PUBLICATION
Assay for transposase-accessible chromatin and circularized chromosome conformation capture, two methods to explore the regulatory landscapes of genes in zebrafish
- Authors
- Fernández-Miñán, A., Bessa, J., Tena, J.J., Gómez-Skarmeta, J.L.
- ID
- ZDB-PUB-160725-15
- Date
- 2016
- Source
- Methods in cell biology 135: 413-30 (Chapter)
- Registered Authors
- Bessa, Jose, Gómez-Skarmeta, José Luis, Tena, Juan
- Keywords
- 3D chromatin structure, 4C-seq, ATAC-seq, Epigenomics, Interactomics, Medaka, Zebrafish, cis-regulation
- MeSH Terms
-
- Animals
- Chromatin/genetics*
- Gene Expression Profiling/methods*
- Gene Expression Regulation/genetics
- High-Throughput Nucleotide Sequencing/methods*
- Transposases/genetics*
- Zebrafish/genetics
- PubMed
- 27443938 Full text @ Meth. Cell. Biol.
Citation
Fernández-Miñán, A., Bessa, J., Tena, J.J., Gómez-Skarmeta, J.L. (2016) Assay for transposase-accessible chromatin and circularized chromosome conformation capture, two methods to explore the regulatory landscapes of genes in zebrafish. Methods in cell biology. 135:413-30.
Abstract
Accurate transcriptional control of genes is fundamental for the correct functioning of organs and developmental processes. This control depends on the interplay between the promoter of genes and other noncoding sequences, whose interaction is mediated by 3D chromatin arrangements. Thus, the detailed description of transcriptional regulatory landscapes is essential to understand the mechanisms of transcriptional regulation. However, to achieve that, two important challenges have to be faced: (1) the identification of the noncoding sequences that contribute to gene transcription and (2) the association of these sequences to the respective genes they control. In this chapter, we describe two protocols that allow overcoming these important challenges: the assay for transposase-accessible chromatin using sequencing (ATAC-seq) and circularized chromosome conformation capture (4C-seq). ATAC-seq is a very efficient technique that, using a very low number of cells as starting material, allows the identification of active chromatin regions genome wide, whereas 4C-seq detects the subset of sequences that interact specifically with the promoter of a given gene. When combined, both techniques provide a comprehensive snapshot of the regulatory landscapes of developmental genes. The protocols we present here have been optimized for teleost fish samples, zebrafish and medaka, allowing the in-depth study of transcriptional regulation in these two emerging animal models. Given the amenability and easy genetic manipulation of these two experimental systems, we anticipate that they will be important in revealing general principles of the vertebrate regulatory genome.
Genes / Markers
Expression
Phenotype
Mutations / Transgenics
Human Disease / Model
Sequence Targeting Reagents
Fish
Orthology
Engineered Foreign Genes
Mapping