Biology subjects

Hwang, I.-S.

Publications and source records attributed to Hwang, I.-S..

3 recordsLinked to original sources

bioRxiv2026

A novel imprinting cluster at the porcine CRSP complex locus defines a species-specific imprinted domain

BackgroundGenomic imprinting is an epigenetic phenomenon that results in parent-of-origin-specific gene expression and has been extensively characterized in mice and humans. However, in pigs, imprinting has been investigated primarily through analyses of orthologs of known imprinted genes in mice and humans. The objective of this study was to examine DNA methylation status and gene expression at a porcine locus containing newly identified imprinted calcitonin receptor-stimulating peptide (CRSP)-encoding genes, to compare orthologous loci in mice and humans, and to investigate a potential underlying mechanism. ResultsAnalyses of differentially methylated regions (DMRs) between porcine parthenogenetic embryos and biparental controls revealed multiple parental DMRs at a locus we term the CRSP complex locus, which harbors CRSP-encoding genes that likely arose through gene duplication. In contrast, orthologous genomic intervals in mice and humans exhibited unmethylated promoters and lacked evidence of imprinting. Consistently, CRSP-encoding genes in pigs showed parent-of-origin-specific monoallelic expression, whereas genes within the orthologous locus in mice and humans were biallelically expressed. Further analysis indicated that porcine CRSP promoters are embedded within oocyte-expressed alternative transcripts and co-occurred with DNA methylation, suggesting a transcription-dependent imprinting mechanism. ConclusionsOur comparative analyses identified CRSP-encoding genes at the porcine CRSP complex locus as novel imprinted genes, indicating species-specific evolution of this imprinted domain. The results further suggest that lineage-specific gene duplication may have contributed to the emergence of imprinting at this locus.

genomics↗

bioRxiv2024

Surface-mediated Bacteriophage Defense Incurs Fitness Tradeoffs for Interbacterial Antagonism

Bacteria in polymicrobial habitats are constantly exposed to biotic threats from bacteriophages (or "phages"), antagonistic bacteria, and predatory eukaryotes. These antagonistic interactions play crucial roles in shaping the evolution and physiology of bacteria. To survive, bacteria have evolved mechanisms to protect themselves from such attacks, but the fitness costs of resisting one threat and rendering bacteria susceptible to others remain unappreciated. Here, we examined the fitness consequences of phage resistance in Salmonella enterica, revealing that phage-resistant variants exhibited significant fitness loss upon co-culture with competitor bacteria. These phage-resistant strains display varying degrees of lipopolysaccharide (LPS) deficiency and increased susceptibility to contact-dependent interbacterial antagonism, such as the type VI secretion system (T6SS). Utilizing mutational analyses and atomic force microscopy, we show that the long-modal length O-antigen of LPS serves as a protective barrier against T6SS-mediated intoxication. Notably, this competitive disadvantage can also be triggered independently by phages possessing LPS-targeting endoglycosidase in their tail spike proteins, which actively cleave the O- antigen upon infection. Our findings reveal two distinct mechanisms of phage-mediated LPS modifications that modulate interbacterial competition, shedding light on the dynamic microbial interplay within mixed populations.

microbiology↗

bioRxiv2024

Lineage-specific genomic imprinting in the ZNF791 locus

BackgroundGenomic imprinting is the primary epigenetic phenomenon that results in parent-of-origin effects on mammalian development and growth. Research on genomic imprinting in domesticated animals has lagged due to a primary focus on orthologous imprinted genes. This emphasis has limited the discovery of imprinted genes specific to livestock. To identify genomic imprinting in pigs, we generated parthenogenetic porcine embryos alongside biparental normal embryos, and then performed whole-genome bisulfite sequencing and RNA sequencing on these samples. ResultsIn our analyses, we discovered a maternally methylated differentially methylated region within the orthologous ZNF791 locus in pigs. Additionally, we identified both a major imprinted isoform of the ZNF791-like gene and an unannotated antisense transcript that has not been previously annotated. Importantly, our comparative analyses of the orthologous ZNF791 gene in various eutherian mammals, including humans, non-human primates, rodents, artiodactyls, and dogs, revealed that this gene is subjected to genomic imprinting exclusively in domesticated animals, thereby highlighting lineage-specific imprinting. Furthermore, we explored the potential mechanisms behind the establishment of maternal DNA methylation imprints in porcine and bovine oocytes, supporting the notion that integration of transposable elements, active transcription, and histone modification may collectively contribute to the methylation of embedded intragenic CpG island promoters. ConclusionsOur findings convey fundamental insights into molecular and evolutionary aspects of livestock species-specific genomic imprinting and provide critical agricultural implications.

genetics↗