scholarly journals Conserved chromatin and repetitive patterns reveal slow genome evolution in frogs

2021 ◽  
Author(s):  
Jessen V. Bredeson ◽  
Austin B. Mudd ◽  
Sofia Medina-Ruiz ◽  
Therese Mitros ◽  
Owen K. Smith ◽  
...  
Keyword(s):  
Tandem Repeats ◽  
Developmental Model ◽  
Model Systems ◽  
Centromeric Chromatin ◽  
Differentiated Cells ◽  
Vertebrate Cell ◽  
Satellite Repeats ◽  
Frog Species ◽  
Hymenochirus Boettgeri ◽  
Clawed Frog

Frogs are an ecologically diverse and phylogenetically ancient group of living amphibians that include important vertebrate cell and developmental model systems, notably the genus Xenopus. Here we report a high-quality reference genome sequence for the western clawed frog, Xenopus tropicalis, along with draft chromosome-scale sequences of three distantly related emerging model frog species, Eleutherodactylus coqui, Engystomops pustulosus and Hymenochirus boettgeri. Frog chromosomes have remained remarkably stable since the Mesozoic Era, with limited Robertsonian (i.e., centric) translocations and end-to-end fusions found among the smaller chromosomes. Conservation of synteny includes conservation of centromere locations, marked by centromeric tandem repeats associated with Cenp-a binding, surrounded by pericentromeric LINE/L1 elements. We explored chromosome structure across frogs, using a dense meiotic linkage map for X. tropicalis and chromatin conformation capture (HiC) data for all species. Abundant satellite repeats occupy the unusually long (~20 megabase) terminal regions of each chromosome that coincide with high rates of recombination. Both embryonic and differentiated cells show reproducible association of centromeric chromatin, and of telomeres, reflecting a Rabl configuration similar to the "bouquet" structure of meiotic cells. Our comparative analyses reveal 13 conserved ancestral anuran chromosomes from which contemporary frog genomes were constructed.

scholarly journals Disruption of VirB6 Paralogs in Anaplasma phagocytophilum Attenuates Its Growth

2020 ◽  
Vol 202 (23) ◽  
Author(s):  
Francy L. Crosby ◽  
Ulrike G. Munderloh ◽  
Curtis M. Nelson ◽  
Michael J. Herron ◽  
Anna M. Lundgren ◽  
...  
Keyword(s):  
Anaplasma Phagocytophilum ◽  
Pathogenic Bacteria ◽  
Tandem Repeats ◽  
Model Systems ◽  
Accession Number ◽  
Secretion Systems ◽  
Altered Expression ◽  
Content Type ◽  
Obligate Intracellular

ABSTRACT Many pathogenic bacteria translocate virulence factors into their eukaryotic hosts by means of type IV secretion systems (T4SS) spanning the inner and outer membranes. Genes encoding components of these systems have been identified within the order Rickettsiales based upon their sequence similarities to other prototypical systems. Anaplasma phagocytophilum strains are obligate intracellular, tick-borne bacteria that are members of this order. The organization of these components at the genomic level was determined in several Anaplasma phagocytophilum strains, showing overall conservation, with the exceptions of the virB2 and virB6 genes. The virB6 loci are characterized by the presence of four virB6 copies (virB6-1 through virB6-4) arranged in tandem within a gene cluster known as the sodB-virB operon. Interestingly, the virB6-4 gene varies significantly in length among different strains due to extensive tandem repeats at the 3′ end. To gain an understanding of how these enigmatic virB6 genes function in A. phagocytophilum, we investigated their expression in infected human and tick cells. Our results show that these genes are expressed by A. phagocytophilum replicating in both cell types and that VirB6-3 and VirB6-4 proteins are surface exposed. Analysis of an A. phagocytophilum mutant carrying the Himar1 transposon within the virB6-4 gene demonstrated that the insertion not only disrupted its expression but also exerted a polar effect on the sodB-virB operon. Moreover, the altered expression of genes within this operon was associated with the attenuated in vitro growth of A. phagocytophilum in human and tick cells, indicating the importance of these genes in the physiology of this obligate intracellular bacterium in such different environments. IMPORTANCE Knowledge of the T4SS is derived from model systems, such as Agrobacterium tumefaciens. The structure of the T4SS in Rickettsiales differs from the classical arrangement. These differences include missing and duplicated components with structural alterations. Particularly, two sequenced virB6-4 genes encode unusual C-terminal structural extensions resulting in proteins of 4,322 (GenBank accession number AGR79286.1) and 9,935 (GenBank accession number ANC34101.1>) amino acids. To understand how the T4SS is used in A. phagocytophilum, we describe the expression of the virB6 paralogs and explore their role as the bacteria replicate within its host cell. Conclusions about the importance of these paralogs for colonization of human and tick cells are supported by the deficient phenotype of an A. phagocytophilum mutant isolated from a sequence-defined transposon insertion library.

scholarly journals Low Structural Variation in the Host-Defense Peptide Repertoire of the Dwarf Clawed Frog Hymenochirus boettgeri (Pipidae)

