Recent Advances in Functional Genomics

A special issue of Life (ISSN 2075-1729). This special issue belongs to the section "Genetics and Genomics".

Deadline for manuscript submissions: 31 December 2025 | Viewed by 4830

Special Issue Editors


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Guest Editor
Department of Molecular Biology and Genetics, Democritus University of Thrace, Dragana, 68100 Alexandroupolis, Greece
Interests: biochemistry; drosophila; metabolism; nuclear pores and disease; proteomics

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Guest Editor
Department of Soil, Plants and Food Sciences, Faculty of Agricultural Science, University of Bari “Aldo Moro”, 70126 Bari, Italy
Interests: genotyping by sequencing; olive germplasm; grapevine; genetic diversity; functional genomics; molecular polymorphism
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Special Issue Information

Dear Colleagues,

For more than two decades, functional genomics has been attempting to unravel the biological functions hidden in the genomes. Most recently, studies have aimed to develop models to link genotype to phenotype, in the context of disease and treatment. From this perspective, functional genomics covers the areas of gene expression profiling, epigenomics, transcriptomics, proteomics, metabolomics and phenomics studies as well as chromatin profiling, epigenome editing, DNA–protein and protein–protein interaction networks. Contributions to this Special Issue should be original research or review articles. Single-cell-omics studies are particularly welcome.

Topics will include but are not limited to the following:

  • Chromatin profiling;
  • CRISPR screens;
  • Crop genomics;
  • Epigenome editing;
  • Epigenomics;
  • Interactomes;
  • Metagenomics;
  • Pharmacogenomics;
  • Phenomics.

Dr. Katerina R. Katsani
Dr. Cinzia Montemurro
Guest Editors

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Keywords

  • chromatin profiling
  • CRISPR screens
  • crop genomics
  • epigenome editing
  • epigenomics
  • interactomes
  • metagenomics
  • pharmacogenomics
  • phenomics

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Published Papers (2 papers)

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Research

15 pages, 5970 KiB  
Article
Epigenetic Modulation Directs Recovery Post LASIK and SMILE Surgery: An Experimental Study
by Rohit Shetty, Pooja Khamar, Ramaraj Kannan, Puja Thacker, Nimisha Rajiv Kumar, Arkasubhra Ghosh and Vrushali Deshpande
Life 2025, 15(2), 246; https://doi.org/10.3390/life15020246 - 6 Feb 2025
Cited by 1 | Viewed by 768
Abstract
Purpose: refractive surgery, such as LASIK and SMILE, induces a wound healing response that leads to significant corneal stromal remodeling. We have shown that the protein profile in the stroma changes dramatically immediately post-surgery. However, the methylation status of the DNA post-refractive surgery [...] Read more.
Purpose: refractive surgery, such as LASIK and SMILE, induces a wound healing response that leads to significant corneal stromal remodeling. We have shown that the protein profile in the stroma changes dramatically immediately post-surgery. However, the methylation status of the DNA post-refractive surgery remains unknown. Design/Participants: DNA methylation study. Refractive surgery (SMILE/LASIK) performed on donor eye globes. Method: we investigated the epigenetic changes post-surgery in relation to long term ECM remodeling in an experimental ex vivo study design. Donor globes (n = 19) were obtained from the eye bank. Three globes served as non-surgical controls while SMILE (-6DS) and LASIK surgery (-6DS) were performed on eight globes each and incubated for 3 days and 2 weeks (n = 4 per group per time point). Here, we compared the DNA methylation landscapes of LASIK and SMILE stroma using the Illumina Infinium Human Methylation 850 EPIC array (HM850). Results: significant changes in DNA methylation patterns were observed post-operatively in both LASIK and SMILE groups. Specific genes involved in the activation of actin cytoskeleton and inflammation (smad3, prkca and ssh2) showed hypomethylation in LASIK after 2 weeks and LASIK SMILE after 3 days, respectively, suggesting their active role in corneal repair. The genes (gaa, gstm1, mgat1, galnt9 and galnt5) involved in sphingolipid metabolism and mucin biosynthesis showed hypomethylation in SMILE after 3 days. Conclusions: our results suggest that altered DNA methylation patterns may have relevance to the development of complications of haze post-refractive surgery. It also presents the opportunity to utilize drugs that regulate chromatin remodeling for optimal outcomes. Full article
(This article belongs to the Special Issue Recent Advances in Functional Genomics)
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17 pages, 4671 KiB  
Article
RNA-Seq of an LPS-Induced Inflammation Model Reveals Transcriptional Profile Patterns of Inflammatory Processes
by Kisung Sheen, Seokho Myung, Dong-Min Lee, Sanghyeon Yu, Yueun Choi, Taeyoon Kim, Jihan Kim, Sang-Gu Ji, Myung-Seo Kim, Wonnam Kim, Yoonsung Lee, Man S. Kim and Yeon-Cheol Park
Life 2024, 14(5), 558; https://doi.org/10.3390/life14050558 - 26 Apr 2024
Cited by 1 | Viewed by 3089
Abstract
The LPS-induced inflammation model is widely used for studying inflammatory processes due to its cost-effectiveness, reproducibility, and faithful representation of key hallmarks. While researchers often validate this model using clinical cytokine markers, a comprehensive understanding of gene regulatory mechanisms requires extending investigation beyond [...] Read more.
The LPS-induced inflammation model is widely used for studying inflammatory processes due to its cost-effectiveness, reproducibility, and faithful representation of key hallmarks. While researchers often validate this model using clinical cytokine markers, a comprehensive understanding of gene regulatory mechanisms requires extending investigation beyond these hallmarks. Our study leveraged multiple whole-blood bulk RNA-seq datasets to rigorously compare the transcriptional profiles of the well-established LPS-induced inflammation model with those of several human diseases characterized by systemic inflammation. Beyond conventional inflammation-associated systems, we explored additional systems indirectly associated with inflammatory responses (i.e., ISR, RAAS, and UPR) using a customized core inflammatory gene list. Our cross-condition-validation approach spanned four distinct conditions: systemic lupus erythematosus (SLE) patients, dengue infection, candidemia infection, and staphylococcus aureus exposure. This analysis approach, utilizing the core gene list aimed to assess the model’s suitability for understanding the gene regulatory mechanisms underlying inflammatory processes triggered by diverse factors. Our analysis resulted in elevated expressions of innate immune-associated genes, coinciding with suppressed expressions of adaptive immune-associated genes. Also, upregulation of genes associated with cellular stresses and mitochondrial innate immune responses underscored oxidative stress as a central driver of the corresponding inflammatory processes in both the LPS-induced and other inflammatory contexts. Full article
(This article belongs to the Special Issue Recent Advances in Functional Genomics)
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