Mapping Mammalian 3D Genomes by Micro-C

Elena Slobodyanyuk; Claudia Cattoglio; Tsung-Han S Hsieh

doi:10.1007/978-1-0716-2497-5_4

Mapping Mammalian 3D Genomes by Micro-C

Methods Mol Biol. 2022:2532:51-71. doi: 10.1007/978-1-0716-2497-5_4.

Authors

Elena Slobodyanyuk^{1

2

3

4}, Claudia Cattoglio^{1

2

3

4}, Tsung-Han S Hsieh^{5

6

7

8

9}

Affiliations

¹ Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA.
² Li Ka Shing Center for Biomedical and Health Sciences, University of California, Berkeley, Berkeley, CA, USA.
³ CIRM Center of Excellence, University of California, Berkeley, Berkeley, CA, USA.
⁴ Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, CA, USA.
⁵ Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA. hsieht@berkeley.edu.
⁶ Li Ka Shing Center for Biomedical and Health Sciences, University of California, Berkeley, Berkeley, CA, USA. hsieht@berkeley.edu.
⁷ CIRM Center of Excellence, University of California, Berkeley, Berkeley, CA, USA. hsieht@berkeley.edu.
⁸ Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, CA, USA. hsieht@berkeley.edu.
⁹ Center for Computational Biology, University of California, Berkeley, Berkeley, CA, USA. hsieht@berkeley.edu.

PMID: 35867245
DOI: 10.1007/978-1-0716-2497-5_4

Abstract

3D genome mapping aims at connecting the physics of chromatin folding to the underlying biological events, and applications of various chromosomal conformation capture (3C) assays continue to discover critical roles of genome folding in regulating nuclear functions. To interrogate the full spectrum of chromatin folding ranging from the level of nucleosomes to full chromosomes in mammals, we developed an enhanced 3C-based method called Micro-C. The protocol employs Micrococcal nuclease (MNase) to fragment the genome, which overcomes the resolution limit of restriction enzyme-based methods, enabling the estimation of contact frequencies between proximal nucleosomes. Such improvements successfully resolve the fine-scale level of chromatin folding, including enhancer-promoter or promoter-promoter interactions, genic and nucleosomal folding, and boost the signal-to-noise ratio in detecting loops and substructures underlying TADs. In this chapter, we will thoroughly discuss the details of the Micro-C protocol and critical parameters to consider for generating high-quality Micro-C maps.

Keywords: 3D genome; Chromosomal conformation capture (3C); Enhancer–promoter interaction; Hi-C; Loop; Micro-C; TAD.

MeSH terms

Animals
Chromatin / genetics
Chromosome Mapping / methods
Genome*
Mammals / genetics
Micrococcal Nuclease
Nucleosomes* / genetics

Substances

Chromatin
Nucleosomes
Micrococcal Nuclease