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: 30 October 2024 | Viewed by 1006

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

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Life is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2600 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

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

Published Papers (1 paper)

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Research

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
Viewed by 805
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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