The Ser19Stop single nucleotide polymorphism (SNP) of human PHYHIPL affects the cerebellum in mice

Sugimoto, Hisako; Horii, Takuro; Hirota, Jun Na; Sano, Yoshitake; Shinoda, Yo; Konno, Ayumu; Hirai, Hirokazu; Ishizaki, Yasuki; Hirase, Hajime; Hatada, Izuho; Furuichi, Teiichi; Sadakata, Tetsushi

doi:10.1186/s13041-021-00766-x

Cited by 3 publications

(3 citation statements)

References 29 publications

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“…S15E ). Although the exact function of the gene PHYHIPL in the human brain is not fully understood, studies have suggested its potential association with cerebellum-related disorders in mice (45). Therefore, further understanding of the transcriptional regulation of this gene is meaningful for subsequent research.…”

Section: Resultsmentioning

confidence: 99%

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Uncovering topologically associating domains from three-dimensional genome maps with TADGATE

Dang,

Zhang,

Dong

et al. 2024

Preprint

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Topologically associating domains (TADs) emerge as indispensable units in three-dimensional (3D) genome organization, playing a critical role in gene regulation. However, accurately identifying TADs from sparse chromatin contact maps and exploring the structural and functional elements within TADs remain challenging. To this end, we develop a graph attention auto-encoder, TADGATE, to accurately identify TADs even from ultra-sparse contact maps and generate the imputed maps while preserving or enhancing the underlying topological structures. TADGATE can capture specific attention patterns, pointing to two types of units with different characteristics in TADs. Moreover, we find that the organization of TADs is closely associated with chromatin compartmentalization, and TAD boundaries in different compartmental environments exhibit distinct biological properties. We also utilize a two-layer Hidden Markov Model to functionally annotate the TADs and their internal regions, revealing the overall properties of TADs and the distribution of the structural and functional elements within TADs. At last, we apply TADGATE to highly sparse and noisy Hi-C contact maps from 21 human tissues or cell lines, enhancing the clarity of TAD structures, investigating the nature of conserved and cell type-specific boundaries, and unveiling the cell type-specific transcriptional regulatory mechanisms associated with topological domains.

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Section: Resultsmentioning

confidence: 99%

Section: Deciphering Tads In the Very Noisy And Sparse Contact Maps O...mentioning

confidence: 99%

Uncovering topologically associating domains from three-dimensional genome maps with TADGATE

Dang,

Zhang,

Dong

et al. 2024

Preprint

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“…Pkd1l1 participates in regulating ciliary drive during development, and plays a key role in establishing left-right asymmetry in vertebrates (Field et al 2011). Phyhipl affects the morphology and signal transduction of Purkinje cells (PC) in cerebellum, which is related to the motor learning ability of organisms (Sugimoto et al 2021). sp8b takes part in the Wnt signaling pathway and affects neural posteriorization during the neural development stage (Mohanty 2017).…”

Section: Discussionmentioning

confidence: 99%

Multi-omics analysis unravels the underlying mechanisms of the escape response of the common strain black carp

Xu,

Dong,

Sewo

et al. 2024

Preprint

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Reducing the escape response of fish during the aquaculture has important economic value and ecological safety significance. This study takes the common strain black carp (Cyprinus carpio var. baisenensis), which is known for its low-escape response, as the main research object. Through a simulated flood experiment, the common strain black carps were divided into the low-escape (BL) group and the high-escape (BH) group. Multi-omics techniques:transcriptome sequencing, LS-MS/MS detection, and 16s sequencing were used to analyze the differences in brain gene transcription levels, liver metabolites, and intestinal microbiota composition between the two groups. In addition, in order to reduce false positives generated by transcriptome experiments, Jian carps (Cyprinus carpio var. Jian) were also grouped into the low-escape (JL) group and the high-escape (JH) group and subjected to transcriptome analysis. According to the differentially expressed genes (DEGs) analysis, 18 DEGs were obtained from both the common strain black carp and Jian carp. Except for the MAP6 gene, which was significantly highly expressed, the remaining 17 genes showed significantly low expression in the BL group, which were almost related to signal transduction, and brain tissue and neuronal development. The results of KEGG signaling pathway annotation, KOG functional annotation, and topGO enrichment analysis showed that there were significant differences in signal transduction between the BL and BH groups, especially in the gama aminobutyric acid (GABA) signaling pathway. The detection of liver metabolites showed that there were differences in tryptophan metabolism between the BL and BH groups of the common strain black carp, with higher tryptophan content in the liver of the BL group fish. This study suggests that the brain activity and development of low-escape fish may be lower than that of high-escape fish. Meanwhile, differences in the brain's GABA signaling pathway and the liver's tryptophan metabolismmay also affect fish's escape response. This study accumulates experimental foundation of fish escape response, and provides a new insight into breeding low-escape fish and developing novel strategies to reduce escape responses during aquaculture.

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Multi-omics analysis unravels the underlying mechanisms of the escape response of the common strain black carp (Cyprinus carpio var. baisenensis)

Xu,

Dong,

Sewo

et al. 2024

Aquacult Int

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The Ser19Stop single nucleotide polymorphism (SNP) of human PHYHIPL affects the cerebellum in mice

Cited by 3 publications

References 29 publications

Uncovering topologically associating domains from three-dimensional genome maps with TADGATE

Uncovering topologically associating domains from three-dimensional genome maps with TADGATE

Multi-omics analysis unravels the underlying mechanisms of the escape response of the common strain black carp

Multi-omics analysis unravels the underlying mechanisms of the escape response of the common strain black carp (Cyprinus carpio var. baisenensis)

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