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Updated: Apr 18, 2026
Isolation of Region-specific Microglia from One Adult Mouse Brain Hemisphere for Deep Single-cell RNA Sequencing
Published on: December 3, 2019
A Comprehensive Profile of ChIP-Seq-Based PU.1/Spi1 Target Genes in Microglia
Jun-Ichi Satoh1, Naohiro Asahina1, Shouta Kitano1
1Department of Bioinformatics and Molecular Neuropathology, Meiji Pharmaceutical University, Kiyose, Tokyo, Japan.
Abstract:
Microglia are resident mononuclear phagocytes that play a principal role in the maintenance of normal tissue homeostasis in the central nervous system (CNS). Microglia, rapidly activated in response to proinflammatory stimuli, are accumulated in brain lesions of neurodegenerative diseases, such as Alzheimer's disease and Parkinson's disease. The E26 transformation-specific (ETS) family transcription factor PU.1/Spi1 acts as a master regulator of myeloid and lymphoid development. PU.1-deficient mice show a complete loss of microglia, indicating that PU.1 plays a pivotal role in microgliogenesis. However, the comprehensive profile of PU.1/Spi1 target genes in microglia remains unknown. By analyzing a chromatin immunoprecipitation followed by deep sequencing (ChIP-Seq) dataset numbered SRP036026 with the Strand NGS program, we identified 5,264 Spi1 target protein-coding genes in BV2 mouse microglial cells. They included Spi1, Irf8, Runx1, Csf1r, Csf1, Il34, Aif1 (Iba1), Cx3cr1, Trem2, and Tyrobp. By motif analysis, we found that the PU-box consensus sequences were accumulated in the genomic regions surrounding ChIP-Seq peaks. By using pathway analysis tools of bioinformatics, we found that ChIP-Seq-based Spi1 target genes show a significant relationship with diverse pathways essential for normal function of monocytes/macrophages, such as endocytosis, Fc receptor-mediated phagocytosis, and lysosomal degradation. These results suggest that PU.1/Spi1 plays a crucial role in regulation of the genes relevant to specialized functions of microglia. Therefore, aberrant regulation of PU.1 target genes might contribute to the development of neurodegenerative diseases with accumulation of activated microglia.
Insights
The transcription factor PU.1 controls microglial development and function by regulating key genes. Aberrant PU.1 target gene regulation may contribute to neurodegenerative diseases like Alzheimer's and Parkinson's.
Area of Science:
- Neuroscience
- Immunology
- Genetics
Background:
- Microglia are crucial for central nervous system (CNS) homeostasis and are implicated in neurodegenerative diseases.
- The transcription factor PU.1 (Spi1) is essential for microglial development, but its target genes in microglia are largely uncharacterized.
- Understanding PU.1's regulatory network is key to deciphering microglial dysfunction in disease.
Purpose of the Study:
- To comprehensively identify PU.1/Spi1 target genes in microglia.
- To investigate the functional pathways regulated by PU.1/Spi1 in microglial cells.
- To explore the potential role of PU.1/Spi1 dysregulation in neurodegenerative diseases.
Main Methods:
- Chromatin immunoprecipitation followed by deep sequencing (ChIP-Seq) was used to identify Spi1 binding sites in BV2 microglial cells.
- Bioinformatic analyses, including motif and pathway analysis, were performed on identified target genes.
- Strand NGS program was utilized for data analysis of the SRP036026 dataset.
Main Results:
- 5,264 Spi1 target protein-coding genes were identified in BV2 microglial cells.
- Key microglial genes such as Csf1r, Cx3cr1, and Trem2 were found to be direct or indirect targets of Spi1.
- Pathway analysis revealed that Spi1 target genes are involved in essential monocyte/macrophage functions like phagocytosis and endocytosis.
Conclusions:
- PU.1/Spi1 is a master regulator of genes critical for specialized microglial functions.
- Dysregulation of PU.1/Spi1 target genes may contribute to the pathogenesis of neurodegenerative diseases characterized by microglial activation.
- This study provides a foundational gene list for understanding microglial biology and disease.