PLoS ONE ◽  
2014 ◽  
Vol 9 (1) ◽  
pp. e86339 ◽  
Author(s):  
Severine Matthijs ◽  
Lumeng Ye ◽  
Benoit Stijlemans ◽  
Pierre Cornelis ◽  
Franky Bossuyt ◽  
...  
Keyword(s):  
Host Defense ◽  
Structural Variation ◽  
Hymenochirus Boettgeri ◽  
Host Defense Peptide ◽  
Clawed Frog

scholarly journals Human 4E-T represses translation of bound mRNAs and enhances microRNA-mediated silencing

2013 ◽  
Vol 42 (5) ◽  
pp. 3298-3313 ◽  
Author(s):  
Anastasiia Kamenska ◽  
Wei-Ting Lu ◽  
Dorota Kubacka ◽  
Helen Broomhead ◽  
Nicola Minshall ◽  
...  
Keyword(s):  
Mammalian Cells ◽  
Translational Regulation ◽  
Binding Protein ◽  
Quantitative Polymerase Chain Reaction ◽  
Mrna Translation ◽  
Developmental Model ◽  
Model Systems ◽  
P Bodies ◽  
Specific Mrnas

Abstract A key player in translation initiation is eIF4E, the mRNA 5′ cap-binding protein. 4E-Transporter (4E-T) is a recently characterized eIF4E-binding protein, which regulates specific mRNAs in several developmental model systems. Here, we first investigated the role of its enrichment in P-bodies and eIF4E-binding in translational regulation in mammalian cells. Identification of the conserved C-terminal sequences that target 4E-T to P-bodies was enabled by comparison of vertebrate proteins with homologues in Drosophila (Cup and CG32016) and Caenorhabditis elegans by sequence and cellular distribution. In tether function assays, 4E-T represses bound mRNA translation, in a manner independent of these localization sequences, or of endogenous P-bodies. Quantitative polymerase chain reaction and northern blot analysis verified that bound mRNA remained intact and polyadenylated. Ectopic 4E-T reduces translation globally in a manner dependent on eIF4E binding its consensus Y30X4Lϕ site. In contrast, tethered 4E-T continued to repress translation when eIF4E-binding was prevented by mutagenesis of YX4Lϕ, and modestly enhanced the decay of bound mRNA, compared with wild-type 4E-T, mediated by increased binding of CNOT1/7 deadenylase subunits. As depleting 4E-T from HeLa cells increased steady-state translation, in part due to relief of microRNA-mediated silencing, this work demonstrates the conserved yet unconventional mechanism of 4E-T silencing of particular subsets of mRNAs.

scholarly journals Impact of Repetitive DNA Elements on Snake Genome Biology and Evolution

Cells ◽  
2021 ◽  
Vol 10 (7) ◽  
pp. 1707
Author(s):  
Syed Farhan Ahmad ◽  
Worapong Singchat ◽  
Thitipong Panthum ◽  
Kornsorn Srikulnath
Keyword(s):  
Repetitive Dna ◽  
Repetitive Elements ◽  
Model Systems ◽  
Satellite Repeats ◽  
Evolutionary Features ◽  
Dna Elements ◽  
Genomic Repeats ◽  
The Impact ◽  
Repetitive Dna Elements

The distinctive biology and unique evolutionary features of snakes make them fascinating model systems to elucidate how genomes evolve and how variation at the genomic level is interlinked with phenotypic-level evolution. Similar to other eukaryotic genomes, large proportions of snake genomes contain repetitive DNA, including transposable elements (TEs) and satellite repeats. The importance of repetitive DNA and its structural and functional role in the snake genome, remain unclear. This review highlights the major types of repeats and their proportions in snake genomes, reflecting the high diversity and composition of snake repeats. We present snakes as an emerging and important model system for the study of repetitive DNA under the impact of sex and microchromosome evolution. We assemble evidence to show that certain repetitive elements in snakes are transcriptionally active and demonstrate highly dynamic lineage-specific patterns as repeat sequences. We hypothesize that particular TEs can trigger different genomic mechanisms that might contribute to driving adaptive evolution in snakes. Finally, we review emerging approaches that may be used to study the expression of repetitive elements in complex genomes, such as snakes. The specific aspects presented here will stimulate further discussion on the role of genomic repeats in shaping snake evolution.

scholarly journals Genome-wide characterization of satellite DNA arrays in a complex plant genome using nanopore reads

2019 ◽  
Author(s):  
Tihana Vondrak ◽  
Laura Ávila Robledillo ◽  
Petr Novák ◽  
Andrea Koblížková ◽  
Pavel Neumann ◽  
...  
Keyword(s):  
Satellite Dna ◽  
Tandem Repeats ◽  
Length Distribution ◽  
Plant Genome ◽  
Ltr Retrotransposons ◽  
Satellite Repeat ◽  
Major Satellite ◽  
Satellite Repeats ◽  
Genome Wide

