scholarly journals Monopolin recruits condensin to organize centromere DNA and repetitive DNA sequences

2013 ◽  
Vol 24 (18) ◽  
pp. 2807-2819 ◽  
Author(s):  
Laura S. Burrack ◽  
Shelly E. Applen Clancey ◽  
Jeremy M. Chacón ◽  
Melissa K. Gardner ◽  
Judith Berman
Keyword(s):  
Chromosome Segregation ◽  
Repetitive Dna ◽  
Dna Sequences ◽  
Meiotic Chromosome ◽  
Higher Order ◽  
Order Structure ◽  
Cross Link ◽  
Microtubule Attachment ◽  
Sister Chromatids ◽  
Repeat Dna

The establishment and maintenance of higher-order structure at centromeres is essential for accurate chromosome segregation. The monopolin complex is thought to cross-link multiple kinetochore complexes to prevent merotelic attachments that result in chromosome missegregation. This model is based on structural analysis and the requirement that monopolin execute mitotic and meiotic chromosome segregation in Schizosaccharomyces pombe, which has more than one kinetochore–microtubule attachment/centromere, and co-orient sister chromatids in meiosis I in Saccharomyces cerevisiae. Recent data from S. pombe suggest an alternative possibility: that the recruitment of condensin is the primary function of monopolin. Here we test these models using the yeast Candida albicans. C. albicans cells lacking monopolin exhibit defects in chromosome segregation, increased distance between centromeres, and decreased stability of several types of repeat DNA. Of note, changing kinetochore–microtubule copy number from one to more than one kinetochore–microtubule/centromere does not alter the requirement for monopolin. Furthermore, monopolin recruits condensin to C. albicans centromeres, and overexpression of condensin suppresses chromosome segregation defects in strains lacking monopolin. We propose that the key function of monopolin is to recruit condensin in order to promote the assembly of higher-order structure at centromere and repetitive DNA.

Driving chromosome segregation: lessons from the human and Drosophila centromere–kinetochore machinery

2010 ◽  
Vol 38 (6) ◽  
pp. 1667-1675 ◽  
Author(s):  
Bernardo Orr ◽  
Olga Afonso ◽  
Tália Feijão ◽  
Claudio E. Sunkel
Keyword(s):  
Chromosome Segregation ◽  
Mitotic Spindle ◽  
Spindle Assembly Checkpoint ◽  
Genomic Stability ◽  
Mitotic Progression ◽  
Chromosomal Locus ◽  
Microtubule Attachment ◽  
Sister Chromatids ◽  
And Function ◽  
Drosophila Cells

The kinetochore is a complex molecular machine that serves as the interface between sister chromatids and the mitotic spindle. The kinetochore assembles at a particular chromosomal locus, the centromere, which is essential to maintain genomic stability during cell division. The kinetochore is a macromolecular puzzle of subcomplexes assembled in a hierarchical manner and fulfils three main functions: microtubule attachment, chromosome and sister chromatid movement, and regulation of mitotic progression though the spindle assembly checkpoint. In the present paper we compare recent results on the assembly, organization and function of the kinetochore in human and Drosophila cells and conclude that, although essential functions are highly conserved, there are important differences that might help define what is a minimal chromosome segregation machinery.

Possible repetitive DNA markers for Eusorghum and Parasorghum and their potential use in examining phylogenetic hypotheses on the origin of Sorghum species

Genome ◽  
1991 ◽  
Vol 34 (2) ◽  
pp. 241-250 ◽  
Author(s):  
Hoang-Tang ◽  
Shyam K. Dube ◽  
George H. Liang ◽  
Shain-Dow Kung
Keyword(s):  
Repetitive Dna ◽  
Dna Sequences ◽  
Meiotic Chromosome ◽  
Repetitive Sequences ◽  
Copy Numbers ◽  
Major Species ◽  
Strong Homology ◽  
Genome Phylogeny ◽  
Genomic Dnas ◽  
Phylogenetic Hypotheses

