Ablation of Vti1a/1b Triggers Neural Progenitor Pool Depletion and Cortical Layer 5 Malformation in Late-embryonic Mouse Cortex

DNA methylation dynamics during yak adipocyte differentiation

In mammals, epigenetic modifications involving DNA methylation are necessary for the completion of the cell differentiation process. However, the global DNA methylation landscape and its dynamics during yak adipocyte differentiation remain unexplored. Here, we performed whole-genome bisulfite sequencing (WGBS) to asses DNA methylation in yak preadipocytes and adipocytes, combining these results with those of our previous studies on changes in chromatin accessibility and gene expression during yak adipogenesis. The results showed that CG methylation levels were lower in promoter than in exon and intron, and gradually decreasing from the distal regions to transcription start site (TSS). There was a significant negative correlation between CG methylation levels located in promoter and gene expression levels. The 46 genes shared by CG differentially methylated regions (DMRs) and differential chromatin accessibility were significantly enriched in Hedgehog and PI3K-Akt signaling pathways. ATAC-seq peaks with high chromatin accessibility located in both promoter (≤ 2 kb from TSS) and distal (> 2 kb from TSS) regions corresponded to low methylation levels. Taken together, these findings demonstrated that DNA methylation and its interactions with chromatin accessibility regulate gene expression during yak adipocyte differentiation, contributing to the understanding of mechanisms of various epigenetic modifications and their interactions in adipogenesis.

Primary neurons lacking the SNAREs vti1a and vti1b show altered neuronal development

BACKGROUND

Neurons are highly specialized cells with a complex morphology generated by various membrane trafficking steps. They contain Golgi outposts in dendrites, which are formed from somatic Golgi tubules. In trafficking membrane fusion is mediated by a specific combination of SNARE proteins. A functional SNARE complex contains four different helices, one from each SNARE subfamily (R-, Qa, Qb and Qc). Loss of the two Qb SNAREs vti1a and vti1b from the Golgi apparatus and endosomes leads to death at birth in mice with massive neurodegeneration in peripheral ganglia and defective axon tracts.

METHODS

Hippocampal and cortical neurons were isolated from Vti1a^-/- Vti1b^-/- double deficient, Vti1a^-/- Vti1b^+/-, Vti1a^+/- Vti1b^-/- and Vti1a^+/- Vti1b^+/- double heterozygous embryos. Neurite outgrowth was determined in cortical neurons and after stimulation with several neurotrophic factors or the Rho-associated protein kinase ROCK inhibitor Y27632, which induces exocytosis of enlargeosomes, in hippocampal neurons. Moreover, postsynaptic densities were isolated from embryonic Vti1a^-/- Vti1b^-/- and Vti1a^+/- Vti1b^+/- control forebrains and analyzed by western blotting.

RESULTS

Golgi outposts were present in Vti1a^-/- Vti1b^+/- and Vti1a^+/- Vti1b^-/- dendrites of hippocampal neurons but not detected in the absence of vti1a and vti1b. The length of neurites was significantly shorter in double deficient cortical neurons. These defects were not observed in Vti1a^-/- Vti1b^+/- and Vti1a^+/- Vti1b^-/- neurons. NGF, BDNF, NT-3, GDNF or Y27632 as stimulator of enlargeosome secretion did not increase the neurite length in double deficient hippocampal neurons. Vti1a^-/- Vti1b^-/- postsynaptic densities contained similar amounts of scaffold proteins, AMPA receptors and NMDA receptors compared to Vti1a^+/- Vti1b^+/-, but much more TrkB, which is the receptor for BDNF.

CONCLUSION

The absence of Golgi outposts did not affect the amount of AMPA and NMDA receptors in postsynaptic densities. Even though TrkB was enriched, BDNF was not able to stimulate neurite elongation in Vti1a^-/- Vti1b^-/- neurons. Vti1a or vti1b function as the missing Qb-SNARE together with VAMP-4 (R-SNARE), syntaxin 16 (Qa-SNARE) and syntaxin 6 (Qc-SNARE) in induced neurite outgrowth. Our data show the importance of vti1a or vti1b for two pathways of neurite elongation.

Spatially resolved epigenomic profiling of single cells in complex tissues

The recent development of spatial omics methods has enabled single-cell profiling of the transcriptome and 3D genome organization with high spatial resolution. Expanding the repertoire of spatial omics tools, a spatially resolved single-cell epigenomics method will accelerate understanding of the spatial regulation of cell and tissue functions. Here, we report a method for spatially resolved epigenomic profiling of single cells using in situ tagmentation and transcription followed by multiplexed imaging. We demonstrated the ability to profile histone modifications marking active promoters, putative enhancers, and silent promoters in individual cells, and generated high-resolution spatial atlas of hundreds of active promoters and putative enhancers in embryonic and adult mouse brains. Our results suggested putative promoter-enhancer pairs and enhancer hubs regulating developmentally important genes. We envision this approach will be generally applicable to spatial profiling of epigenetic modifications and DNA-binding proteins, advancing our understanding of how gene expression is spatiotemporally regulated by the epigenome.

The Role of Vti1a in Biological Functions and Its Possible Role in Nervous System Disorders

Vesicle transport through interaction with t-SNAREs 1A (Vti1a), a member of the N-ethylmaleimide-sensitive factor attachment protein receptor protein family, is involved in cell signaling as a vesicular protein and mediates vesicle trafficking. Vti1a appears to have specific roles in neurons, primarily by regulating upstream neurosecretory events that mediate exocytotic proteins and the availability of secretory organelles, as well as regulating spontaneous synaptic transmission and postsynaptic efficacy to control neurosecretion. Vti1a also has essential roles in neural development, autophagy, and unconventional extracellular transport of neurons. Studies have shown that Vti1a dysfunction plays critical roles in pathological mechanisms of Hepatic encephalopathy by influencing spontaneous neurotransmission. It also may have an unknown role in amyotrophic lateral sclerosis. A VTI1A variant is associated with the risk of glioma, and the fusion product of the VTI1A gene and the adjacent TCF7L2 gene is involved in glioma development. This review summarizes Vti1a functions in neurons and highlights the role of Vti1a in the several nervous system disorders.