Evolution and Origin of Genomes

A special issue of Life (ISSN 2075-1729). This special issue belongs to the section "Origin of Life".

Deadline for manuscript submissions: closed (31 October 2017)

Special Issue Editor


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Guest Editor
Department of Evolutionary and Environmental Biology, The Institute of Evolution, University of Haifa, Haifa, Israel
Interests: DNA structure; chromatin; nucleosome positioning; bioinformatics; multiple alignment; ranking; genomics; evolutionary microbiology; COVID-19
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Special Issue Information

Dear Colleagues,

The present Special Issue of Life is devoted to a relatively new field of science, Evolutionary Genomics. In principle, we welcome all kind of manuscripts related to any question that can be asked about the evolution of genomes, especially prokaryotic genomes. Here are some examples:

  • Which factors affect the size of prokaryotic genomes during evolution?
  • Why do some prokaryotes have more paralogs than expected?
  • Why do some species have more coding DNA (that is, more genes or longer genes) than other species?
  • Why are some genes unique to each species, while usually genes are common to many species?
  • When have genomic changes occurred?
  • What is the origin of Mycoplasmas?
  • How should we describe the evolution of viruses?
  • Can we predict emerging viruses?
  • What are the new facts regarding the role of viruses in the evolution of their hosts?

Prof. Dr. Alexander Bolshoy
Guest Editor

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Keywords

  • gene structure evolution
  • GC-content
  • number of paralogs
  • gene length
  • origin of ORFans
  • gene duplication
  • bacterial sex
  • archaeal chromatin

Published Papers (1 paper)

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Research

15 pages, 4367 KiB  
Article
The Diverging Routes of BORIS and CTCF: An Interactomic and Phylogenomic Analysis
by Kamel Jabbari, Peter Heger, Ranu Sharma and Thomas Wiehe
Life 2018, 8(1), 4; https://doi.org/10.3390/life8010004 - 30 Jan 2018
Cited by 8 | Viewed by 5248
Abstract
The CCCTC-binding factor (CTCF) is multi-functional, ubiquitously expressed, and highly conserved from Drosophila to human. It has important roles in transcriptional insulation and the formation of a high-dimensional chromatin structure. CTCF has a paralog called “Brother of Regulator of Imprinted Sites” (BORIS) or [...] Read more.
The CCCTC-binding factor (CTCF) is multi-functional, ubiquitously expressed, and highly conserved from Drosophila to human. It has important roles in transcriptional insulation and the formation of a high-dimensional chromatin structure. CTCF has a paralog called “Brother of Regulator of Imprinted Sites” (BORIS) or “CTCF-like” (CTCFL). It binds DNA at sites similar to those of CTCF. However, the expression profiles of the two proteins are quite different. We investigated the evolutionary trajectories of the two proteins after the duplication event using a phylogenomic and interactomic approach. We find that CTCF has 52 direct interaction partners while CTCFL only has 19. Almost all interactors already existed before the emergence of CTCF and CTCFL. The unique secondary loss of CTCF from several nematodes is paralleled by a loss of two of its interactors, the polycomb repressive complex subunit SuZ12 and the multifunctional transcription factor TYY1. In contrast to earlier studies reporting the absence of BORIS from birds, we present evidence for a multigene synteny block containing CTCFL that is conserved in mammals, reptiles, and several species of birds, indicating that not the entire lineage of birds experienced a loss of CTCFL. Within this synteny block, BORIS and its genomic neighbors seem to be partitioned into two nested chromatin loops. The high expression of SPO11, RAE1, RBM38, and PMEPA1 in male tissues suggests a possible link between CTCFL, meiotic recombination, and fertility-associated phenotypes. Using the 65,700 exomes and the 1000 genomes data, we observed a higher number of intergenic, non-synonymous, and loss-of-function mutations in CTCFL than in CTCF, suggesting a reduced strength of purifying selection, perhaps due to less functional constraint. Full article
(This article belongs to the Special Issue Evolution and Origin of Genomes)
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