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Evolution of Non-coding Elements in Genome Biology
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Evolution of Non-coding Elements in Genome Biology

A special issue of Genes (ISSN 2073-4425). This special issue belongs to the section "Population and Evolutionary Genetics and Genomics".

Deadline for manuscript submissions: closed (20 February 2025) | Viewed by 6384

Special Issue Editor

Dr. David Lando

E-Mail Website
Guest Editor
Department of Biochemistry, University of Cambridge, Cambridge, UK
Interests: chromatin structure and function; enhancer–promoter communication; molecular basis of pluripotency

Special Issue Information

Dear Colleagues,

The evolutionary process through which species mutate to change their heritable characteristics over time is one of the most fundamental processes that govern biological life on earth. While some mutational changes occur in gene coding regions, the vast majority occur in the non-coding portion of the genome, which contains many transposable elements and DNA repeats. Recent improvements in DNA sequencing and computational analysis are starting to reveal the role of these regions in the cis-regulation of gene expression. What is becoming apparent is that these changes can alter the binding of transcription factors and their chromatin regulators to change genome organization and function. In addition, genome-wide association studies have shown that a large number of disease-associated variants reside in these noncoding sequences.

With this Special Issue, we will be focussing on the recent advances achieved in our understanding of the evolution of non-coding elements in genome biology. We encourage submissions that discuss novel findings or concepts concerning the structure, function, organisation and expression of genomes in the context of their relationship with either cis-regulatory transposable elements, natural genome diversity or disease progression.

Dr. David Lando
Guest 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 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. Genes 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

  • genome organisation
  • evolution
  • non-coding
  • transposable element
  • chromatin
  • cis-regulatory element
  • enhancer
  • transcription factor

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Published Papers (3 papers)

