Functional Diversification of Chromatin on Rapid Evolutionary Timescales

2021 ◽  
Vol 55 (1) ◽  
pp. 401-425
Author(s):  
Cara L. Brand ◽  
Mia T. Levine
Keyword(s):  
Close Relative ◽  
Dna Repeats ◽  
Selfish Genetic Elements ◽  
Cellular Processes ◽  
Chromosome Transmission ◽  
Intragenomic Conflict ◽  
Dna Repeat ◽  
Chromatin Proteins ◽  
Species Specific ◽  
New Research

Repeat-enriched genomic regions evolve rapidly and yet support strictly conserved functions like faithful chromosome transmission and the preservation of genome integrity. The leading resolution to this paradox is that DNA repeat–packaging proteins evolve adaptively to mitigate deleterious changes in DNA repeat copy number, sequence, and organization. Exciting new research has tested this model of coevolution by engineering evolutionary mismatches between adaptively evolving chromatin proteins of one species and the DNA repeats of a close relative. Here, we review these innovative evolution-guided functional analyses. The studies demonstrate that vital, chromatin-mediated cellular processes, including transposon suppression, faithful chromosome transmission, and chromosome retention depend on species-specific versions of chromatin proteins that package species-specific DNA repeats. In many cases, the ever-evolving repeats are selfish genetic elements, raising the possibility that chromatin is a battleground of intragenomic conflict.

scholarly journals Chromosome Evolution in the Thermotogales: Large-Scale Inversions and Strain Diversification of CRISPR Sequences

2006 ◽  
Vol 188 (7) ◽  
pp. 2364-2374 ◽  
Author(s):  
Robert T. DeBoy ◽  
Emmanuel F. Mongodin ◽  
Joanne B. Emerson ◽  
Karen E. Nelson
Keyword(s):  
Sequence Analysis ◽  
Large Scale ◽  
Thermotoga Maritima ◽  
Chromosomal Rearrangements ◽  
Pcr Amplification ◽  
Trna Genes ◽  
Thermotoga Neapolitana ◽  
Dna Repeats ◽  
Dna Rearrangements ◽  
Dna Repeat

ABSTRACT In the present study, the chromosomes of two members of the Thermotogales were compared. A whole-genome alignment of Thermotoga maritima MSB8 and Thermotoga neapolitana NS-E has revealed numerous large-scale DNA rearrangements, most of which are associated with CRISPR DNA repeats and/or tRNA genes. These DNA rearrangements do not include the putative origin of DNA replication but move within the same replichore, i.e., the same replicating half of the chromosome (delimited by the replication origin and terminus). Based on cumulative GC skew analysis, both the T. maritima and T. neapolitana lineages contain one or two major inverted DNA segments. Also, based on PCR amplification and sequence analysis of the DNA joints that are associated with the major rearrangements, the overall chromosome architecture was found to be conserved at most DNA joints for other strains of T. neapolitana. Taken together, the results from this analysis suggest that the observed chromosomal rearrangements in the Thermotogales likely occurred by successive inversions after their divergence from a common ancestor and before strain diversification. Finally, sequence analysis shows that size polymorphisms in the DNA joints associated with CRISPRs can be explained by expansion and possibly contraction of the DNA repeat and spacer unit, providing a tool for discerning the relatedness of strains from different geographic locations.

scholarly journals Citrus Peel Flavonoids as Potential Cancer Prevention Agents

2020 ◽  
Vol 4 (5) ◽  
Author(s):  
Nooshin Koolaji ◽  
Balakrishnan Shammugasamy ◽  
Aaron Schindeler ◽  
Qihan Dong ◽  
Fariba Dehghani ◽  
...  
Keyword(s):  
Citrus Fruit ◽  
In Vivo Studies ◽  
Citrus Peel ◽  
Cellular Processes ◽  
New Research ◽  
Cycle Regulation ◽  
Potential Cancer ◽  
Cell Signaling Pathways

ABSTRACT Citrus fruit and in particular flavonoid compounds from citrus peel have been identified as agents with utility in the treatment of cancer. This review provides a background and overview regarding the compounds found within citrus peel with putative anticancer potential as well as the associated in vitro and in vivo studies. Historical studies have identified a number of cellular processes that can be modulated by citrus peel flavonoids including cell proliferation, cell cycle regulation, apoptosis, metastasis, and angiogenesis. More recently, molecular studies have started to elucidate the underlying cell signaling pathways that are responsible for the flavonoids’ mechanism of action. These growing data support further research into the chemopreventative potential of citrus peel extracts, and purified flavonoids in particular. This critical review highlights new research in the field and synthesizes the pathways modulated by flavonoids and other polyphenolic compounds into a generalized schema.

scholarly journals Genome sequences of Aegilops species of section Sitopsis reveal phylogenetic relationships and provide resources for wheat improvement

