Systematic investigation of imprinted gene expression and enrichment in the mouse brain explored at single-cell resolution

Abstract

Over 200 murine imprinted genes have currently been identified, many are expressed in the brain, and a subset have been associated with neurological and behavioural phenotypes. These studies have led to the suggestion that imprinted genes show enriched expression in certain key brain functions; however, this has never been formally tested. Here we use fifteen available single-cell RNA sequencing datasets to investigate imprinted gene over-representation in the brain, with the aim of identifying key hotspots of expression and, by extension, function. We establish that imprinted genes are indeed over-represented in the adult brain compared to other adult tissues, and in neurons specifically compared to other cell-types. Brain wide datasets allowed us to demonstrate enrichment of imprinted genes in the hypothalamus, ventral midbrain, pons and medulla. Finally, using scRNA-seq datasets focusing on these regions of enrichment, we were able to identify hypothalamic neuroendocrine populations and the monoaminergic hindbrain neurons as specific hotspots of imprinted gene expression. These analyses provide a robust assessment of the neural systems on which imprinted genes converge and in turn suggest the neuronal regulation of motivated behaviours such as feeding, parental behaviour and sleep as functional hotspots for imprinting.

Parenting deficits inMagel2-null mice predicted from systematic investigation of imprinted gene expression in galanin neurons of the hypothalamus

“…Our systematic analysis of imprinted gene expression, and behavioural/molecular biology analysis of an exemplar candidate, taken together with our previous findings (32), strongly support the idea that parental care is indeed a physiological focus for genomic imprinting. Interestingly, loss of paternal Magel2 in pups leads to reduced USV production which in turn impacts upon solicitation of parental care from wild-type mums (36), supporting the idea that genomic imprinting has evolved to coordinate the activity of parenting between mother and offspring (22,23).…”

“…Imprinted gene expression data for the Mouse Brain Atlas (2) and Whole Hypothalamus (5) were produced in our previous analysis (32) and all files can be found at our OSF repository (https://osf.io/jx7kr/) but are also provided as Supplemental Data. Imprinted gene expression data can be found as an 'Upregulated_IGs.csv' file for each analysis.…”

“…Utilising a variety of publicly available single cell transcriptomic data, we have previously demonstrated that imprinted genes show over-representation in the adult mouse brain, and more specifically gene set enrichment in the neurons and neuroendocrine cells of the hypothalamus (32).…”

The imprinted Zdbf2 gene finely tunes control of feeding and growth in neonates

“…The three hypothalamic clusters where Zdbf2 was the most highly expressed were both glutamatergic (Glu13 and Glu15) and GABAergic (GABA17) neurons from the arcuate and the periventricular hypothalamic regions (Figure 1-figure supplement 1C). Same results were recently reported using different scRNA-seq datasets (Higgs et al, 2021).Interestingly, these nuclei synthesize peptides that stimulate hormone production from the pituitary gland, or that control energy balance -food intake, energy expenditure and body temperature-by directly acting on the brain and/or more distal organs (Saper & Lowell, 2014).…”

“…Imprinting-related postnatal effects are recurrently linked to dysfunction of the hypothalamus (Ivanova & Kelsey, 2011), a key organ for orchestrating whole body homeostasis through a complex network of nuclei that produce and deliver neuropeptides to distinct targets, including the pituitary gland that in turn secretes endocrine hormones such as the growth hormone (GH). Accordingly, the hypothalamus appears as a privileged site for imprinted gene expression (Gregg et al, 2010;Higgs et al, 2021). A typical illustration of such association is provided by a cluster of hypothalamic genes whose dosage is altered in Prader-Willi syndrome (PWS).…”