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Research

27 pages, 5317 KiB  
Article
ARGONAUTE2 Localizes to Sites of Sporocysts in the Schistosome-Infected Snail, Biomphalaria glabrata
by Phong Phan, Conor E. Fogarty, Andrew L. Eamens, Mary G. Duke, Donald P. McManus, Tianfang Wang and Scott F. Cummins
Genes 2024, 15(8), 1023; https://doi.org/10.3390/genes15081023 - 3 Aug 2024
Cited by 1 | Viewed by 1869
Abstract
MicroRNAs (miRNAs) are a class of small regulatory RNA that are generated via core protein machinery. The miRNAs direct gene-silencing mechanisms to mediate an essential role in gene expression regulation. In mollusks, miRNAs have been demonstrated to be required to regulate gene expression [...] Read more.
MicroRNAs (miRNAs) are a class of small regulatory RNA that are generated via core protein machinery. The miRNAs direct gene-silencing mechanisms to mediate an essential role in gene expression regulation. In mollusks, miRNAs have been demonstrated to be required to regulate gene expression in various biological processes, including normal development, immune responses, reproduction, and stress adaptation. In this study, we aimed to establishment the requirement of the miRNA pathway as part of the molecular response of exposure of Biomphalaria glabrata (snail host) to Schistosoma mansoni (trematode parasite). Initially, the core pieces of miRNA pathway protein machinery, i.e., Drosha, DGCR8, Exportin-5, Ran, and Dicer, together with the central RNA-induced silencing complex (RISC) effector protein Argonaute2 (Ago2) were elucidated from the B. glabrata genome. Following exposure of B. glabrata to S. mansoni miracidia, we identified significant expression up-regulation of all identified pieces of miRNA pathway protein machinery, except for Exportin-5, at 16 h post exposure. For Ago2, we went on to show that the Bgl-Ago2 protein was localized to regions surrounding the sporocysts in the digestive gland of infected snails 20 days post parasite exposure. In addition to documenting elevated miRNA pathway protein machinery expression at the early post-exposure time point, a total of 13 known B. glabrata miRNAs were significantly differentially expressed. Of these thirteen B. glabrata miRNAs responsive to S. mansoni miracidia exposure, five were significantly reduced in their abundance, and correspondingly, these five miRNAs were determined to putatively target six genes with significantly elevated expression and that have been previously associated with immune responses in other animal species, including humans. In conclusion, this study demonstrates the central importance of a functional miRNA pathway in snails, which potentially forms a critical component of the immune response of snails to parasite exposure. Further, the data reported in this study provide additional evidence of the complexity of the molecular response of B. glabrata to S. mansoni infection: a molecular response that could be targeted in the future to overcome parasite infection and, in turn, human schistosomiasis. Full article
(This article belongs to the Special Issue Evolution of Non-coding Elements in Genome Biology)
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11 pages, 733 KiB  
Article
Variation of the 3’RR1 HS1.2 Enhancer and Its Genomic Context
by Carla Jodice, Patrizia Malaspina, Bianca Maria Ciminelli, Cristina Martinez-Labarga, Michela Biancolella, Giuseppe Novelli and Andrea Novelletto
Genes 2024, 15(7), 856; https://doi.org/10.3390/genes15070856 - 29 Jun 2024
Cited by 1 | Viewed by 1299
Abstract
In humans, the HS1.2 enhancer in the Ig heavy-chain locus is modular, with length polymorphism. Previous studies have shown the following features for this variation: (i) strong population structuring; (ii) association with autoimmune diseases; and (iii) association with developmental changes in Ig expression. [...] Read more.
In humans, the HS1.2 enhancer in the Ig heavy-chain locus is modular, with length polymorphism. Previous studies have shown the following features for this variation: (i) strong population structuring; (ii) association with autoimmune diseases; and (iii) association with developmental changes in Ig expression. The HS1.2 region could then be considered as a contributor to inter-individual diversity in humoral response in adaptive immunity. We experimentally determined the HS1.2-length class genotype in 72 of the 1000 Genomes CEU cell lines and assigned the HS1.2 alleles to haplotypes defined by 18 landmark SNPs. We also sequenced the variable portion and ~200 bp of the flanking DNA of 34 HS1.2 alleles. Furthermore, we computationally explored the ability of different allelic arrangements to bind transcription factors. Non-random association between HS1.2 and Gm allotypes in the European population clearly emerged. We show a wealth of variation in the modular composition of HS1.2, with five SNPs further contributing to diversity. Longer alleles offer more potential sites for binding but, for same-length alleles, SNP variation creates/destroys potential binding sites. Altogether, the arrangements of modules and SNP alleles both inside and outside HS1.2 denote an organization of diversity far from randomness. In the context of the strong divergence of human populations for this genomic region and the reported disease associations, our results suggest that selective forces shaped the pattern of its diversity. Full article
(This article belongs to the Special Issue Evolution of Non-coding Elements in Genome Biology)
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16 pages, 6601 KiB  
Article
Dynamic Evolution of Repetitive Elements and Chromatin States in Apis mellifera Subspecies
by Nick Panyushev, Max Selitskiy, Vasilina Melnichenko, Egor Lebedev, Larisa Okorokova and Leonid Adonin
Genes 2024, 15(1), 89; https://doi.org/10.3390/genes15010089 - 11 Jan 2024
Cited by 1 | Viewed by 2308
Abstract
In this study, we elucidate the contribution of repetitive DNA sequences to the establishment of social structures in honeybees (Apis mellifera). Despite recent advancements in understanding the molecular mechanisms underlying the formation of honeybee castes, primarily associated with Notch signaling, the [...] Read more.
In this study, we elucidate the contribution of repetitive DNA sequences to the establishment of social structures in honeybees (Apis mellifera). Despite recent advancements in understanding the molecular mechanisms underlying the formation of honeybee castes, primarily associated with Notch signaling, the comprehensive identification of specific genomic cis-regulatory sequences remains elusive. Our objective is to characterize the repetitive landscape within the genomes of two honeybee subspecies, namely A. m. mellifera and A. m. ligustica. An observed recent burst of repeats in A. m. mellifera highlights a notable distinction between the two subspecies. After that, we transitioned to identifying differentially expressed DNA elements that may function as cis-regulatory elements. Nevertheless, the expression of these sequences showed minimal disparity in the transcriptome during caste differentiation, a pivotal process in honeybee eusocial organization. Despite this, chromatin segmentation, facilitated by ATAC-seq, ChIP-seq, and RNA-seq data, revealed a distinct chromatin state associated with repeats. Lastly, an analysis of sequence divergence among elements indicates successive changes in repeat states, correlating with their respective time of origin. Collectively, these findings propose a potential role of repeats in acquiring novel regulatory functions. Full article
(This article belongs to the Special Issue Evolution of Non-coding Elements in Genome Biology)
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