2021 ◽  
Author(s):  
Raz Avni ◽  
Thomas Lux ◽  
Anna Minz-Dub ◽  
Eitan Millet ◽  
Hanan Sela ◽  
...  
Keyword(s):  
Haplotype Block ◽  
Close Relative ◽  
Whole Genome ◽  
Aegilops Species ◽  
Wheat Improvement ◽  
Genome Wide ◽  
Triticum Spp ◽  
Species Specific ◽  
Genomic Regions ◽  
Genome Assemblies

Aegilops is a close relative of wheat (Triticum spp.), and Aegilops species in the section Sitopsis represent a rich reservoir of genetic diversity for improvement of wheat. To understand their diversity and advance their utilization, we produced whole-genome assemblies of Ae. longissima and Ae. speltoides. Whole-genome comparative analysis, along with the recently sequenced Ae. sharonensis genome, showed that the Ae. longissima and Ae. sharonensis genomes are highly simiar and most closely related to the wheat D subgenome. By contrast, the Ae. speltoides genome is more closely related to the B subgenome. Haplotype block analysis supported the idea that Ae. speltoides is the closest ancestor of the wheat B subgenome and highlighted variable and similar genomic regions between the three Aegilops species and wheat. Genome-wide analysis of nucleotide-binding site leucine rich repeat (NLR) genes revealed species-specific and lineage-specific NLR genes and variants, demonstrating the potential of Aegilops genomes for wheat improvement.

scholarly journals The bacterial chromatin protein HupA can remodel DNA and associates with the nucleoid in Clostridium difficile

2018 ◽  
Author(s):  
Ana M. Oliveira Paiva ◽  
Annemieke H. Friggen ◽  
Liang Qin ◽  
Roxanne Douwes ◽  
Remus T. Dame ◽  
...  
Keyword(s):  
Protein A ◽  
Chromatin Protein ◽  
Chromosomal Organization ◽  
Cellular Processes ◽  
Hu Proteins ◽  
Architectural Proteins ◽  
Chromatin Proteins

AbstractThe maintenance and organization of the chromosome plays an important role in the development and survival of bacteria. Bacterial chromatin proteins are architectural proteins that bind DNA, modulate its conformation and by doing so affect a variety of cellular processes. No bacterial chromatin proteins of C. difficile have been characterized to date.Here, we investigate aspects of the C. difficile HupA protein, a homologue of the histone-like HU proteins of Escherichia coli. HupA is a 10 kDa protein that is present as a homodimer in vitro and self-interacts in vivo. HupA co-localizes with the nucleoid of C. difficile. It binds to the DNA without a preference for the DNA G+C content. Upon DNA binding, HupA induces a conformational change in the substrate DNA in vitro and leads to compaction of the chromosome in vivo.The present study is the first to characterize a bacterial chromatin protein in C. difficile and opens the way to study the role of chromosomal organization in DNA metabolism and on other cellular processes in this organism.

scholarly journals Cross-species incompatibility between a DNA satellite and a chromatin protein poisons germline genome integrity

2021 ◽  
Author(s):  
Cara L Brand ◽  
Mia T Levine
Keyword(s):  
Satellite Dna ◽  
Rapid Evolution ◽  
Genome Integrity ◽  
Dna Repeats ◽  
Chromatin Protein ◽  
Genetic Rescue ◽  
Chromatin Proteins ◽  
Genomic Regions ◽  
Female Germline ◽  
Nuclear Processes

Satellite DNA spans megabases of eukaryotic genome sequence. These vast stretches of tandem DNA repeats undergo high rates of sequence turnover, resulting in radically different satellite DNA landscapes between closely related species. Such extreme evolutionary plasticity suggests that satellite DNA accumulates mutations with no functional consequence. Paradoxically, satellite-rich genomic regions support essential, conserved nuclear processes, including chromosome segregation, dosage compensation, and nuclear structure. A leading resolution to this paradox is that deleterious alterations to satellite DNA trigger adaptive evolution of chromatin proteins to preserve these essential functions. Here we experimentally test this model of coevolution between chromatin proteins and DNA satellites by conducting an evolution-guided manipulation of both protein and satellite. We focused on an adaptively evolving, ovary-enriched chromatin protein, called Maternal Haploid (MH) from Drosophila. MH co-localizes with an 11 Mb 359-bp satellite array present in Drosophila melanogaster but absent in its sister species, D. simulans. Using CRISPR/Cas9-mediated transgenesis, we swapped the D. simulans version of MH into D. melanogaster. We discovered that D. melanogaster females encoding only the D. simulans mh (mh[sim]) do not phenocopy the mh null mutation. Instead, MH[sim] is toxic to D. melanogaster ovaries: we observed elevated ovarian cell death, reduced ovary size, and subfertility in mh[sim] females. Using both cell biological and genetic approaches, we demonstrate that MH[sim] poisons oogenesis through a DNA damage pathway. Remarkably, deleting the D. melanogaster-specific 359 satellite array from mh[sim] females completely restores female germline genome integrity and fertility. This genetic rescue offers experimental evidence that rapid evolution resulted in a cross-species incompatibility between the 359 satellite and MH. These data suggest that coevolution between ostensibly inert repetitive DNA and essential chromatin proteins preserves germline genome integrity.

