Decision letter: Specification of diverse cell types during early neurogenesis of the mouse cerebellum

The cerebellum is a well-studied brain structure with diverse roles in motor learning, coordination, cognition, and autonomic regulation. Nonetheless, a complete inventory of cerebellar cell types is presently lacking. We used high-throughput transcriptional profiling to molecularly define cell types across individual lobules of the adult mouse cerebellum. Purkinje and granule neurons showed considerable regional specialization, with the greatest diversity occurring in the posterior lobules. For multiple types of cerebellar interneurons, the molecular variation within each type was more continuous, rather than discrete. For the unipolar brush cells (UBCs)—an interneuron population previously subdivided into two discrete populations—the continuous variation in gene expression was associated with a graded continuum of electrophysiological properties. Most surprisingly, we found that molecular layer interneurons (MLIs) were composed of two molecularly and functionally distinct types. Both show a continuum of morphological variation through the thickness of the molecular layer, but electrophysiological recordings revealed marked differences between the two types in spontaneous firing, excitability, and electrical coupling. Together, these findings provide the first comprehensive cellular atlas of the cerebellar cortex, and outline a methodological and conceptual framework for the integration of molecular, morphological, and physiological ontologies for defining brain cell types.

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Mutations affecting neurogenesis and brain morphology in the zebrafish, Danio rerio

Development ◽

10.1242/dev.123.1.205 ◽

1996 ◽

Vol 123 (1) ◽

pp. 205-216 ◽

Cited By ~ 34

Author(s):

Y.J. Jiang ◽

M. Brand ◽

C.P. Heisenberg ◽

D. Beuchle ◽

M. Furutani-Seiki ◽

...

Keyword(s):

Cell Types ◽

Brain Morphology ◽

Abnormal Development ◽

Radial Glial Cells ◽

Complementation Groups ◽

Early Neurogenesis ◽

Radial Glial ◽

General Organization ◽

Neurogenic Mutants ◽

The Brain

In a screen for embryonic mutants in the zebrafish a large number of mutants were isolated with abnormal brain morphology. We describe here 26 mutants in 13 complementation groups that show abnormal development of large regions of the brain. Early neurogenesis is affected in white tail (wit). During segmentation stages, homozygous wit embryos display an irregularly formed neural keel, particularly in the hindbrain. Using a variety of molecular markers, a severe increase in the number of various early differentiating neurons can be demonstrated. In contrast, late differentiating neurons, radial glial cells and some nonneural cell types, such as the neural crest-derived melanoblasts, are much reduced. Somitogenesis appears delayed. In addition, very reduced numbers of melanophores are present posterior to the mid-trunk. The wit phenotype is reminiscent of neurogenic mutants in Drosophila, such as Notch or Delta. In mutant parachute (pac) embryos the general organization of the hindbrain is disturbed and many rounded cells accumulate loosely in the hindbrain and midbrain ventricles. Mutants in a group of 6 genes, snakehead(snk), natter (nat), otter (ott), fullbrain (ful), viper (vip) and white snake (wis) develop collapsed brain ventricles, before showing signs of general degeneration. atlantis (atl), big head (bid), wicked brain (win), scabland (sbd) and eisspalte (ele) mutants have different malformation of the brain folds. Some of them have transient phenotypes, and mutant individuals may grow up to adults.

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The regulatory landscape of cells in the developing mouse cerebellum

10.1101/2021.01.29.428632 ◽

2021 ◽

Author(s):

Ioannis Sarropoulos ◽

Mari Sepp ◽

Robert Frömel ◽

Kevin Leiss ◽

Nils Trost ◽

...

Keyword(s):

Evolutionary Dynamics ◽

Cell Types ◽

Regulatory Elements ◽

Specific Gene ◽

Regulatory Change ◽

Evolutionary Constraint ◽

Organ Development ◽

Mouse Cerebellum ◽

Cerebellar Cell ◽

Time Specific

AbstractOrgan development is orchestrated by cell- and time-specific gene regulatory networks. Here we investigated the regulatory basis of mouse cerebellum development from early neurogenesis to adulthood. By acquiring snATAC-seq profiles for ~90,000 cells spanning eleven stages, we mapped all major cerebellar cell types and identified candidate cis-regulatory elements (CREs). We detected extensive spatiotemporal heterogeneity among progenitor cells and characterized the regulatory programs underlying the differentiation of cerebellar neurons. Although CRE activity is predominantly cell type- and time-specific, periods of greater regulatory change are shared across cell types. There is a universal decrease in CRE conservation and pleiotropy during development and differentiation, but the degree of evolutionary constraint differs between cerebellar cell types. Our work delineates the developmental and evolutionary dynamics of gene regulation in cerebellar cells and provides general insights into mammalian organ development.

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Specification of diverse cell types during early neurogenesis of the mouse cerebellum

10.1101/440818 ◽

2018 ◽

Author(s):

John W. Wizeman ◽

Qiuxia Guo ◽

Elliot Wilion ◽

James Y.H. Li

Keyword(s):

Cell Fate ◽

Developmental Trajectories ◽

Ventricular Zone ◽

Cell Types ◽

Genome Wide ◽

Integral Role ◽

Cerebellar Cell ◽

Early Neurogenesis ◽

And Function ◽

Developing Cerebellum

SUMMARYWe applied single-cell RNA sequencing to profile genome-wide gene expression in about 9,400 individual cerebellar cells from the mouse embryo at embryonic day 13.5. Reiterative clustering identified the major cerebellar cell types and subpopulations of different lineages. Through pseudotemporal ordering to reconstruct developmental trajectories, we identified novel transcriptional programs controlling cell fate specification of populations arising from the ventricular zone and the anterior rhombic lip, two distinct germinal zones of the embryonic cerebellum. Together, our data revealed cell-specific markers for studying the cerebellum, important specification decisions, and a number of previously unknown subpopulations that may play an integral role in the formation and function of the cerebellum. Importantly, we identified a potential mechanism of vermis formation, which is affected by multiple congenital cerebellar defects. Our findings will facilitate new discovery by providing insights into the molecular and cell type diversity in the developing cerebellum.

