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: 25 August 2024 | Viewed by 1414

Special Issue Editor


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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

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Keywords

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

Published Papers (1 paper)

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Research

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
Viewed by 1100
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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