scholarly journals Short-Sequence DNA Repeats in Prokaryotic Genomes

1998 ◽  
Vol 62 (2) ◽  
pp. 275-293 ◽  
Author(s):  
Alex van Belkum ◽  
Stewart Scherer ◽  
Loek van Alphen ◽  
Henri Verbrugh
Keyword(s):  
Pathogenic Bacteria ◽  
Gene Expression Regulation ◽  
Epidemiological Studies ◽  
Phenotypic Flexibility ◽  
Dna Repeats ◽  
Sequence Motifs ◽  
Short Sequence ◽  
Bacterial Cell Division ◽  
Dna Repeat ◽  
Prokaryotic Genomes

SUMMARY Short-sequence DNA repeat (SSR) loci can be identified in all eukaryotic and many prokaryotic genomes. These loci harbor short or long stretches of repeated nucleotide sequence motifs. DNA sequence motifs in a single locus can be identical and/or heterogeneous. SSRs are encountered in many different branches of the prokaryote kingdom. They are found in genes encoding products as diverse as microbial surface components recognizing adhesive matrix molecules and specific bacterial virulence factors such as lipopolysaccharide-modifying enzymes or adhesins. SSRs enable genetic and consequently phenotypic flexibility. SSRs function at various levels of gene expression regulation. Variations in the number of repeat units per locus or changes in the nature of the individual repeat sequences may result from recombination processes or polymerase inadequacy such as slipped-strand mispairing (SSM), either alone or in combination with DNA repair deficiencies. These rather complex phenomena can occur with relative ease, with SSM approaching a frequency of 10−4 per bacterial cell division and allowing high-frequency genetic switching. Bacteria use this random strategy to adapt their genetic repertoire in response to selective environmental pressure. SSR-mediated variation has important implications for bacterial pathogenesis and evolutionary fitness. Molecular analysis of changes in SSRs allows epidemiological studies on the spread of pathogenic bacteria. The occurrence, evolution and function of SSRs, and the molecular methods used to analyze them are discussed in the context of responsiveness to environmental factors, bacterial pathogenicity, epidemiology, and the availability of full-genome sequences for increasing numbers of microorganisms, especially those that are medically relevant.

Low levels of extra-pair paternity in southern emu-wrens (Aves : Maluridae)

2008 ◽  
Vol 56 (2) ◽  
pp. 79 ◽  
Author(s):  
Grainne S. Maguire ◽  
Raoul A. Mulder
Keyword(s):  
Mate Choice ◽  
Cooperative Breeding ◽  
Paternal Care ◽  
Close Relative ◽  
High Frequencies ◽  
Extra Pair Paternity ◽  
Genetic Mating System ◽  
Low Levels ◽  
Alternative Sources ◽  
Species Specific

The frequency of extra-pair paternity (EPP) among birds varies considerably, with the highest rates (56–76%) reported in several species of fairy-wren (Maluridae). According to the ‘constrained female’ hypothesis, such high frequencies arise when females are emancipated from constraints on mate choice because they have access to alternative sources of parental care (cooperative breeding). We investigated the genetic mating system of a close relative of the fairy-wrens within the Maluridae, the southern emu-wren (Stipiturus malachurus). Southern emu-wrens share several life-history attributes with the fairy-wrens, but show relatively low levels of cooperation, providing an opportunity to assess how the frequency of cooperative breeding correlates with the frequency of EPP. We assessed paternity for 50 offspring within 27 emu-wren broods using species-specific microsatellite markers. Overall, only 12% of genotyped offspring resulted from extra-pair paternity, and 15% of broods contained at least one extra-pair offspring. We argue that opportunities for mate choice by female emu-wrens are restricted by their dependence on paternal care for offspring survival, as suggested by the constrained female hypothesis. The low occurrence of cooperative breeding in the southern emu-wren may thus help explain the extreme variation in the frequency of extra-pair paternity within this family.