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Selective demethylation of two CpG sites causes postnatal activation of the Dao gene and consequent removal of d-serine within the mouse cerebellum

Clinical Epigenetics ◽

10.1186/s13148-019-0732-z ◽

2019 ◽

Vol 11 (1) ◽

Cited By ~ 7

Author(s):

Mariella Cuomo ◽

Simona Keller ◽

Daniela Punzo ◽

Tommaso Nuzzo ◽

Ornella Affinito ◽

...

Keyword(s):

Amino Acids ◽

Dna Methylation ◽

Single Molecule ◽

Developmental Stages ◽

Cell Types ◽

Epigenetic Modifications ◽

Specific Cell ◽

Cpg Sites ◽

Brain Levels ◽

Mouse Cerebellum

Abstract Background Programmed epigenetic modifications occurring at early postnatal brain developmental stages may have a long-lasting impact on brain function and complex behavior throughout life. Notably, it is now emerging that several genes that undergo perinatal changes in DNA methylation are associated with neuropsychiatric disorders. In this context, we envisaged that epigenetic modifications during the perinatal period may potentially drive essential changes in the genes regulating brain levels of critical neuromodulators such as d-serine and d-aspartate. Dysfunction of this fine regulation may contribute to the genesis of schizophrenia or other mental disorders, in which altered levels of d-amino acids are found. We recently demonstrated that Ddo, the d-aspartate degradation gene, is actively demethylated to ultimately reduce d-aspartate levels. However, the role of epigenetics as a mechanism driving the regulation of appropriate d-ser levels during brain development has been poorly investigated to date. Methods We performed comprehensive ultradeep DNA methylation and hydroxymethylation profiling along with mRNA expression and HPLC-based d-amino acids level analyses of genes controlling the mammalian brain levels of d-serine and d-aspartate. DNA methylation changes occurring in specific cerebellar cell types were also investigated. We conducted high coverage targeted bisulfite sequencing by next-generation sequencing and single-molecule bioinformatic analysis. Results We report consistent spatiotemporal modifications occurring at the Dao gene during neonatal development in a specific brain region (the cerebellum) and within specific cell types (astrocytes) for the first time. Dynamic demethylation at two specific CpG sites located just downstream of the transcription start site was sufficient to strongly activate the Dao gene, ultimately promoting the complete physiological degradation of cerebellar d-serine a few days after mouse birth. High amount of 5′-hydroxymethylcytosine, exclusively detected at relevant CpG sites, strongly evoked the occurrence of an active demethylation process. Conclusion The present investigation demonstrates that robust and selective demethylation of two CpG sites is associated with postnatal activation of the Dao gene and consequent removal of d-serine within the mouse cerebellum. A single-molecule methylation approach applied at the Dao locus promises to identify different cell-type compositions and functions in different brain areas and developmental stages.

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Modulation of the notch signaling by Mash1 and Dlx1/2regulates sequential specification and differentiation of progenitor cell types in the subcortical telencephalon

Development ◽

10.1242/dev.129.21.5029 ◽

2002 ◽

Vol 129 (21) ◽

pp. 5029-5040 ◽

Cited By ~ 7

Author(s):

Kyuson Yun ◽

Seth Fischman ◽

Jane Johnson ◽

Martin Hrabe de Angelis ◽

Gerry Weinmaster ◽

...

Keyword(s):

Transcription Factors ◽

Notch Signaling ◽

Cell Fate ◽

Progenitor Cell ◽

Cell Types ◽

Cell Fate Specification ◽

Early Neurogenesis ◽

Molecular Phenotypes ◽

Postmitotic Cell ◽

Homeobox Transcription Factors

Notch signaling has a central role in cell fate specification and differentiation. We provide evidence that the Mash1 (bHLH) andDlx1 and Dlx2 (homeobox) transcription factors have complementary roles in regulating Notch signaling, which in turn mediates the temporal control of subcortical telencephalic neurogenesis in mice. We defined progressively more mature subcortical progenitors (P1, P2 and P3) through their combinatorial expression of MASH1 and DLX2, as well as the expression of proliferative and postmitotic cell markers at E10.5-E11.5. In the absence ofMash1, Notch signaling is greatly reduced and `early' VZ progenitors(P1 and P2) precociously acquire SVZ progenitor (P3) properties. Comparing the molecular phenotypes of the delta-like 1 and Mash1 mutants, suggests that Mash1 regulates early neurogenesis through Notch-and Delta-dependent and -independent mechanisms. While Mash1 is required for early neurogenesis (E10.5), Dlx1 and Dlx2 are required to downregulate Notch signaling during specification and differentiation steps of `late' progenitors (P3). We suggest that alternate cell fate choices in the developing telencephalon are controlled by coordinated functions of bHLH and homeobox transcription factors through their differential affects on Notch signaling.

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