Biology subjects

Xun Gu

Publications and source records attributed to Xun Gu.

3 recordsLinked to original sources

bioRxiv2016

Case study: Paralog diverged features may help reduce off-target effects of drugs

Side effects from targeted drugs is a serious concern. One reason is the nonselective binding of a drug to unintended proteins such as its paralogs, which are highly homologous in sequences and exhibit similar structures and drug-binding pockets. In this study, we analyzed amino acid residues with type-II functional divergence, i.e., sites that are conserved in sequence constraints but differ in physicochemical properties between paralogs, to identify targetable differences between two paralogs. We analyzed paralogous protein receptors in the glucagon-like subfamily, glucagon receptor (GCGR) and glucagon-like peptide-1 receptor (GLP-1R), which are clinically validated drug targets in patients with type 2 diabetes and exhibit divergence in ligands, showing opposing roles in regulating glucose homeostasis. We identified 8 residues related to type-II functional divergence, which are conserved in functional constraints but differ in physicochemical properties between GCGR and GLP-1R. We detected significant enrichment of predicted residues in binding sites of the antagonist MK-0893 to GCGR. We also identified a type-II functional divergence-related residue involved in ligand-specific effects that was critical for agonist-mediated activation of GLP-1R. We describe the important role of type-II functional divergence-related sites in paralog discrimination, enabling the identification of binding sites to reduce undesirable side effects and increase the target specificity of drugs.

Bioinformatics↗

bioRxiv2016

Tissue-Driven Hypothesis of Transcriptome Evolution: An Update

In past decade, many reports have demonstrated that tissues in multi-cellular organisms may play important roles to shape the pattern of genome evolution. The tissue-driven hypothesis was then coined, claiming that tissue-specific factor as the common resource of functional constrain may underlie the positive correlations between tissue expression divergence, sequence divergence, or the expression tolerance of duplication divergence. However, the original version of tissue-driven hypothesis cannot rule out the tissue-specific effect of mutational variance. In this perspective, we solve this problem by modifying the evolutionary model that underlies the tissue expression evolution. Reanalysis of the microarray data reanalysis has revealed the relative importancebetween tissue-specific functional constraints and mutational variances in the tissue evolution. Finally, we outline how to utilize RNA-seq technology to further investigate the tissue expression evolution in the case of multiple tissues and species.

Genetics↗

bioRxiv2015

Genome-wide and single-base resolution DNA methylomes of the Sea Lamprey (Petromyzon marinus) Reveal Gradual Transition of the Genomic Methylation Pattern in Early Vertebrates

In eukaryotes, cytosine methylation is a primary heritable epigenetic modification of the genome that regulates many cellular processes. While the whole-genome methylation pattern has been generally conserved in different eukaryotic groups, invertebrates and vertebrates exhibit two distinct patterns. Whereas almost all CpG sites are methylated in most vertebrates, with the exception of short unmethylated regions call CpG islands, the most frequent pattern in invertebrate animals is mosaic methylation, comprising domains of heavily methylated DNA interspersed with domains that are methylation free. The mechanism by which the genome methylation pattern transited from a mosaic to a global pattern and the role of the one or two-round whole-genome duplication in this transition remain largely elusive, partly owing to the lack of methylome data from early vertebrates. In this study, we used the whole-genome bisulfite-sequencing technology to investigate the genome-wide methylation in three tissues (heart, muscle, and sperm) from the sea lamprey, an extant Agarthan vertebrate. Analyses of methylation level and the extent of CpG dinucleotide depletion of geneencoding, intergenic and promoter regions revealed a gradual increase in the methylation level from invertebrates to vertebrates, with the sea lamprey exhibiting an intermediate position. In addition, the methylation level of the majority of CpGs was intermediate in each sea lamprey tissue, indicating a high level of heterogeneity of methylation status between individual cells. In this regard, we defined the genomic methylation pattern of sea lamprey as \"global genomic DNA intermediate methylation\". The methylation features in different genomic regions, such as the transcription start site (TSS) region of the gene body, exon-intron boundaries, transposons, as well as genes grouping with different expression levels, supported the gradual methylation transition hypothesis. We further discussed that the copy number difference in DNA methylation transferases and the loss of the PWWP domain and/or DNTase domain in DNMT3 sub-family enzymes may have contributed to the methylation pattern transition in early vertebrates. These findings demonstrate an intermediate genomic methylation pattern between invertebrates and jawed vertebrates, providing evidence that supports the hypothesis that methylation patterns underwent a gradual transition from invertebrates (mosaic) to vertebrates (global).

Evolutionary Biology↗