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New Insights into Gene Expression Regulation in the Next-Generation Sequencing (NGS) Era

A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Molecular Genetics and Genomics".

Deadline for manuscript submissions: 30 June 2024 | Viewed by 403

Special Issue Editor

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Guest Editor
Department of Pathology, Faculty of Medicine, University of Thessaly, 41500 Larissa, Greece
Interests: urothelial carcinomas genetics and genomics; epigenetics; cancer biology; molecular subtypes; mutations; signaling pathways; miRNAs

Special Issue Information

Dear Colleagues,

Somatic cells exhibit different phenotypes, though they share the same DNA sequences. Gene expression regulation is achieved through transcriptional, post-transcriptional, translational, and post-translational mechanisms. Epigenetic factors modulate gene expression through DNA methylation, histone protein modifications, and RNA-molecule interaction processes. Next-generation sequencing (NGS) is a high-throughput technique that has boosted gene regulation studies. RNA sequencing (RNA-seq) allows transcriptome analysis and provides evidence about gene regulation, alternative splicing, and non-coding RNA molecules. Tissue heterogeneity and the microenvironment also add to the complexity. NGS-based approaches, such as single-cell or spatial RNA sequencing, can evaluate the mRNA expressions of all cells included in a specific microenvironment, providing evidence about cell–cell interactions. Methyl-seq or CHIP-seq NGS approaches will permit epigenome understanding through studies on DNA methylation patterns and histone modifications. The human microbiome is also a key player in gene expression regulation. Thus, the use of the NGS technique in metagenomic studies will highlight the role and mechanisms of microbiome interaction with human host cells.

I propose that the scope of this Special Issue of IJMS include a wide range of studies that use NGS-based approaches to investigate various aspects of gene expression regulation. Submission formats may include research articles, reviews, perspectives, and communications.

Dr. Maria Samara
Guest Editor

Manuscript Submission Information

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  • alternative splicing
  • DNA methylation
  • histone modification
  • RNA sequencing
  • epigenome
  • metagenomics
  • single-cell sequencing
  • spatial sequencing
  • microenvironment
  • microbiome profile

Published Papers (1 paper)

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8 pages, 1877 KiB  
Next-Generation Sequencing of the Human Aqueous Humour Microbiome
by Günther Schlunck, Philip Maier, Barbara Maier, Wolfgang Maier, Sebastian Strempel, Thomas Reinhard and Sonja Heinzelmann
Int. J. Mol. Sci. 2024, 25(11), 6128; https://doi.org/10.3390/ijms25116128 - 1 Jun 2024
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The microbiome of the ocular surface has been characterised, but only limited information is available on a possible silent intraocular microbial colonisation in normal eyes. Therefore, we performed next-generation sequencing (NGS) of 16S rDNA genes in the aqueous humour. The aqueous humour was [...] Read more.
The microbiome of the ocular surface has been characterised, but only limited information is available on a possible silent intraocular microbial colonisation in normal eyes. Therefore, we performed next-generation sequencing (NGS) of 16S rDNA genes in the aqueous humour. The aqueous humour was sampled from three patients during cataract surgery. Air swabs, conjunctival swabs from patients as well as from healthy donors served as controls. Following DNA extraction, the V3 and V4 hypervariable regions of the 16S rDNA gene were amplified and sequenced followed by denoising. The resulting Amplicon Sequence Variants were matched to a subset of the Ribosomal Database Project 16S database. The deduced bacterial community was then statistically analysed. The DNA content in all samples was low (0–1.49 ng/µL) but sufficient for analysis. The main phyla in the samples were Acinetobacteria (48%), Proteobacteria (26%), Firmicutes (14%), Acidobacteria (8%), and Bacteroidetes (2%). Patients’ conjunctival control samples and anterior chamber fluid showed similar patterns of bacterial species containing many waterborne species. Non-disinfected samples showed a different bacterial spectrum than the air swab samples. The data confirm the existence of an ocular surface microbiome. Meanwhile, a distinct intraocular microbiome was not discernible from the background, suggesting the absence of an intraocular microbiome in normal eyes. Full article
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