Genomic structures of two major species in section Eusorghum (Sorghum), Sorghum bicolor and Sorghum halepense, and their phylogenetic relationships with a species in section Parasorghum, Sorghum versicolor, were studied by using cloned repetitive DNA sequences from the three species. Of the five repetitive DNA clones isolated from S. bicolor and S. halepense, four produced qualitatively similar hybridization patterns with detectable variations in copy numbers of some of the restriction fragments on the Southern blots of the two genomic DNAs. One clone was shown to be diagnostic for S. halepense. Molecular analysis at the DNA level indicates that S. bicolor and S. halepense have similar but not identical genomes, consonant with differences in karyotypes, meiotic chromosome behaviors, morphology, and physiology of the species. In addition to five repetitive clones isolated from S. bicolor and S. halepense, eight more sequences were cloned from S. versicolor. Nine clones were found to be specific for either S. bicolor and S. halepense or S. versicolor. The remaining four had a moderate to strong homology with sequences present in all Sorghum species studied. We speculate that the genome in the common ancestor of Sorghum has differentiated to give rise to genomes of at least three major chromosome sizes; large, medium, and small, as seen at present. Amplifications, eliminations, rearrangements, and new syntheses of repetitive sequences may have been involved in genome differentiation of these species. The results also suggest that the S. versicolor genome has strongly diverged from the genomes of the two species in section Eusorghum.Key words: repetitive DNA, genome, phylogeny, Eusorghum, Parasorghum, Sorghum.

scholarly journals Parity-dependent hairpin configurations of repetitive DNA sequence promote slippage associated with DNA expansion

2017 ◽  
Vol 114 (36) ◽  
pp. 9535-9540 ◽  
Author(s):  
Tze-Yun Huang ◽  
Chung-ke Chang ◽  
Ya-Fen Kao ◽  
Chih-Hao Chin ◽  
Cheng-Wei Ni ◽  
...  
Keyword(s):  
Repetitive Dna ◽  
Single Molecule ◽  
Dna Sequences ◽  
Hot Spots ◽  
Neurological Diseases ◽  
Repeat Expansion ◽  
Single Molecule Spectroscopy ◽  
Dna Repeats ◽  
Structural Polymorphism ◽  
Repeat Dna

Repetitive DNA sequences are ubiquitous in life, and changes in the number of repeats often have various physiological and pathological implications. DNA repeats are capable of interchanging between different noncanonical and canonical conformations in a dynamic fashion, causing configurational slippage that often leads to repeat expansion associated with neurological diseases. In this report, we used single-molecule spectroscopy together with biophysical analyses to demonstrate the parity-dependent hairpin structural polymorphism of TGGAA repeat DNA. We found that the DNA adopted two configurations depending on the repeat number parity (even or odd). Transitions between these two configurations were also observed for longer repeats. In addition, the ability to modulate this transition was found to be enhanced by divalent ions. Based on the atomic structure, we propose a local seeding model where the kinked GGA motifs in the stem region of TGGAA repeat DNA act as hot spots to facilitate the transition between the two configurations, which may give rise to disease-associated repeat expansion.

scholarly journals A stochastic model of kinetochore–microtubule attachment accurately describes fission yeast chromosome segregation

2012 ◽  
Vol 196 (6) ◽  
pp. 757-774 ◽  
Author(s):  
Guillaume Gay ◽  
Thibault Courtheoux ◽  
Céline Reyes ◽  
Sylvie Tournier ◽  
Yannick Gachet
Keyword(s):  
Fission Yeast ◽  
Chromosome Segregation ◽  
Aurora B ◽  
Segregation Behavior ◽  
Microtubule Attachment ◽  
Anaphase Onset ◽  
Sister Chromatids ◽  
Yeast Chromosome ◽  
Spindle Microtubules ◽  
Early Mitosis

In fission yeast, erroneous attachments of spindle microtubules to kinetochores are frequent in early mitosis. Most are corrected before anaphase onset by a mechanism involving the protein kinase Aurora B, which destabilizes kinetochore microtubules (ktMTs) in the absence of tension between sister chromatids. In this paper, we describe a minimal mathematical model of fission yeast chromosome segregation based on the stochastic attachment and detachment of ktMTs. The model accurately reproduces the timing of correct chromosome biorientation and segregation seen in fission yeast. Prevention of attachment defects requires both appropriate kinetochore orientation and an Aurora B–like activity. The model also reproduces abnormal chromosome segregation behavior (caused by, for example, inhibition of Aurora B). It predicts that, in metaphase, merotelic attachment is prevented by a kinetochore orientation effect and corrected by an Aurora B–like activity, whereas in anaphase, it is corrected through unbalanced forces applied to the kinetochore. These unbalanced forces are sufficient to prevent aneuploidy.

scholarly journals Condensin restructures chromosomes in preparation for meiotic divisions

2004 ◽  
Vol 167 (4) ◽  
pp. 613-625 ◽  
Author(s):  
Raymond C. Chan ◽  
Aaron F. Severson ◽  
Barbara J. Meyer
Keyword(s):  
Caenorhabditis Elegans ◽  
Chromosome Segregation ◽  
Germ Cells ◽  
Protein Complex ◽  
Mitotic Chromosome ◽  
Meiotic Chromosome ◽  
Ordered Structure ◽  
Homologous Chromosomes ◽  
Sister Chromatids ◽  
Chromosome Resolution

