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Quantifying Genomic Imprinting at Tissue and Cell Resolution in the Brain

1
Institut de Génomique Fonctionnelle (IGF), Univ. Montpellier, CNRS, INSERM, 34094 Montpellier, France
2
Montpellier GenomiX (MGX), Univ. Montpellier, CNRS, INSERM, 34094 Montpellier, France
*
Author to whom correspondence should be addressed.
Received: 17 July 2020 / Revised: 24 August 2020 / Accepted: 1 September 2020 / Published: 4 September 2020
Imprinted genes are a group of ~150 genes that are preferentially expressed from one parental allele owing to epigenetic marks asymmetrically distributed on inherited maternal and paternal chromosomes. Altered imprinted gene expression causes human brain disorders such as Prader-Willi and Angelman syndromes and additional rare brain diseases. Research data principally obtained from the mouse model revealed how imprinted genes act in the normal and pathological brain. However, a better understanding of imprinted gene functions calls for building detailed maps of their parent-of-origin-dependent expression and of associated epigenetic signatures. Here we review current methods for quantifying genomic imprinting at tissue and cell resolutions, with a special emphasis on methods to detect parent-of-origin dependent expression and their applications to the brain. We first focus on bulk RNA-sequencing, the main method to detect parent-of-origin-dependent expression transcriptome-wide. We discuss the benefits and caveats of bulk RNA-sequencing and provide a guideline to use it on F1 hybrid mice. We then review methods for detecting parent-of-origin-dependent expression at cell resolution, including single-cell RNA-seq, genetic reporters, and molecular probes. Finally, we provide an overview of single-cell epigenomics technologies that profile additional features of genomic imprinting, including DNA methylation, histone modifications and chromatin conformation and their combination into sc-multimodal omics approaches, which are expected to yield important insights into genomic imprinting in individual brain cells. View Full-Text
Keywords: genomic imprinting; allele-specific RNA-seq; scRNA-seq; brain genomic imprinting; allele-specific RNA-seq; scRNA-seq; brain
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MDPI and ACS Style

Varrault, A.; Dubois, E.; Le Digarcher, A.; Bouschet, T. Quantifying Genomic Imprinting at Tissue and Cell Resolution in the Brain. Epigenomes 2020, 4, 21. https://0-doi-org.brum.beds.ac.uk/10.3390/epigenomes4030021

AMA Style

Varrault A, Dubois E, Le Digarcher A, Bouschet T. Quantifying Genomic Imprinting at Tissue and Cell Resolution in the Brain. Epigenomes. 2020; 4(3):21. https://0-doi-org.brum.beds.ac.uk/10.3390/epigenomes4030021

Chicago/Turabian Style

Varrault, Annie; Dubois, Emeric; Le Digarcher, Anne; Bouschet, Tristan. 2020. "Quantifying Genomic Imprinting at Tissue and Cell Resolution in the Brain" Epigenomes 4, no. 3: 21. https://0-doi-org.brum.beds.ac.uk/10.3390/epigenomes4030021

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