Single nucleus multi-omics regulatory landscape of the murine pituitary

Abstract

To provide a multi-omics resource and investigate transcriptional regulatory mechanisms, we profile the transcriptome, chromatin accessibility, and methylation status of over 70,000 single nuclei (sn) from adult mouse pituitaries. Paired snRNAseq and snATACseq datasets from individual animals highlight a continuum between developmental epigenetically-encoded cell types and transcriptionally-determined transient cell states. Co-accessibility analysis-based identification of a putative Fshb cis-regulatory domain that overlaps the fertility-linked rs11031006 human polymorphism, followed by experimental validation illustrate the use of this resource for hypothesis generation. We also identify transcriptional and chromatin accessibility programs distinguishing each major cell type. Regulons, which are co-regulated gene sets sharing binding sites for a common transcription factor driver, recapitulate cell type clustering. We identify both cell type-specific and sex-specific regulons that are highly correlated with promoter accessibility, but not with methylation state, supporting the centrality of chromatin accessibility in shaping cell-defining transcriptional programs. The sn multi-omics atlas is accessible at snpituitaryatlas.princeton.edu.

TGFBR3L is an inhibin B co-receptor that regulates female fertility

“…1, A and B , and fig. S1, A and B) ( 23 ). Tgfbr3l mRNA is also selectively expressed in rat gonadotropes ( 24 ), and the TGFBR3L protein was recently reported to be a gonadotrope-specific membrane protein of unknown function in human pituitary ( 25 ).…”

Postnatal developmental trajectory of sex-biased gene expression in the mouse pituitary gland

“…At PD27, when puberty has occurred in a subset of our mice ( Figure 1A ), we observed the emergence of male bias in somatotrope cell proportions and female bias in lactotrope cell proportions ( Figure 5C ). The emergence of sex differences in relative cell proportions at ages leading up to and including puberty suggest that pubertal transition may be a key time window for the establishment of sex-biased proportions of hormone-producing cells observed in adult mice (Ho et al, 2020; Ruf-Zamojski et al, 2021; Sasaki and Iwama, 1988).…”

“…While currently cost-prohibitive, our results suggest that a similar experimental design in the future with single-cell technologies (multiple replicates of male and female mice at multiple postnatal timepoints) will provide more specific insight into the mechanisms underlying sex-biased gene expression and the molecular mechanisms that give rise to cell-type proportion differences during postnatal development in the pituitary. Support for this approach is seen in the aforementioned recent work which used scRNA-seq and scATAC-seq to characterize the sex-biased specific regulatory landscape of the mouse pituitary (Ruf-Zamojski et al, 2021). In this study, the authors highlighted a group of genes with female-biased expression using latent variable analysis.…”

“…However, these transcriptional regulators were predicted using datasets generated in other cellular environments, and hence future experiments in both sexes of the mouse pituitary, such as ATAC-seq and ChIP-seq, would be of interest to further identify sex differences in chromatin accessibility and TF binding. Recently, Ruf-Zamojski et al performed scRNA-seq and scATAC- seq in male and female adult mice (10-12 weeks) (Ruf-Zamojski et al, 2021). While the authors discussed limited examples of sex-biased regulons, their dataset serves as a valuable resource to study the cis-regulation of sex-biased gene expression in a cell-type-specific manner and a model for future single-cell studies aiming at further dissecting sex-biased gene regulatory networks.…”

“…However, inferences may be made based on the expression of host genes for mirtrons. For example, Sgcz , the host gene of female-biased miR- 383-5p, displays specific expression in a putative lactosomatotrope population (Ruf-Zamojski et al, 2021), suggesting miR-383-5p may also be expressed from a similar population of cells.…”