The production of haploid gametes from diploid germ cells requires two rounds of meiotic chromosome segregation after one round of replication. Accurate meiotic chromosome segregation involves the remodeling of each pair of homologous chromosomes around the site of crossover into a highly condensed and ordered structure. We showed that condensin, the protein complex needed for mitotic chromosome compaction, restructures chromosomes during meiosis in Caenorhabditis elegans. In particular, condensin promotes both meiotic chromosome condensation after crossover recombination and the remodeling of sister chromatids. Condensin helps resolve cohesin-independent linkages between sister chromatids and alleviates recombination-independent linkages between homologues. The safeguarding of chromosome resolution by condensin permits chromosome segregation and is crucial for the formation of discrete, individualized bivalent chromosomes.

scholarly journals Eco1-dependent cohesin acetylation anchors chromatin loops and cohesion to define functional meiotic chromosome domains

2021 ◽  
Author(s):  
Rachael E Barton ◽  
Lucia F Massari ◽  
Daniel Robertson ◽  
Adele L Marston
Keyword(s):  
Chromosome Segregation ◽  
Sister Chromatid ◽  
Meiotic Chromosome ◽  
Chromatin Loops ◽  
Meiotic Chromosomes ◽  
Sister Chromatids ◽  
Gamete Formation ◽  
Chromosome Domains ◽  
Chromatid Cohesion ◽  
Cohesin Subunit

Cohesin organizes the genome by forming intra-chromosomal loops and inter-sister chromatid linkages. During gamete formation by meiosis, chromosomes are reshaped to support crossover recombination and two consecutive rounds of chromosome segregation. Here we show that Eco1 acetyltransferase positions both chromatin loops and sister chromatid cohesion to organize meiotic chromosomes into functional domains in budding yeast. Eco1 acetylates the Smc3 cohesin subunit in meiotic S phase to establish chromatin boundaries, independently of DNA replication. Boundary formation by Eco1 is critical for prophase exit and for the maintenance of cohesion until meiosis II, but is independent of the ability of Eco1 to antagonize the cohesin-release factor, Wpl1. Conversely, prevention of cohesin release by Wpl1 is essential for centromeric cohesion, kinetochore monoorientation and co-segregation of sister chromatids in meiosis I. Our findings establish Eco1 as a key determinant of chromatin boundaries and cohesion positioning, revealing how local chromosome structuring directs genome transmission into gametes.

Similarity Detection for Higher-Order Structure of DNA Sequences

2017 ◽  
Vol 3 (2) ◽  
pp. 28
Author(s):  
Nguyen Thi Ngoc Anh ◽  
Ho Phan Hieu ◽  
Tran Anh Kiet ◽  
Vo Trung Hung
Keyword(s):  
Feature Extraction ◽  
Dna Sequences ◽  
Missing Values ◽  
Computation Time ◽  
Data Representation ◽  
Higher Order ◽  
High Order ◽  
Order Structure ◽  
Similarity Detection ◽  
The Matrix

With the advances in data collection and storage capabilities, large amount of multidimensional dataset, known as higher-order data representation, has been generated on bioinformatics applications recently, especially in DNA sequences recognition. This paper thus proposes a mathematical modeling could be capable of the multidimensional problem of DNA similarity detection with high accuracy and reliability. To this end, the paper covers the central issues of multidimensional DNA gene expression data, including: (1) formulating multidimensional DNA data into higher-order representation; (2) recovering missing values; (3) decomposing high-order DNA data directly from their tensorial representation to extracted useful information for classification. Consequently, an exploring a novel type of third-order microarray expression, termed as gene - sample - time (GST), is presented for biological sample classification. The contributions will be distributed along two main thrusts of effectiveness; including latent modeling setting for imputing missing values based on the High-Order Kalman Filter and feature extraction based on Tensor Discriminative Feature Extraction. The experimental performance on real dataset of DNA sequences corroborates the advantages of the proposed approaches upon those of the matrix-based algorithms and recent tensor-based, discriminant-decomposition, in terms of missing values completion, classification accuracy and computation time.

