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Adam D. Leaché - One of the best experts on this subject based on the ideXlab platform.

  • characterization of a pericentric inversion in plateau fence lizards sceloporus tristichus evidence from chromosome scale genomes
    G3: Genes Genomes Genetics, 2021
    Co-Authors: Ana M Bedoya, Adam D. Leaché
    Abstract:

    Spiny lizards in the genus Sceloporus are a model system among squamate reptiles for studies of chromosomal evolution. While most pleurodont iguanians retain an ancestral karyotype formula of 2n = 36 chromosomes, Sceloporus exhibits substantial karyotype variation ranging from 2n =  22 to 46 chromosomes. We present two annotated chromosome-scale genome assemblies for the Plateau Fence Lizard (Sceloporus tristichus) to facilitate research on the role of pericentric inversion polymorphisms on adaptation and speciation. Based on previous karyotype work using conventional staining, the S. tristichus genome is characterized as 2n =  22 with six pairs of macrochromosomes and five pairs of microchromosomes and a pericentric inversion polymorphism on chromosome 7 that is geographically variable. We provide annotated, chromosome-scale genomes for two lizards located at opposite ends of a dynamic hybrid zone that are each fixed for different inversion polymorphisms. The assembled genomes are 1.84-1.87 Gb (1.72 Gb for scaffolds mapping to chromosomes) with a scaffold N50 of 267.5 Mb. Functional annotation of the genomes resulted in ∼15K predicted gene models. Our assemblies confirmed the presence of a 4.62-Mb pericentric inversion on chromosome 7, which contains 62 annotated coding genes with known functions. In addition, we collected population genomics data using double digest RAD-sequencing for 44 S. tristichus to estimate population structure and phylogeny across the Colorado Plateau. These new genomic resources provide opportunities to perform genomic scans and investigate the formation and spread of pericentric inversions in a naturally occurring hybrid zone.

  • characterization of a large pericentric inversion in plateau fence lizards sceloporus tristichus evidence from chromosome scale genomes
    bioRxiv, 2020
    Co-Authors: Adam D. Leaché, Ana M Bedoya
    Abstract:

    Spiny lizards in the genus Sceloporus are a model system among squamate reptiles for studies of chromosomal evolution. While most pleurodont iguanians retain an ancestral karyotype formula of 2n=36 chromosomes, Sceloporus exhibits substantial kary- otype variation ranging from 2n=22 to 2n=46 chromosomes. In this study, we present two annotated chromosome-scale genome assemblies for the Plateau Fence Lizard (Sceloporus tristichus) in order to facilitate research on the role of pericentric inversion polymorphisms on adaptation and speciation. Based on previous karyotype work using conventional staining, the S. tristichus genome is characterized as 2n=22 with 6 pairs of macrochromosomes and 5 pairs of microchromosomes with a large pericentric inversion polymorphism on chromosome seven that is geographically variable. We provide annotated, chromosome-scale genomes for two lizards located at opposite ends of a dynamic hybrid zone that are each fixed for different inversion polymorphisms. The assembled genomes are 1.84 to 1.87 Gb (1.72 Gb for scaffolds mapping to chromosomes) with a scaffold N50 of 267.5 Mb. Functional annotation of the genomes resulted in 65,417 annotated genes, 16,426 of which were deduced to have a function. We confirmed the presence of a 4.62 Mb pericentric inversion on chromosome seven, which contains 59 annotated coding genes with known functions. These new genomic resources provide opportunities to perform genomic scans and investigate the formation and spread of pericentric inversions in a naturally occurring hybrid zone. Key words: chromosome rearrangement, de novo assembly, hybrid zone, pericentric inversion, phrynosomatidae, Sceloporus, genome sequencing.

Stephen J Doxsey - One of the best experts on this subject based on the ideXlab platform.

  • membrane type 1 matrix metalloproteinase mt1 mmp exhibits an important intracellular cleavage function and causes chromosome instability
    Journal of Biological Chemistry, 2005
    Co-Authors: Vladislav S Golubkov, Stephen J Doxsey, Sarah Elizabeth Boyd, Alexei Y Savinov, Alexei V Chekanov, Andrei L Osterman, Albert G Remacle, Dmitri V Rozanov, Alex Y Strongin
    Abstract:

