Topical Collection "Feature Papers in Molecular Genetics"

A topical collection in Biomolecules (ISSN 2218-273X). This collection belongs to the section "Molecular Genetics".

Editor

Prof. Dr. Jürg Bähler
E-Mail Website
Collection Editor
Department of Genetics, Evolution & Environment and Institute of Healthy Ageing, University College London, Darwin Building, Gower Street, London WC1E 6BT, UK
Interests: gene regulation; genomics; transcriptomics; non-coding RNAs; genome function and evolution; fission yeast; cellular quiescence and ageing
Special Issues, Collections and Topics in MDPI journals

Topical Collection Information

Dear Colleagues,

This Topical Collection, “Feature Papers in Molecular Genetics”, will bring together high-quality research articles, review articles, and communications on all aspects of molecular genetics. It is dedicated to diverse recent advances in genetics research, as highlighted in the topics below, and comprises a selection of exclusive papers from the Editorial Board Members (EBMs) of the Molecular Genetics Section as well as invited papers from relevant experts. We also welcome established experts in the field to make contributions to this Topical Collection. Please note that all invited papers will be published online once accepted. We aim to represent our Section as an attractive open access publishing platform for molecular genetics research.

Topics include, without being limited to:

    Chromosome biology;
    Epigenetics;
    Gene editing and genetic variants;
    Gene regulation and transcriptomics;
    Genetic assays and methods;
    Genetic screens and gene-function analyses;
    Genome function and evolution;
    Genotype-phenotype relationships;
    Medical genetics and disease biology;
    Molecular evolution;
    Non-coding RNAs;
    Population genetics and complex traits;
    Synthetic biology.

Prof. Dr. Jürg Bähler
Collection Editor

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 collection 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. Biomolecules 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 2100 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.

Published Papers (5 papers)