Genomic DNA repeat from Leishmania (Viannia) braziliensis (Venezuelan strain) containing simple repeats and microsatellites

Parasitology ◽  
1997 ◽  
Vol 115 (4) ◽  
pp. 349-358 ◽  
Author(s):  
N. RODRIGUEZ ◽  
H. DE LIMA ◽  
A. RODRIGUEZ ◽  
S. BREWSTER ◽  
D. C. BARKER
Keyword(s):  
Repetitive Dna ◽  
Dna Sequences ◽  
Genomic Dna ◽  
Nuclear Genome ◽  
Cosmid Library ◽  
Simple Repeat ◽  
Mucocutaneous Leishmaniasis ◽  
Dna Repeat ◽  
Repeat Dna ◽  
Species Specific

In this paper the Leishmania (Viannia) braziliensis complex is defined as containing all species of the actual subgenus Viannia. Organisms of the L. (V) braziliensis complex are the causative agents of localized human cutaneous and mucocutaneous leishmaniasis in South America, much of Central America and some areas of North America. In our search for better species and subspecies diagnostic probes we focused our research on repetitive DNA, since it provides a greater number of target sites for hybridization. In this work we report the isolation and sequencing of a 1·8 kb DNA region, LbJ38, which is probably tandemly repeated or dispersed at least 4 times along one chromosome and is naturally present in L. (V) braziliensis genomic DNA. This region contains microsatellites and simple repeat DNA sequences and was isolated by screening a genomic DNA cosmid library with complex- and species-specific probes. No homology was found with other Leishmania microsatellite or repetitive DNA. The utility of this repetitive sequence and primers derived from it in the identification of L. (V) braziliensis is demonstrated. As far as we are aware, this is the first report of sequence characterized repetitive microsatellite and GC rich simple repeat DNA from the nuclear genome of New World Leishmania.

scholarly journals An unbiased, quantitative and versatile method for determining misaligned and lagging chromosome during mitosis

2020 ◽  
Author(s):  
Luciano Gama Braga ◽  
Diogjena Katerina Prifti ◽  
Chantal Garand ◽  
Pawan Kumar Saini ◽  
Sabine Elowe
Keyword(s):  
Chromosome Segregation ◽  
Hallmarks Of Cancer ◽  
Analytical Geometry ◽  
Daughter Cells ◽  
Chromosome Missegregation ◽  
Microtubule Attachment ◽  
Sister Chromatids ◽  
Chromosome Congression ◽  
Chromosome Alignment ◽  
Lagging Chromosome

ABSTRACTAccurate chromosome alignment at metaphase facilitates the equal segregation of sister chromatids to each of the nascent daughter cells. Lack of proper metaphase alignment is an indicator of defective chromosome congression and aberrant kinetochore-microtubule attachments which in turn promotes chromosome missegregation and aneuploidy, hallmarks of cancer. Therefore, tools to sensitively and quantitatively measure chromosome alignment at metaphase will facilitate understanding of how changes in the composition and regulation of the microtubule attachment machinery impinge on this process. In this work, we have developed and validated a method based on analytical geometry to measure several indicators of chromosome misalignment. We generated semi-automated and flexible ImageJ2/Fiji pipelines to quantify kinetochore misalignment at metaphase plates as well as lagging chromosomes at anaphase. These tools will ultimately allow sensitive, unbiased, and systematic quantitation of these chromosome segregation defects in cells undergoing mitosis.

DNA methylation in satellite repeats disorders

2019 ◽  
Vol 63 (6) ◽  
pp. 757-771 ◽  
Author(s):  
Claire Francastel ◽  
Frédérique Magdinier
Keyword(s):  
Dna Methylation ◽  
Human Genome ◽  
Repetitive Dna ◽  
Dna Sequences ◽  
Satellite Repeats ◽  
Tremendous Progress ◽  
Genes Encoding ◽  
Dna Elements ◽  
Near Future

Abstract Despite the tremendous progress made in recent years in assembling the human genome, tandemly repeated DNA elements remain poorly characterized. These sequences account for the vast majority of methylated sites in the human genome and their methylated state is necessary for this repetitive DNA to function properly and to maintain genome integrity. Furthermore, recent advances highlight the emerging role of these sequences in regulating the functions of the human genome and its variability during evolution, among individuals, or in disease susceptibility. In addition, a number of inherited rare diseases are directly linked to the alteration of some of these repetitive DNA sequences, either through changes in the organization or size of the tandem repeat arrays or through mutations in genes encoding chromatin modifiers involved in the epigenetic regulation of these elements. Although largely overlooked so far in the functional annotation of the human genome, satellite elements play key roles in its architectural and topological organization. This includes functions as boundary elements delimitating functional domains or assembly of repressive nuclear compartments, with local or distal impact on gene expression. Thus, the consideration of satellite repeats organization and their associated epigenetic landmarks, including DNA methylation (DNAme), will become unavoidable in the near future to fully decipher human phenotypes and associated diseases.

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