Abstract
Transcription factor (TF) networks orchestrate the regulation of gene programs in mammalian cells, including white and brown adipocytes. In this protocol, we outline how genomics and transcriptomics data can be integrated to infer causal TFs of a given cellular response or cell type using "Integrated analysis of Motif Activity and Gene Expression changes of transcription factors" (IMAGE). Here, we show how key regulatory TFs controlling white and brown adipocyte gene programs can be predicted from chromatin accessibility and RNA-seq data. Furthermore, we demonstrate how information about target sites and target genes of the predicted key regulators can be integrated to propose testable hypotheses regarding the role and mechanisms of TFs.
| Original language | English |
|---|---|
| Title of host publication | Brown Adipose Tissue : Methods and Protocols |
| Editors | David A. Guertin, Christian Wolfrum |
| Number of pages | 21 |
| Publisher | Springer |
| Publication date | 2022 |
| Pages | 155-175 |
| ISBN (Print) | 978-1-0716-2086-1 |
| ISBN (Electronic) | 978-1-0716-2087-8 |
| DOIs | |
| Publication status | Published - 2022 |
| Series | Methods in Molecular Biology |
|---|---|
| Volume | 2448 |
| ISSN | 1064-3745 |
Bibliographical note
Publisher Copyright:© 2022. The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature.
Keywords
- Chromatin accessibility
- Enhancer activity
- Genome-wide sequencing
- IMAGE
- Motif activity
- Transcription factor
- Transcriptional regulation
- Chromatin
- Adipocytes/metabolism
- Gene Expression Regulation
- Transcription Factors/genetics
- Gene Regulatory Networks
- Animals