2022

Jump to: 2021

Article
CAPTURE of the Human U2 snRNA Genes Expands the Repertoire of Associated Factors
Biomolecules 2022, 12(5), 704; https://doi.org/10.3390/biom12050704 - 14 May 2022
Viewed by 265
Abstract
In order to identify factors involved in transcription of human snRNA genes and 3′ end processing of the transcripts, we have carried out CRISPR affinity purification in situ of regulatory elements (CAPTURE), which is deadCas9-mediated pull-down, of the tandemly repeated U2 snRNA genes [...] Read more.
In order to identify factors involved in transcription of human snRNA genes and 3′ end processing of the transcripts, we have carried out CRISPR affinity purification in situ of regulatory elements (CAPTURE), which is deadCas9-mediated pull-down, of the tandemly repeated U2 snRNA genes in human cells. CAPTURE enriched many factors expected to be associated with these human snRNA genes including RNA polymerase II (pol II), Cyclin-Dependent Kinase 7 (CDK7), Negative Elongation Factor (NELF), Suppressor of Ty 5 (SPT5), Mediator 23 (MED23) and several subunits of the Integrator Complex. Suppressor of Ty 6 (SPT6); Cyclin K, the partner of Cyclin-Dependent Kinase 12 (CDK12) and Cyclin-Dependent Kinase 13 (CDK13); and SWI/SNF chromatin remodelling complex-associated SWI/SNF-related, Matrix-associated, Regulator of Chromatin (SMRC) factors were also enriched. Several polyadenylation factors, including Cleavage and Polyadenylation Specificity Factor 1 (CPSF1), Cleavage Stimulation Factors 1 and 2 (CSTF1,and CSTF2) were enriched by U2 gene CAPTURE. We have already shown by chromatin immunoprecipitation (ChIP) that CSTF2—and Pcf11 and Ssu72, which are also polyadenylation factors—are associated with the human U1 and U2 genes. ChIP-seq and ChIP-qPCR confirm the association of SPT6, Cyclin K, and CDK12 with the U2 genes. In addition, knockdown of SPT6 causes loss of subunit 3 of the Integrator Complex (INTS3) from the U2 genes, indicating a functional role in snRNA gene expression. CAPTURE has therefore expanded the repertoire of transcription and RNA processing factors associated with these genes and helped to identify a functional role for SPT6. Full article
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Review
PrimPol: A Breakthrough among DNA Replication Enzymes and a Potential New Target for Cancer Therapy
Biomolecules 2022, 12(2), 248; https://doi.org/10.3390/biom12020248 - 03 Feb 2022
Viewed by 867 | Correction
Abstract
DNA replication can encounter blocking obstacles, leading to replication stress and genome instability. There are several mechanisms for evading this blockade. One mechanism consists of repriming ahead of the obstacles, creating a new starting point; in humans, PrimPol is responsible for carrying out [...] Read more.
DNA replication can encounter blocking obstacles, leading to replication stress and genome instability. There are several mechanisms for evading this blockade. One mechanism consists of repriming ahead of the obstacles, creating a new starting point; in humans, PrimPol is responsible for carrying out this task. PrimPol is a primase that operates in both the nucleus and mitochondria. In contrast with conventional primases, PrimPol is a DNA primase able to initiate DNA synthesis de novo using deoxynucleotides, discriminating against ribonucleotides. In vitro, PrimPol can act as a DNA primase, elongating primers that PrimPol itself sythesizes, or as translesion synthesis (TLS) DNA polymerase, elongating pre-existing primers across lesions. However, the lack of evidence for PrimPol polymerase activity in vivo suggests that PrimPol only acts as a DNA primase. Here, we provide a comprehensive review of human PrimPol covering its biochemical properties and structure, in vivo function and regulation, and the processes that take place to fill the gap-containing lesion that PrimPol leaves behind. Finally, we explore the available data on human PrimPol expression in different tissues in physiological conditions and its role in cancer. Full article
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Article
Regulation of Melanocortin-3 and -4 Receptors by Isoforms of Melanocortin-2 Receptor Accessory Protein 1 and 2
Biomolecules 2022, 12(2), 244; https://doi.org/10.3390/biom12020244 - 02 Feb 2022
Viewed by 548
Abstract
The neural melanocortin receptors (MCRs), melanocortin-3 and -4 receptors (MC3R and MC4R), play essential non-redundant roles in the regulation of energy homeostasis. Interaction of neural MCRs and melanocortin-2 receptor accessory proteins (MRAPs, MRAP1 and MRAP2) is suggested to play pivotal roles in MC3R [...] Read more.
The neural melanocortin receptors (MCRs), melanocortin-3 and -4 receptors (MC3R and MC4R), play essential non-redundant roles in the regulation of energy homeostasis. Interaction of neural MCRs and melanocortin-2 receptor accessory proteins (MRAPs, MRAP1 and MRAP2) is suggested to play pivotal roles in MC3R and MC4R signaling. In the present study, we identified two new human (h) MRAP2 splice variants, MRAP2b (465 bp open reading frame) and MRAP2c (381 bp open reading frame). Human MRAP2s are different in C-termini. We investigated the effects of five isoforms of MRAPs, hMRAP1a, hMRAP1b, hMRAP2a, hMRAP2b, and hMRAP2c, on MC3R and MC4R pharmacology. At the hMC3R, hMRAP1a and hMRAP2c increased and hMRAP1b decreased the cell surface expression. hMRAP1a increased affinity to ACTH. Four MRAPs (hMRAP1a, hMRAP1b, hMRAP2a, and hMRAP2c) decreased the maximal responses in response to α-MSH and ACTH. For hMC4R, hMRAP1a, hMRAP2a, and hMRAP2c increased the cell surface expression of hMC4R. Human MRAP1b significantly increased affinity to ACTH while MRAP2a decreased affinity to ACTH. Human MRAP1a increased ACTH potency. MRAPs also affected hMC4R basal activities, with hMRAP1s increasing and hMRAP2s decreasing the basal activities. In summary, the newly identified splicing variants, hMRAP2b and hMRAP2c, could regulate MC3R and MC4R pharmacology. The two MRAP1s and three MRAP2s had differential effects on MC3R and MC4R trafficking, binding, and signaling. These findings led to a better understanding of the regulation of neural MCRs by MRAP1s and MRAP2s. Full article
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Review
Folic Acid, Folinic Acid, 5 Methyl TetraHydroFolate Supplementation for Mutations That Affect Epigenesis through the Folate and One-Carbon Cycles
Biomolecules 2022, 12(2), 197; https://doi.org/10.3390/biom12020197 - 24 Jan 2022
Cited by 1 | Viewed by 1366
Abstract
Methylation is an essential biochemical mechanism that is central to the transmission of life, and crucially responsible for regulating gametogenesis and continued embryo development. The methylation of DNA and histones drives cell division and regulation of gene expression through epigenesis and imprinting. Brain [...] Read more.
Methylation is an essential biochemical mechanism that is central to the transmission of life, and crucially responsible for regulating gametogenesis and continued embryo development. The methylation of DNA and histones drives cell division and regulation of gene expression through epigenesis and imprinting. Brain development and its maturation also depend on correct lipid methylation, and continued neuronal function depends on biogenic amines that require methylation for their synthesis. All methylation processes are carried out via a methyltransferase enzyme and its unique co-factor S-adenosylmethionine (SAM); the transfer of a methyl group to a target molecule results in the release of SAH (SA homocysteine), and then homocysteine (Hcy). Both of these molecules are toxic, inhibiting methylation in a variety of ways, and Hcy recycling to methionine is imperative; this is achieved via the one carbon cycle, supported by the folates cycle. Folate deficiency causes hyperhomocysteinaemia, with several associated diseases; during early pregnancy, deficiency interferes with closure of the neural tube at the fourth week of gestation, and nutraceutical supplementation has been routinely prescribed to prevent neural tube defects, mainly involving B vitamins, Zn and folates. The two metabolic pathways are subject to single nucleotide polymorphisms that alter their activity/capacity, often severely, impairing specific physiological functions including fertility, brain and cardiac function. The impact of three types of nutraceutical supplements, folic acid (FA), folinic acid (FLA) and 5 Methyl THF (MTHF), will be discussed here, with their positive effects alongside potentially hazardous secondary effects. The issue surrounding FA and its association with UMFA (unmetabolized folic acid) syndrome is now a matter of concern, as UMFA is currently found in the umbilical cord of the fetus, and even in infants’ blood. We will discuss its putative role in influencing the acquisition of epigenetic marks in the germline, acquired during embryogenesis, as well as the role of FA in the management of cancerous disease. Full article
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2021

