Analysis of Genome-Wide Monoallelic Expression Patterns in Three Major Cell Types of Mouse Visual Cortex Using Laser Capture Microdissection.
Genomic imprinting is an epigenetic mechanism causing monoallelic expression in a parent-of-origin-specific manner. Disruption of imprinted genes causes various neurological and psychiatric disorders. However, the role of imprinted genes in the brain is largely unknown. Different cell types within distinct brain regions can influence the genomic imprinting status, but imprinted genes in single cell types within distinct brain regions have not been characterized on a genome-wide scale. To address this critical question, we used a multi-stage approach, which combined genetically engineered mice with fluorescence-based laser capture microdissection (LCM) to capture excitatory neurons, inhibitory neurons and astrocytes as single cells in layer 2/3 of mouse visual cortex. RNA sequencing determined parental expression patterns on a genome-wide scale in the captured cells within specific brain regions. The expression level of cell-type-specific genes for excitatory neurons (13 genes), inhibitory neurons (16 genes) and astrocytes (20 genes) confirmed the LCM-captured cells maintained their cellular identities. The parent-of-origin-specific expression pattern of imprinted genes, including maternally expressed Meg3 and paternally expressed Peg3, provided evidence that the status of known imprinted genes was also maintained. Although our platform remains to be improved, our findings demonstrate the parental expression pattern can be analysed not only at the level of a single cell type but also at the level of specific cortical layers. Our approach has the potential to reveal novel regulatory modules associated with plasticity through genomic imprinting mechanisms in different cell types, not only in the visual cortex but also in other brain regions.
Graduate Institute of Brain and Mind Sciences, College of Medicine, National Taiwan University, Taipei, Taiwan.
Chia-Yi
CY
Lin
Graduate Institute of Brain and Mind Sciences, College of Medicine, National Taiwan University, Taipei, Taiwan.
Shih-Chuan
SC
Huang
Graduate Institute of Brain and Mind Sciences, College of Medicine, National Taiwan University, Taipei, Taiwan.
Chun-Che
CC
Tung
Graduate Institute of Brain and Mind Sciences, College of Medicine, National Taiwan University, Taipei, Taiwan.
Chih-Hsuan
CH
Chou
Graduate Institute of Brain and Mind Sciences, College of Medicine, National Taiwan University, Taipei, Taiwan.|Department of Psychiatry, College of Medicine, National Taiwan University, Taipei, Taiwan.|Clinical Center for Neuroscience and Behavior, National Taiwan University Hospital, Taipei, Taiwan.|Neurobiology and Cognitive Science Center, National Taiwan University, Taipei, Taiwan.
Susan Shur-Fen
SS
Gau
Graduate Institute of Brain and Mind Sciences, College of Medicine, National Taiwan University, Taipei, Taiwan.|Clinical Center for Neuroscience and Behavior, National Taiwan University Hospital, Taipei, Taiwan.|Neurobiology and Cognitive Science Center, National Taiwan University, Taipei, Taiwan.|Ph.D. Program in Translational Medicine, National Taiwan University and Academia Sinica, Taipei, Taiwan.|Neurodevelopment Club in Taiwan, Taipei, Taiwan.
Hsien-Sung
http://orcid.org/0000-0003-2657-3635
HS
Huang
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