FokI DNA repeats in the genome of Vicia faba: species specificity, structure, redundancy modulation, and nuclear organization

Genome ◽  
1995 ◽  
Vol 38 (6) ◽  
pp. 1255-1261 ◽  
Author(s):  
F. Maggini ◽  
R. D'Ovidio ◽  
M. T. Gelati ◽  
M. Frediani ◽  
R. Cremonini ◽  
...  
Keyword(s):  
Vicia Faba ◽  
Dna Sequences ◽  
Nuclear Organization ◽  
Chromosome Complement ◽  
Dna Repeats ◽  
Repeated Dna ◽  
Repeated Dna Sequences ◽  
Functional Roles ◽  
Species Specific ◽  
Tandemly Repeated Dna

Tandemly repeated DNA sequences about 60 bp in length, which may be isolated by digestion with FokI restriction endonuclease, were studied by means of molecular and cytological hybridizations in Vicia faba and other Vicia species. The results obtained can be summarized as follows: (i) FokI repeats are almost species specific to V. faba, since they hybridize to a minimum extent to the genomic DNA of only two out of five related species; (ii) these tandemly repeated elements display variability in structure even within one and the same array, where different repeats may share not more than 71% homology; (iii) their redundancy in the genome of V. faba is remarkably high and varies largely between land races (copy numbers per haploid, 1C, genome range from 21.51 × 106 to 5.39 × 106); (iv) FokI repeats are clustered in differing amounts in each subtelocentric pair of the chromosome complement and are missing or present in a nondetectable amount in the submetacentric pair; (vi) chromosome regions that bear these repeats associate closely to varying degrees in interphase nuclei. These results are discussed in relation to possible functional roles that tandemly repeated DNA sequences such as the FokI elements might play.Key words: FokI, intraspecific DNA changes, nuclear organization, repeated DNA sequences, Vicia faba.

scholarly journals Chromosomal organization of Xenopus laevis oocyte and somatic 5S rRNA genes in vivo.

1992 ◽  
Vol 12 (1) ◽  
pp. 45-55 ◽  
Author(s):  
C C Chipev ◽  
A P Wolffe
Keyword(s):  
Xenopus Laevis ◽  
Rrna Genes ◽  
Dna Repeats ◽  
5S Rna ◽  
Chromosomal Organization ◽  
Dna Repeat ◽  
5S Dna ◽  
Nuclease Digestion ◽  
5S Rna Genes ◽  
Rna Genes

We describe the chromosomal organization of the major oocyte and somatic 5S RNA genes of Xenopus laevis in chromatin isolated from erythrocyte nuclei. Both major oocyte and somatic 5S DNA repeats are associated with nucleosomes; however, differences exist in the organization of chromatin over the oocyte and somatic 5S RNA genes. The repressed oocyte 5S RNA gene is protected from nuclease digestion by incorporation into a nucleosome, and the entire oocyte 5S DNA repeat is assembled into a loosely positioned array of nucleosomes. In contrast, the potentially active somatic 5S RNA gene is accessible to nuclease digestion, and the majority of somatic 5S RNA genes appear not to be incorporated into positioned nucleosomes. Evidence is presented supporting the stable association of transcription factors with the somatic 5S RNA genes. Histone H1 is shown to have a role both in determining the organization of nucleosomes over the oocyte 5S DNA repeat and in repressing transcription of the oocyte 5S RNA genes.

scholarly journals Does polyandry control population sex ratio via regulation of a selfish gene?

2014 ◽  
Vol 281 (1783) ◽  
pp. 20133259 ◽  
Author(s):  
Tom A. R. Price ◽  
Amanda Bretman ◽  
Ana C. Gradilla ◽  
Julia Reger ◽  
Michelle L. Taylor ◽  
...  
Keyword(s):  
Sex Ratio ◽  
Natural Populations ◽  
Low Frequency ◽  
Evolution Of Cooperation ◽  
Northern Population ◽  
Selfish Gene ◽  
Selfish Genetic Elements ◽  
Sex Ratio Bias ◽  
Intragenomic Conflict ◽  
The Usa

The extent of female multiple mating (polyandry) can strongly impact on the intensity of sexual selection, sexual conflict, and the evolution of cooperation and sociality. More subtly, polyandry may protect populations against intragenomic conflicts that result from the invasion of deleterious selfish genetic elements (SGEs). SGEs commonly impair sperm production, and so are likely to be unsuccessful in sperm competition, potentially reducing their transmission in polyandrous populations. Here, we test this prediction in nature. We demonstrate a heritable latitudinal cline in the degree of polyandry in the fruitfly Drosophila pseudoobscura across the USA, with northern population females remating more frequently in both the field and the laboratory. High remating was associated with low frequency of a sex-ratio-distorting meiotic driver in natural populations. In the laboratory, polyandry directly controls the frequency of the driver by undermining its transmission. Hence we suggest that the cline in polyandry represents an important contributor to the cline in sex ratio in nature. Furthermore, as the meiotic driver causes sex ratio bias, variation in polyandry may ultimately determine population sex ratio across the USA, a dramatic impact of female mating decisions. As SGEs are ubiquitous it is likely that the reduction of intragenomic conflict by polyandry is widespread.

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