Biomedical subjects

Yucheng Xu

Publications and source records attributed to Yucheng Xu.

4 recordsLinked to original sources

PubMed2025

SIGEL: a context-aware genomic representation learning framework for spatial genomics analysis.

Spatial transcriptomics (ST) integrates spatial information into genomics, yet methods for generating spatially-informed gene representations are limited and computationally intensive. We present SIGEL, a cost-effective framework that derives gene manifolds from ST data by exploiting spatial genomic context. The resulting SIGEL-generated gene representations (SGRs) are context-aware, biologically meaningful, and robust across samples, making them highly effective for key downstream tasks, including imputing missing genes, detecting spatial expression patterns, identifying disease-related genes and interactions, and improving spatial clustering. Extensive experiments across diverse ST datasets validate SIGEL's effectiveness and highlight its potential in advancing spatial genomics research.

Genomics↗

PubMed2007

Physical dissection of the CCAAT/enhancer-binding protein alpha in regulating the mouse amelogenin gene.

The amelogenin gene is tightly regulated at the temporal and spatial level in accord with the developmental requirement for tooth formation. Previous studies have shown that CCAAT/enhancer-binding protein alpha (C/EBPalpha) is a transactivator of the mouse X-chromosomal amelogenin gene. C/EBPalpha contains four highly conserved regions (CR) named CR1, CR2, CR3, and CR4. Transient transfection assays showed that CR2 in isolation had an exceptional capacity to enhance transcription from the 2.3 kb mouse amelogenin promoter. The remaining conserved regions of C/EBPalpha, either in isolation or in selected combinations, were less effective in amelogenin transactivation than the full length C/EBPalpha. Msx2 has previously been shown to antagonize C/EBPalpha through protein-protein interactions with C/EBPalpha, and the carboxyl-terminus of Msx2 is required for protein-protein interactions. Co-immunoprecipitation analyses identified that the carboxyl-terminal domain (residues 218-359) of C/EBPalpha is required for the C/EBPalpha-Msx2 protein-protein interactions.

Ameloblasts↗

PubMed2006

NF-Y and CCAAT/enhancer-binding protein alpha synergistically activate the mouse amelogenin gene.

Amelogenin is the major protein component of the forming enamel matrix. In situ hybridization revealed a periodicity for amelogenin mRNA hybridization signals ranging from low to high transcript abundance on serial sections of developing mouse teeth. This in vivo observation led us to examine the amelogenin promoter for the activity of transcription factor(s) that account for this expression aspect of the regulation for the amelogenin gene. We have previously shown that CCAAT/enhancer-binding protein alpha (C/EBPalpha) is a potent transactivator of the mouse X-chromosomal amelogenin gene acting at the C/EBPalpha cis-element located in the -70/+52 minimal promoter. The minimal promoter contains a reversed CCAAT box (-58/-54) that is four base pairs downstream from the C/EBPalpha binding site. Similar to the C/EBPalpha binding site, the integrity of the reversed CCAAT box is also required for maintaining the activity of the basal promoter. We therefore focused on transcription factors that interact with the reversed CCAAT box. Using electrophoretic mobility shift assays we demonstrated that NF-Y was directly bound to this reversed CCAAT site. Co-transfection of C/EBPalpha and NF-Y synergistically increased the promoter activity. In contrast, increased expression of NF-Y alone had only marginal effects on the promoter. A dominant-negative DNA binding-deficient NF-Y mutant (NF-YAm29) dramatically decreased the promoter activity both in the absence or presence of exogenous expression of C/EBPalpha. We identified protein-protein interactions between C/EBPalpha and NF-Y by a co-immunoprecipitation analysis. These results suggest that C/EBPalpha and NF-Y synergistically activate the mouse amelogenin gene and can contribute to its physiological regulation during amelogenesis.

Amelogenin↗

PubMed2006

Transcription factor sumoylation and factor YY1 serve to modulate mouse amelogenin gene expression.

Amelogenin proteins are essential in the control of enamel biomineralization and the amelogenin gene therefore is spatiotemporally regulated to ensure proper amelogenin protein expression. In this study, we examined the role of sumoylation to alter CCAAT/enhancer-binding protein alpha (C/EBPalpha) activity, and performed a search using a protein/DNA array system for other proteins that act co-operatively with C/EBPalpha to alter amelogenin expression. We observed that C/EBPalpha was modified by sumoylation, and that this modification played an indirect inhibitory role on the regulation of C/EBPalpha activity which appeared to act through other transcription factors. The protein/DNA array allowed us to single out the transcription factor, YY1, which acts in the absence of direct DNA binding to repress both the basal amelogenin promoter activity and C/EBPalpha-mediated transactivation. Taken together, these pathways may account for part of the physiological modulation of the amelogenin gene expression in accordance with tooth developmental and enamel biomineralization requirements.

Amelogenesis↗