    Elevated expression of membrane type-1 matrix metalloproteinase (MT1-MMP) is closely associated with malignancies. There is a consensus among scientists that cell surface-associated MT1-MMP is a key player in pericellular proteolytic events. Now we have identified an intracellular, hitherto unknown, function of MT1-MMP. We demonstrated that MT1-MMP is trafficked along the tubulin cytoskeleton. A fraction of cellular MT1-MMP accumulates in the centrosomal compartment. MT1-MMP targets an integral centrosomal protein, Pericentrin. Pericentrin is known to be essential to the normal functioning of centrosomes and to mitotic spindle formation. Expression of MT1-MMP stimulates mitotic spindle aberrations and aneuploidy in non-malignant cells. Volumes of data indicate that chromosome instability is an early event of carcinogenesis. In agreement, the presence of MT1-MMP activity correlates with degraded Pericentrin in tumor biopsies, whereas normal tissues exhibit intact Pericentrin. We believe that our data show a novel proteolytic pathway to chromatin instability and elucidate the close association of MT1-MMP with malignant transformation.

  • direct interaction of Pericentrin with cytoplasmic dynein light intermediate chain contributes to mitotic spindle organization
    Journal of Cell Biology, 1999
    Co-Authors: Aruna Purohit, Richard B Vallee, Sharon H. Tynan, Stephen J Doxsey
    Abstract:

    Pericentrin is a conserved protein of the centrosome involved in microtubule organization. To better understand Pericentrin function, we overexpressed the protein in somatic cells and assayed for changes in the composition and function of mitotic spindles and spindle poles. Spindles in Pericentrin-overexpressing cells were disorganized and mispositioned, and chromosomes were misaligned and missegregated during cell division, giving rise to aneuploid cells. We unexpectedly found that levels of the molecular motor cytoplasmic dynein were dramatically reduced at spindle poles. Cytoplasmic dynein was diminished at kinetochores also, and the dynein-mediated organization of the Golgi complex was disrupted. Dynein coimmunoprecipitated with overexpressed Pericentrin, suggesting that the motor was sequestered in the cytoplasm and was prevented from associating with its cellular targets. Immunoprecipitation of endogenous Pericentrin also pulled down cytoplasmic dynein in untransfected cells. To define the basis for this interaction, Pericentrin was coexpressed with cytoplasmic dynein heavy (DHCs), intermediate (DICs), and light intermediate (LICs) chains, and the dynamitin and p150Glued subunits of dynactin. Only the LICs coimmunoprecipitated with Pericentrin. These results provide the first physiological role for LIC, and they suggest that a Pericentrin–dynein interaction in vivo contributes to the assembly, organization, and function of centrosomes and mitotic spindles.

  • Pericentrin and gamma tubulin form a protein complex and are organized into a novel lattice at the centrosome
    Journal of Cell Biology, 1998
    Co-Authors: Jason B Dictenberg, Aaron Isadore Young, Wendy Zimmerman, Cynthia A Sparks, Charles A Vidair, Yixian Zheng, Walter A Carrington, Fredric S Fay, Stephen J Doxsey
    Abstract:

    Pericentrin and γ-tubulin are integral centrosome proteins that play a role in microtubule nucleation and organization. In this study, we examined the relationship between these proteins in the cytoplasm and at the centrosome. In extracts prepared from Xenopus eggs, the proteins were part of a large complex as demonstrated by sucrose gradient sedimentation, gel filtration and coimmunoprecipitation analysis. The Pericentrin–γ-tubulin complex was distinct from the previously described γ-tubulin ring complex (γ-TuRC) as purified γ-TuRC fractions did not contain detectable Pericentrin. When assembled at the centrosome, the two proteins remained in close proximity as shown by fluorescence resonance energy transfer. The three- dimensional organization of the centrosome-associated fraction of these proteins was determined using an improved immunofluorescence method. This analysis revealed a novel reticular lattice that was conserved from mammals to amphibians, and was organized independent of centrioles. The lattice changed dramatically during the cell cycle, enlarging from G1 until mitosis, then rapidly disassembling as cells exited mitosis. In cells colabeled to detect centrosomes and nucleated microtubules, lattice elements appeared to contact the minus ends of nucleated microtubules. Our results indicate that Pericentrin and γ-tubulin assemble into a unique centrosome lattice that represents the higher-order organization of microtubule nucleating sites at the centrosome.

