Single-Molecule Mapping of Chromatin Accessibility Using NOMe-seq/dSMF

Michaela Hinks; Georgi K Marinov; Anshul Kundaje; Lacramioara Bintu; William J Greenleaf

doi:10.1007/978-1-0716-2899-7_8

Single-Molecule Mapping of Chromatin Accessibility Using NOMe-seq/dSMF

Methods Mol Biol. 2023:2611:101-119. doi: 10.1007/978-1-0716-2899-7_8.

Authors

Michaela Hinks¹, Georgi K Marinov², Anshul Kundaje^{2

3}, Lacramioara Bintu⁴, William J Greenleaf^{5

6

7

8}

Affiliations

¹ Department of Genetics, Stanford University, Stanford, CA, USA. mhinks@stanford.edu.
² Department of Genetics, Stanford University, Stanford, CA, USA.
³ Department of Computer Science, Stanford University, Stanford, CA, USA.
⁴ Department of Bioengineering, Stanford University, Stanford, CA, USA.
⁵ Department of Genetics, Stanford University, Stanford, CA, USA. wjg@stanford.edu.
⁶ Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA, USA. wjg@stanford.edu.
⁷ Department of Applied Physics, Stanford University, Stanford, CA, USA. wjg@stanford.edu.
⁸ Chan Zuckerberg Biohub, San Francisco, CA, USA. wjg@stanford.edu.

PMID: 36807067
DOI: 10.1007/978-1-0716-2899-7_8

Abstract

The bulk of gene expression regulation in most organisms is accomplished through the action of transcription factors (TFs) on cis-regulatory elements (CREs). In eukaryotes, these CREs are generally characterized by nucleosomal depletion and thus higher physical accessibility of DNA. Many methods exploit this property to map regions of high average accessibility, and thus putative active CREs, in bulk. However, these techniques do not provide information about coordinated patterns of accessibility along the same DNA molecule, nor do they map the absolute levels of occupancy/accessibility. SMF (Single-Molecule Footprinting) fills these gaps by leveraging recombinant DNA cytosine methyltransferases (MTase) to mark accessible locations on individual DNA molecules. In this chapter, we discuss current methods and important considerations for performing SMF experiments.

Keywords: Chromatin accessibility; Enhancers; High-throughput sequencing; Promoters; SMF.

Publication types

Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't

MeSH terms

Chromatin*
DNA Methylation
High-Throughput Nucleotide Sequencing / methods
Nucleosomes*
Sequence Analysis, DNA / methods
Transcription Factors / metabolism

Substances

Chromatin
Nucleosomes
Transcription Factors

Abstract

Publication types

MeSH terms

Substances

Grants and funding