SSP, a single-stranded sequencing library preparation method for nuclease-digested chromatin that enables simultaneous mapping of TF and nucleosome positions. As a proof of concept, we apply MNase-SSP toward the genome-wide, high-resolution mapping of nucleosome and TF occupancy in murine embryonic stem cells (mESCs). Compared with existing MNase-seq protocols, MNase-SSP markedly enriches for short DNA fragments, enabling detection of binding by subnucleosomal particles and TFs, in addition to nucleosomes. From these same data, we identify multiple, sequence-dependent binding modes of the architectural TF Ctcf and extend this analysis to the TF Nrsf/Rest. Looking forward, we anticipate that single stranded protocol (SSP) adaptations of any protein-DNA interaction mapping technique (e.g., ChIP-exo and CUT&RUN) will enhance the information content of the resulting data.

Citations

Oct 8, 2019·Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences·A E SantoroS M Laperriere
Mar 3, 2020·Yakugaku zasshi : Journal of the Pharmaceutical Society of Japan·Nozomu Mori
Sep 3, 2020·Open Biology·Alexis ZukowskiSrinivas Ramachandran
Nov 30, 2019·Chromosome Research : an International Journal on the Molecular, Supramolecular and Evolutionary Aspects of Chromosome Biology·David C Klein, Sarah J Hainer
Dec 3, 2020·ELife·Nour J AbdulhayVijay Ramani
Sep 18, 2020·Methods : a Companion to Methods in Enzymology·Itika Arora, Trygve O Tollefsbol
Aug 13, 2021·PLoS Genetics·Savannah D SavadelHank W Bass

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Methods Mentioned

BETA
cleavage sequencing
MNase-seq
immunoprecipitation
Illumina sequencing
ChIP-exo
ChIP-seq
ChIP
atomic force microscopy
footprinting
PCR

Software Mentioned

ggplot2
bowtie2
PySAM
PySAM API
ChIP
learn
MEME
R
scikit
Python script

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