  • Pericentrin a highly conserved centrosome protein involved in microtubule organization
    Cell, 1994
    Co-Authors: Stephen J Doxsey, Pascal Stein, Louise Evans, Patricia D Calarco, Marc W Kirschner
    Abstract:

    Abstract Antisera from scleroderma patients that react widely with centrosomes in plants and animals were used to isolate cDNAs encoding a novel centrosomal protein. The nucleotide sequence is consistent with a 7 kb mRNA and contains an open reading frame encoding a protein with a putative large coiled-coil domain flanked by noncoiled ends. Antisera recognize a 220 kd protein and stain centrosomes and acentriolar microtubule-organizing centers, where the protein is localized to the pericentriolar material (hence, the name Pericentrin). Anti-Pericentrin antibodies disrupt mitotic and meiotic divisions in vivo and block microtubule aster formation in Xenopus extracts, but do not block γ-tubulin assembly or microtubule nucleation from mature centrosomes. These results suggest that Pericentrin is a conserved integral component of the filamentous matrix of the centrosome involved in the initial establishment of organized microtubule arrays.

Ana M Bedoya - One of the best experts on this subject based on the ideXlab platform.

  • characterization of a pericentric inversion in plateau fence lizards sceloporus tristichus evidence from chromosome scale genomes
    G3: Genes Genomes Genetics, 2021
    Co-Authors: Ana M Bedoya, Adam D. Leaché
    Abstract:

    Spiny lizards in the genus Sceloporus are a model system among squamate reptiles for studies of chromosomal evolution. While most pleurodont iguanians retain an ancestral karyotype formula of 2n = 36 chromosomes, Sceloporus exhibits substantial karyotype variation ranging from 2n =  22 to 46 chromosomes. We present two annotated chromosome-scale genome assemblies for the Plateau Fence Lizard (Sceloporus tristichus) to facilitate research on the role of pericentric inversion polymorphisms on adaptation and speciation. Based on previous karyotype work using conventional staining, the S. tristichus genome is characterized as 2n =  22 with six pairs of macrochromosomes and five pairs of microchromosomes and a pericentric inversion polymorphism on chromosome 7 that is geographically variable. We provide annotated, chromosome-scale genomes for two lizards located at opposite ends of a dynamic hybrid zone that are each fixed for different inversion polymorphisms. The assembled genomes are 1.84-1.87 Gb (1.72 Gb for scaffolds mapping to chromosomes) with a scaffold N50 of 267.5 Mb. Functional annotation of the genomes resulted in ∼15K predicted gene models. Our assemblies confirmed the presence of a 4.62-Mb pericentric inversion on chromosome 7, which contains 62 annotated coding genes with known functions. In addition, we collected population genomics data using double digest RAD-sequencing for 44 S. tristichus to estimate population structure and phylogeny across the Colorado Plateau. These new genomic resources provide opportunities to perform genomic scans and investigate the formation and spread of pericentric inversions in a naturally occurring hybrid zone.

  • characterization of a large pericentric inversion in plateau fence lizards sceloporus tristichus evidence from chromosome scale genomes
    bioRxiv, 2020
    Co-Authors: Adam D. Leaché, Ana M Bedoya
    Abstract:

    Spiny lizards in the genus Sceloporus are a model system among squamate reptiles for studies of chromosomal evolution. While most pleurodont iguanians retain an ancestral karyotype formula of 2n=36 chromosomes, Sceloporus exhibits substantial kary- otype variation ranging from 2n=22 to 2n=46 chromosomes. In this study, we present two annotated chromosome-scale genome assemblies for the Plateau Fence Lizard (Sceloporus tristichus) in order to facilitate research on the role of pericentric inversion polymorphisms on adaptation and speciation. Based on previous karyotype work using conventional staining, the S. tristichus genome is characterized as 2n=22 with 6 pairs of macrochromosomes and 5 pairs of microchromosomes with a large pericentric inversion polymorphism on chromosome seven that is geographically variable. We provide annotated, chromosome-scale genomes for two lizards located at opposite ends of a dynamic hybrid zone that are each fixed for different inversion polymorphisms. The assembled genomes are 1.84 to 1.87 Gb (1.72 Gb for scaffolds mapping to chromosomes) with a scaffold N50 of 267.5 Mb. Functional annotation of the genomes resulted in 65,417 annotated genes, 16,426 of which were deduced to have a function. We confirmed the presence of a 4.62 Mb pericentric inversion on chromosome seven, which contains 59 annotated coding genes with known functions. These new genomic resources provide opportunities to perform genomic scans and investigate the formation and spread of pericentric inversions in a naturally occurring hybrid zone. Key words: chromosome rearrangement, de novo assembly, hybrid zone, pericentric inversion, phrynosomatidae, Sceloporus, genome sequencing.

Maria M. Viveiros - One of the best experts on this subject based on the ideXlab platform.

