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Updated: Jun 3, 2025
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Improved Protocol for Chromatin Immunoprecipitation from Mouse Skeletal Muscle
Published on: November 6, 2017
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Integrative Analysis of Chromatin Accessibility and Transcriptional Landscape Identifies Key Genes During Muscle
Dongjie Zhang1, Qian Zhang2, Xiaoxu Wu2
1Institute of Animal Husbandry, Heilongjiang Academy of Agricultural Sciences, Harbin 150086, China.
Cells
|January 8, 2025
Summary
This study reveals key epigenetic regulators of skeletal muscle development in pigs. It identifies critical genes and transcription factors, including KLF5, that control muscle growth through dynamic chromatin accessibility changes.
Area of Science:
- Epigenetics
- Molecular Biology
- Animal Science
Background:
- Skeletal muscle development is crucial for animal productivity.
- Understanding the epigenetic mechanisms, particularly chromatin accessibility, is vital for regulating gene expression during muscle growth.
- Current knowledge on dynamic chromatin accessibility changes in skeletal muscle development is limited.
Purpose of the Study:
- To investigate dynamic changes in chromatin accessibility during skeletal muscle development in Min pigs.
- To identify key genes, transcription factors, and regulatory regions involved in muscle development.
- To elucidate the functional roles of identified regulatory elements and transcription factors.
Main Methods:
- Assay for transposase-accessible chromatin with high-throughput sequencing (ATAC-seq) to analyze chromatin accessibility.
- RNA sequencing (RNA-seq) to identify differentially expressed genes.
- Integrated analysis of ATAC-seq and RNA-seq data.
- Molecular biology techniques to validate gene regulation by transcription factors.
Main Results:
- 16,301 differentially accessible regions (DARs) and 7,455 associated genes were identified across developmental stages.
- Seven of eight tested DARs significantly regulated reporter gene expression.
- 2,219 differentially expressed genes (DEGs) were identified.
- 54 DEG_DAR_genes and 61 transcription factors (TFs) were characterized as critical for muscle development.
- Kruppel-like factor 5 (KLF5) was identified as a key TF regulating multiple genes, including SLPI and APOA1.
Conclusions:
- Dynamic changes in chromatin accessibility play a significant role in skeletal muscle development.
- Key transcription factors, such as KLF5, are critical for regulating gene expression during muscle growth.
- The identified regulatory regions, TFs, and genes provide novel insights into the epigenetic regulation of muscle development in pigs.
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