AbstractBackgroundAmplification of monomer sequences into long contiguous arrays is the main feature distinguishing satellite DNA from other tandem repeats, yet it is also the main obstacle in its investigation because these arrays are in principle difficult to assemble. Here we explore an alternative, assembly-free approach that utilizes ultra-long Oxford Nanopore reads to infer the length distribution of satellite repeat arrays, their association with other repeats and the prevailing sequence periodicities.ResultsWe have developed a computational workflow for similarity-based detection and downstream analysis of satellite repeats in individual nanopore reads that led to genome-wide characterization of their properties. Using the satellite DNA-rich legume plantLathyrus sativusas a model, we demonstrated this approach by analyzing eleven major satellite repeats using a set of nanopore reads ranging from 30 to over 200 kb in length and representing 0.73x genome coverage. We found surprising differences between the analyzed repeats because only two of them were predominantly organized in long arrays typical for satellite DNA. The remaining nine satellites were found to be derived from short tandem arrays located within LTR-retrotransposons that occasionally expanded in length. While the corresponding LTR-retrotransposons were dispersed across the genome, this array expansion occurred mainly in the primary constrictions of theL. sativuschromosomes, which suggests that these genome regions are favorable for satellite DNA accumulation.ConclusionsThe presented approach proved to be efficient in revealing differences in long-range organization of satellite repeats that can be used to investigate their origin and evolution in the genome.

Emerging developmental model systems

2006 ◽  
Vol 235 (10) ◽  
pp. 2895-2899 ◽  
Author(s):  
Julie C. Kiefer
Keyword(s):  
Developmental Model ◽  
Model Systems

scholarly journals On the wrong DNA track: Molecular mechanisms of repeat-mediated genome instability

2020 ◽  
Vol 295 (13) ◽  
pp. 4134-4170 ◽  
Author(s):  
Alexandra N. Khristich ◽  
Sergei M. Mirkin
Keyword(s):  
Molecular Mechanisms ◽  
Tandem Repeats ◽  
Genome Instability ◽  
Current Knowledge ◽  
Model Systems ◽  
Dna Repeats ◽  
Repeat Instability ◽  
Repeat Expansions ◽  
Induced Mutagenesis ◽  
Simple Tandem Repeats

Expansions of simple tandem repeats are responsible for almost 50 human diseases, the majority of which are severe, degenerative, and not currently treatable or preventable. In this review, we first describe the molecular mechanisms of repeat-induced toxicity, which is the connecting link between repeat expansions and pathology. We then survey alternative DNA structures that are formed by expandable repeats and review the evidence that formation of these structures is at the core of repeat instability. Next, we describe the consequences of the presence of long structure-forming repeats at the molecular level: somatic and intergenerational instability, fragility, and repeat-induced mutagenesis. We discuss the reasons for gender bias in intergenerational repeat instability and the tissue specificity of somatic repeat instability. We also review the known pathways in which DNA replication, transcription, DNA repair, and chromatin state interact and thereby promote repeat instability. We then discuss possible reasons for the persistence of disease-causing DNA repeats in the genome. We describe evidence suggesting that these repeats are a payoff for the advantages of having abundant simple-sequence repeats for eukaryotic genome function and evolvability. Finally, we discuss two unresolved fundamental questions: (i) why does repeat behavior differ between model systems and human pedigrees, and (ii) can we use current knowledge on repeat instability mechanisms to cure repeat expansion diseases?

scholarly journals Genome-Wide Distribution of Novel Ta-3A1 Mini-Satellite Repeats and Its Use for Chromosome Identification in Wheat and Related Species

Agronomy ◽  
2019 ◽  
Vol 9 (2) ◽  
pp. 60 ◽  
Author(s):  
Tao Lang ◽  
Guangrong Li ◽  
Zhihui Yu ◽  
Jiwei Ma ◽  
Qiheng Chen ◽  
...  
Keyword(s):  
Satellite Dna ◽  
Tandem Repeats ◽  
Chromosomal Rearrangements ◽  
Wide Distribution ◽  
Fish Analysis ◽  
Satellite Repeats ◽  
Genome Wide ◽  
Rapid Sequence ◽  
Group 5

A large proportion of the genomes of grasses is comprised of tandem repeats (TRs), which include satellite DNA. A mini-satellite DNA sequence with a length of 44 bp, named Ta-3A1, was found to be highly accumulated in wheat genome, as revealed by a comprehensive sequence analysis. The physical distribution of Ta-3A1 in chromosomes 3A, 5A, 5B, 5D, and 7A of wheat was confirmed by nondenaturing fluorescence in situ hybridization (ND-FISH) after labeling the oligonucleotide probe. The analysis of monomer variants indicated that rapid sequence amplification of Ta-3A1 occurred first on chromosomes of linkage group 5, then groups 3 and 7. Comparative ND-FISH analysis suggested that rapid changes occurred in copy number and chromosomal locations of Ta-3A1 among the different species in the tribe Triticeae, which may have been associated with chromosomal rearrangements during speciation and polyploidization. The labeling and subsequent use of Ta-3A1 by ND-FISH may assist in the precise identification and documentation of novel wheat germplasm engineered by chromosome manipulation.

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