  • Depletion of Pericentrin in mouse oocytes disrupts microtubule organizing center function and meiotic spindle organization.
    Molecular reproduction and development, 2014
    Co-Authors: Maria M. Viveiros
    Abstract:

    SUMMARY Accurate chromosome segregation is dependent on the formation and stability of the microtubule spindle apparatus. Meiotic spindle assembly in oocytes differs from the process used during mitosis, and is regulated by unique microtubule organizing centers (MTOCs) that lack centrioles. To gain insight into the molecular composition and function of acentriolar MTOCs in mouse oocytes, we assessed the role of a key MTOC-associated protein, Pericentrin (PCNT). In somatic cells, Pericentrin functions as a scaffold that binds specific proteins at MTOCs, including γ-tubulin, which is necessary for microtubule nucleation. Pericentrin is expressed in oocytes, but the conservation of its function is not known. Pericentrin localizes specifically to MTOCs during prophase-I arrest in mouse oocytes recovered from pre-ovulatory ovarian follicles, and remains associated with MTOCs at spindle poles during metaphase-I and -II. To test function, specific siRNAs were used to knock down Pcnt transcripts in mouse oocytes. Efficient protein depletion was confirmed by Western blot as well as immunofluorescence analysis. Notably, meiotic spindle structure and chromosome alignment were disrupted in Pcnt-depleted oocytes. Disorganized spindle structures with reduced microtubule density and misaligned chromosomes were observed in the majority of these oocytes (∼70%). In addition, γ-tubulin localization to MTOCs was significantly reduced and microtubule regrowth, following cold treatment, was delayed in Pcnt-depleted oocytes. Thus, Pericentrin is a key functional component of the unique acentriolar MTOCs of mouse oocytes, and plays an important role in regulating meiotic spindle assembly and/or stability. Mol. Reprod. Dev. 81: 1019–1029, 2014. © 2014 Wiley Periodicals, Inc.

  • Protein kinase C delta (PKCδ) interacts with microtubule organizing center (MTOC)-associated proteins and participates in meiotic spindle organization
    Developmental biology, 2008
    Co-Authors: Jessica A. Koch, Maria M. Viveiros
    Abstract:

    Defects in meiotic spindle structure can lead to chromosome segregation errors and genomic instability. In this study the potential role of protein kinase C delta (PKCdelta) on meiotic spindle organization was evaluated in mouse oocytes. PKCdelta was previously shown to be phosphorylated during meiotic maturation and concentrate on the meiotic spindle during metaphases I and II. Currently we show that when phosphorylated on Threonine 505 (pPKCdelta(Thr505)), within the activation loop of its C4 domain, PKCdelta expression was restricted to the meiotic spindle poles and a few specific cytoplasmic foci. In addition, pPKCdelta(Thr505) co-localized with two key microtubule organizing center (MTOC)-associated proteins, Pericentrin and gamma-tubulin. An interaction between pPKCdelta(Thr505) and Pericentrin as well as gamma-tubulin was confirmed by co-immunoprecipitation analysis using both fetal fibroblast cells and oocytes. Notably, targeted knockdown of PKCdelta expression in oocytes using short interfering RNAs effectively reduced pPKCdelta(Thr505) protein expression at MTOCs and leads to a significant (P < 0.05) disruption of meiotic spindle organization and chromosome alignment during MI and MII. Moreover, both gamma-tubulin and Pericentrin expression at MTOCs were decreased in pPKCdelta(Thr505)-depleted oocytes. In sum, these results indicate that pPKCdelta(Thr505) interacts with MTOC-associated proteins and plays a role in meiotic spindle organization in mammalian oocytes.

Kerry Bloom - One of the best experts on this subject based on the ideXlab platform.

  • individual pericentromeres display coordinated motion and stretching in the yeast spindle
    Journal of Cell Biology, 2013
    Co-Authors: Andrew D Stephens, Julian Haase, Chloe E Snider, Rachel A Haggerty, Paula A Vasquez, Gregory M Forest, Kerry Bloom
    Abstract:

    The mitotic segregation apparatus composed of microtubules and chromatin functions to faithfully partition a duplicated genome into two daughter cells. Microtubules exert extensional pulling force on sister chromatids toward opposite poles, whereas pericentric chromatin resists with contractile springlike properties. Tension generated from these opposing forces silences the spindle checkpoint to ensure accurate chromosome segregation. It is unknown how the cell senses tension across multiple microtubule attachment sites, considering the stochastic dynamics of microtubule growth and shortening. In budding yeast, there is one microtubule attachment site per chromosome. By labeling several chromosomes, we find that pericentromeres display coordinated motion and stretching in metaphase. The pericentromeres of different chromosomes exhibit physical linkage dependent on centromere function and structural maintenance of chromosomes complexes. Coordinated motion is dependent on condensin and the kinesin motor Cin8, whereas coordinated stretching is dependent on pericentric cohesin and Cin8. Linking of pericentric chromatin through cohesin, condensin, and kinetochore microtubules functions to coordinate dynamics across multiple attachment sites.

