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Editorial Board Members’ Collection Series: Human Traits and Genomics
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Editorial Board Members’ Collection Series: Human Traits and Genomics

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: 31 July 2024 | Viewed by 413

Special Issue Editors

Dr. Giovanni Malerba

E-Mail Website
Guest Editor
GM Lab, Department of Neurosciences, Biomedicine and Movement Sciences, University of Verona, 37134 Verona, Italy
Interests: genomics and transcriptomics of Mendelian and complex traits; association and Linkage analyses; statistical genetics and bioinformatics
Special Issues, Collections and Topics in MDPI journals
Prof. Dr. Lidia Larizza

E-Mail Website
Guest Editor
Experimental Research Laboratory of Medical Cytogenetics and Molecular Genetics, IRCCS Istituto Auxologico Italiano, Via Ariosto 13, 20145 Milan, Italy
Interests: rare disorders of chromatin regulators; Rubinstein-Taybi and related syndromes of the epigenetic machinery; chromosomal/genomic instability syndromes with cancer predisposition; imprinting disorders affecting growth; neurodevelopmental imprinting disorders; genomic disorders; MARK4 gene; c-kit gene
Special Issues, Collections and Topics in MDPI journals
Prof. Dr. Salvatore Saccone

E-Mail Website
Guest Editor
Department Biological, Geological and Environmental Sciences, University of Catania, 95124 Catania, Italy
Interests: genetics; genomics; molecular cytogenetics; chromosomes; nuclear chromatin organization; evolutionary genetics; developmental genetics; forensic genetics; environmental mutagenesis; epigenetics
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Studies of the genetic component that is associated with human traits rely on a variety of strategies encompassing case–control and linkage (family-based) designs, along with the integration of evolutionary models to assess the likelihood of different classes of mutations. Despite the advances in genomic sequencing technology, a significant portion of the genetic causes of rare and common traits remain elusive, as functional variants often extend beyond coding regions; this poses challenges to identification. The availability of new data and tools, such as the telomere-to-telomere reference sequence of the human genome, the introduction of a human pangenome reflecting the haplotypic diversity of a population, and the utilization of cutting-edge technologies for genome analysis, such as long-read sequencing technology, single-cell sequencing, and the introduction of deep learning methods to extract knowledge from genomic data, offer new dimensions with which to unravel the molecular basis associated with trait inheritance and development in humans. This collection series aims to gather papers illustrating the latest and most innovative approaches in genetic data analysis for human traits. These approaches aim to uncover the patterns that associate genomic profiles with Mendelian or complex traits, thus contributing to a deeper understanding of the intricate mechanisms that govern trait inheritance in the human population.

Dr. Giovanni Malerba
Prof. Dr. Lidia Larizza
Prof. Dr. Salvatore Saccone
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. International Journal of Molecular Sciences is an international peer-reviewed open access semimonthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. There is an Article Processing Charge (APC) for publication in this open access journal. For details about the APC please see here. 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

  • genetic data analysis
  • genomic profiling
  • trait inheritance
  • DNA and RNA sequencing approaches
  • deep learning methods

Published Papers (1 paper)

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Research

15 pages, 3730 KiB  
Article
The Chromatin Organization Close to SNP rs12913832, Involved in Eye Color Variation, Is Evolutionary Conserved in Vertebrates
by Desiree Brancato, Francesca Bruno, Elvira Coniglio, Valentina Sturiale, Salvatore Saccone and Concetta Federico
Int. J. Mol. Sci. 2024, 25(12), 6602; https://doi.org/10.3390/ijms25126602 - 15 Jun 2024
Viewed by 240
Abstract
The most significant genetic influence on eye color pigmentation is attributed to the intronic SNP rs12913832 in the HERC2 gene, which interacts with the promoter region of the contiguous OCA2 gene. This interaction, through the formation of a chromatin loop, modulates the transcriptional [...] Read more.
The most significant genetic influence on eye color pigmentation is attributed to the intronic SNP rs12913832 in the HERC2 gene, which interacts with the promoter region of the contiguous OCA2 gene. This interaction, through the formation of a chromatin loop, modulates the transcriptional activity of OCA2, directly affecting eye color pigmentation. Recent advancements in technology have elucidated the precise spatial organization of the genome within the cell nucleus, with chromatin architecture playing a pivotal role in regulating various genome functions. In this study, we investigated the organization of the chromatin close to the HERC2/OCA2 locus in human lymphocyte nuclei using fluorescence in situ hybridization (FISH) and high-throughput chromosome conformation capture (Hi-C) data. The 3 Mb of genomic DNA that belonged to the chromosomal region 15q12-q13.1 revealed the presence of three contiguous chromatin loops, which exhibited a different level of compaction depending on the presence of the A or G allele in the SNP rs12913832. Moreover, the analysis of the genomic organization of the genes has demonstrated that this chromosomal region is evolutionarily highly conserved, as evidenced by the analysis of syntenic regions in species from other Vertebrate classes. Thus, the role of rs12913832 variant is relevant not only in determining the transcriptional activation of the OCA2 gene but also in the chromatin compaction of a larger region, underscoring the critical role of chromatin organization in the proper regulation of the involved genes. It is crucial to consider the broader implications of this finding, especially regarding the potential regulatory role of similar polymorphisms located within intronic regions, which do not influence the same gene by modulating the splicing process, but they regulate the expression of adjacent genes. Therefore, caution should be exercised when utilizing whole-exome sequencing for diagnostic purposes, as intron sequences may provide valuable gene regulation information on the region where they reside. Thus, future research efforts should also be directed towards gaining a deeper understanding of the precise mechanisms underlying the role and mode of action of intronic SNPs in chromatin loop organization and transcriptional regulation. Full article
(This article belongs to the Special Issue Editorial Board Members’ Collection Series: Human Traits and Genomics)
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