Jump to: 2022

Review
Genome Editing among Bioethics and Regulatory Practices
Biomolecules 2022, 12(1), 13; https://doi.org/10.3390/biom12010013 - 22 Dec 2021
Viewed by 972
Abstract
In the last decade, genome editing technologies became very effective and several clinical trials have been started in order to use them for treating some genetic diseases. Interestingly, despite more than 50 years of discussion about the frontiers of genetics in human health [...] Read more.
In the last decade, genome editing technologies became very effective and several clinical trials have been started in order to use them for treating some genetic diseases. Interestingly, despite more than 50 years of discussion about the frontiers of genetics in human health and evolution, the debate about the bioethics and the regulatory practices of genome editing is still far from satisfactory answers. This delay results from an excessive emphasis on the effectiveness of the genome editing technologies that is relevant for the regulatory practices, but not at a bioethical level. Indeed, other factors (such as accessibility and acceptability) could make these techniques not accepted at the bioethical level, even in the presence of their 100% effectiveness. Full article
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Planned Papers

The below list represents only planned manuscripts. Some of these manuscripts have not been received by the Editorial Office yet. Papers submitted to MDPI journals are subject to peer-review.

Title: Genome editing among bioethics and regulatory practices
Authors: Mauro Mandrioli; et al.
Affiliation: University of Modena and Reggio Emilia

Title: CAPTURE of the human U2 genes confirms the association of several polyadenylation factors
Authors: Shona Murphy; et al.
Affiliation: Sir William Dunn School of Pathology, University of Oxford, South Park Roads, Oxford, OX1 3RE, U

Title: 5 MTHF instead of folic acids
Authors: Pr Yves MENEZO et al
Affiliation: Intl ART Scientific adviser, Laboratoire Clement PARIS

Title: To be determined
Authors: Wolf-Dietrich Heyer; et al
Affiliation: University of California

Title: To be determined
Authors: Jungsu Kim; et al
Affiliation: Indiana University School of Medicine

Title: TMEM16x in genetic diseases
Authors: Paolo Scudieri; et al
Affiliation: U.O.C. Genetica Medica, IRCCS Istituto Giannina Gaslini, 16147 Genova, Italy

Title: To be determined
Authors: Michael Ibba; et al
Affiliation: Ohio State University

Title: Functional characterization of a novel gene involved in a genetic neurodevelopmental disorder
Authors: Paolo Scudieri; et al.
Affiliation: U.O.C. Genetica Medica, IRCCS Istituto Giannina Gaslini, 16147 Genova, Italy

Title: To be determined
Authors: Yves Menezo; et al.
Affiliation: Laboratoire Clement, Paris, France

Title: The artificial intelligence (AI)-powered analytic approaches in precision cancer genomics
Authors: Dr. Meng-Ru Shen; et al.
Affiliation: National Cheng Kung University Hospital

Title: Mutations in G protein-coupled receptor-specific molecular chaperones and disease
Authors: Dr. Ya Xiong Tao; et al.
Affiliation: Auburn University College of Veterinary Medicinedisabled, Auburn, United States

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