  • bub1 kinase and sgo1 modulate pericentric chromatin in response to altered microtubule dynamics
    Current Biology, 2012
    Co-Authors: Julian Haase, Andrew D Stephens, Jolien S Verdaasdonk, Elaine Y Yeh, Kerry Bloom
    Abstract:

    Summary Background Tension sensing of bioriented chromosomes is essential for the fidelity of chromosome segregation. The spindle assembly checkpoint (SAC) conveys lack of tension or attachment to the anaphase promoting complex. Components of the SAC (Bub1) phosphorylate histone H2A (S121) and recruit the protector of cohesin, Shugoshin (Sgo1), to the inner centromere. How the chromatin structural modifications of the inner centromere are integrated into the tension sensing mechanisms and the checkpoint are not known. Results We have identified a Bub1/Sgo1-dependent structural change in the geometry and dynamics of kinetochores and the pericentric chromatin upon reduction of microtubule dynamics. The cluster of inner kinetochores contract, whereas the pericentric chromatin and cohesin that encircle spindle microtubules undergo a radial expansion. Despite its increased spatial distribution, the pericentric chromatin is less dynamic. The change in dynamics is due to histone H2A phosphorylation and Sgo1 recruitment to the pericentric chromatin, rather than microtubule dynamics. Conclusions Bub1 and Sgo1 act as a rheostat to regulate the chromatin spring and maintain force balance. Through histone H2A S121 phosphorylation and recruitment of Sgo1, Bub1 kinase softens the chromatin spring in response to changes in microtubule dynamics. The geometric alteration of all 16 kinetochores and pericentric chromatin reflect global changes in the pericentromeric region and provide mechanisms for mechanically amplifying damage at a single kinetochore microtubule.

  • Cohesin, condensin, and the intramolecular centromere loop together generate the mitotic chromatin spring
    Journal of Cell Biology, 2011
    Co-Authors: Andrew D Stephens, Leandra Vicci, Russell M. Taylor, Julian Haase, Kerry Bloom
    Abstract:

    Sister chromatid cohesion provides the mechanistic basis, together with spindle microtubules, for generating tension between bioriented chromosomes in metaphase. Pericentric chromatin forms an intramolecular loop that protrudes bidirectionally from the sister chromatid axis. The centromere lies on the surface of the chromosome at the apex of each loop. The cohesin and condensin structural maintenance of chromosomes (SMC) protein complexes are concentrated within the pericentric chromatin, but whether they contribute to tension-generating mechanisms is not known. To understand how pericentric chromatin is packaged and resists tension, we map the position of cohesin (SMC3), condensin (SMC4), and pericentric LacO arrays within the spindle. Condensin lies proximal to the spindle axis and is responsible for axial compaction of pericentric chromatin. Cohesin is radially displaced from the spindle axis and confines pericentric chromatin. Pericentric cohesin and condensin contribute to spindle length regulation and dynamics in metaphase. Together with the intramolecular centromere loop, these SMC complexes constitute a molecular spring that balances spindle microtubule force in metaphase.

  • function and assembly of dna looping clustering and microtubule attachment complexes within a eukaryotic kinetochore
    Molecular Biology of the Cell, 2009
    Co-Authors: Marybeth Anderson, Julian Haase, Kerry Bloom
    Abstract:

    The kinetochore is a complex protein–DNA assembly that provides the mechanical linkage between microtubules and the centromere DNA of each chromosome. Centromere DNA in all eukaryotes is wrapped around a unique nucleosome that contains the histone H3 variant CENP-A (Cse4p in Saccharomyces cerevisiae). Here, we report that the inner kinetochore complex (CBF3) is required for pericentric DNA looping at the Cse4p-containing nucleosome. DNA within the pericentric loop occupies a spatially confined area that is radially displaced from the interpolar central spindle. Microtubule-binding kinetochore complexes are not involved in pericentric DNA looping but are required for the geometric organization of DNA loops around the spindle microtubules in metaphase. Thus, the mitotic segregation apparatus is a composite structure composed of kinetochore and interpolar microtubules, the kinetochore, and organized pericentric DNA loops. The linkage of microtubule-binding to centromere DNA-looping complexes positions the pericentric chromatin loops and stabilizes the dynamic properties of individual kinetochore complexes in mitosis.