Analysis of Genome-Wide Monoallelic Expression Patterns in Three Major Cell Types of Mouse Visual Cortex Using Laser Capture Microdissection

PLoS One. 2016 Sep 23;11(9):e0163663. doi: 10.1371/journal.pone.0163663. eCollection 2016.

Abstract

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.

Grants and funding

This work was supported by the National Health Research Institutes, Miaoli, Taiwan (http://english.nhri.org.tw/NHRI_WEB/nhriw001Action.do) (Career Development Grant, NHRI-EX103-10316NC to H.-S.H.), the National Taiwan University, Taipei, Taiwan (http://www.ntu.edu.tw/english/)(AIM for Top University Excellent Research Project, 102C101-42, 103C101-C1, 104C101-B1, 105R3701 to S.S.G. and H.-S.H), the National Taiwan University Hospital (http://www.ntuh.gov.tw/en/default_P.aspx) (NTHU-UN104-018, NTUH-UN105-014 to S.S.G. and H.-S.H.) and the Foundation for the Advancement of Outstanding Scholarship, Taipei, Taiwan (http://www.faos.org.tw/English/aboutus.html) (Young Scholars’ Creativity Award, to H.-S.H). Ministry of Science and Technology, Taipei, Taiwan (https://www.most.gov.tw/en/public) (General Research Project, MOST 105-2628-B-002-033-MY3 to H.-S.H. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.