Low Input Targeted Chromatin Capture (Low-T2C)

Ilias Boltsis; Karol Nowosad; Rutger W W Brouwer; Przemko Tylzanowski; Wilfred F J van IJcken; Danny Huylebroeck; Frank Grosveld; Petros Kolovos

doi:10.1007/978-1-0716-1597-3_9

Low Input Targeted Chromatin Capture (Low-T2C)

Methods Mol Biol. 2021:2351:165-179. doi: 10.1007/978-1-0716-1597-3_9.

Authors

Ilias Boltsis¹, Karol Nowosad^{1

2

3}, Rutger W W Brouwer^{1

4}, Przemko Tylzanowski^{2

5}, Wilfred F J van IJcken^{1

4}, Danny Huylebroeck^{1

6}, Frank Grosveld⁷, Petros Kolovos⁸

Affiliations

¹ Department of Cell Biology, Erasmus Medical Center, Rotterdam, The Netherlands.
² Department of Biochemistry and Molecular Biology, Medical University of Lublin, Lublin, Poland.
³ The Postgraduate School of Molecular Medicine, Medical University of Warsaw, Warsaw, Poland.
⁴ Center for Biomics, Erasmus Medical Center, Rotterdam, The Netherlands.
⁵ Department of Development and Regeneration, Skeletal Biology and Engineering Research Center, University of Leuven, Leuven, Belgium.
⁶ Department of Development and Regeneration, KU Leuven, Leuven, Belgium.
⁷ Department of Cell Biology, Erasmus Medical Center, Rotterdam, The Netherlands. [email protected].
⁸ Department of Molecular Biology and Genetics, Democritus University of Thrace, University Campus Dragana, Alexandroupolis, Greece.

PMID: 34382189
DOI: 10.1007/978-1-0716-1597-3_9

Abstract

Targeted chromatin capture (T2C) is a 3C-based method and is used to study the 3D chromatin organization, interactomes and structural changes associated with gene regulation, progression through the cell cycle, and cell survival and development. Low input targeted chromatin capture (low-T2C) is an optimized version of the T2C protocol for low numbers of cells. Here, we describe the protocol for low-T2C, including all experimental steps and bioinformatics tools in detail.

Keywords: C-technologies; Chromatin; Chromatin conformation capture; Genome architecture; T2C; Three-dimensional (3D) organization; Topologically associating domains (TADs).

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Chromatin / chemistry
Chromatin / genetics*
Chromatin / metabolism
Chromatin Assembly and Disassembly*
Chromosome Mapping
Computational Biology / methods*
Gene Expression Regulation
Gene Library
Genomics / methods
Reproducibility of Results

Substances

Chromatin