Quantifying Changes in Chromosome Position to Assess Chromokinesin Activity

2022 ◽  
pp. 139-149
Author(s):  
Alex F. Thompson ◽  
Sarah Vandal ◽  
Jason Stumpff
Keyword(s):  
Chromosome Position

scholarly journals Motile kinetochores and polar ejection forces dictate chromosome position on the vertebrate mitotic spindle

1994 ◽  
Vol 124 (3) ◽  
pp. 223-233 ◽  
Author(s):  
CL Rieder ◽  
ED Salmon
Keyword(s):  
Mitotic Spindle ◽  
Constant Velocity ◽  
Molecular Mechanisms ◽  
Dynamic Instability ◽  
Microtubule Dynamic ◽  
Pole Motion ◽  
Microtubule Motors ◽  
Chromosome Position ◽  
Pulling Forces

We argue that hypotheses for how chromosomes achieve a metaphase alignment, that are based solely on a tug-of-war between poleward pulling forces produced along the length of opposing kinetochore fibers, are no longer tenable for vertebrates. Instead, kinetochores move themselves and their attached chromosomes, poleward and away from the pole, on the ends of relatively stationary but shortening/elongating kinetochore fiber microtubules. Kinetochores are also "smart" in that they switch between persistent constant-velocity phases of poleward and away from the pole motion, both autonomously and in response to information within the spindle. Several molecular mechanisms may contribute to this directional instability including kinetochore-associated microtubule motors and kinetochore microtubule dynamic instability. The control of kinetochore directional instability, to allow for congression and anaphase, is likely mediated by a vectorial mechanism whose magnitude and orientation depend on the density and orientation or growth of polar microtubules. Polar microtubule arrays have been shown to resist chromosome poleward motion and to push chromosomes away from the pole. These "polar ejection forces" appear to play a key role in regulating kinetochore directional instability, and hence, positions achieved by chromosomes on the spindle.

scholarly journals VariantKey: A Reversible Numerical Representation of Human Genetic Variants

2018 ◽  
Author(s):  
Nicola Asuni ◽  
Steven Wilder
Keyword(s):  
Open Source Software ◽  
Genetic Variants ◽  
Data Representation ◽  
Lookup Table ◽  
Memory Allocation ◽  
Computer Memory ◽  
Numerical Representation ◽  
Chromosome Position ◽  
The Individual ◽  
Genomic Regions

AbstractHuman genetic variants are usually represented by four values with variable length: chromosome, position, reference and alternate alleles. There is no guarantee that these components are represented in a consistent way across different data sources, and processing variant-based data can be inefficient because four different comparison operations are needed for each variant, three of which are string comparisons. Existing variant identifiers do not typically represent every possible variant we may be interested in, nor they are directly reversible. Similarly, genomic regions are typically represented inconsistently by three or four values. Working with strings, in contrast to numbers, poses extra challenges on computer memory allocation and data-representation. To overcome these limitations, a novel reversible numerical encoding schema for human genetic variants (VariantKey) and genomics regions (RegionKey), is presented here alongside a multi-language open-source software implementation (https://github.com/Genomicsplc/variantkey). VariantKey and RegionKey represents variants and regions as single 64 bit numeric entities, while preserving the ability to be searched and sorted by chromosome and position. The individual components of short variants can be directly read back from the VariantKey, while long variants are supported with a fast lookup table.

scholarly journals Degradation of the Repetitive Genomic Landscape in a Close Relative of Caenorhabditis elegans

2020 ◽  
Vol 37 (9) ◽  
pp. 2549-2567 ◽  
Author(s):  
Gavin C Woodruff ◽  
Anastasia A Teterina
Keyword(s):  
Caenorhabditis Elegans ◽  
Recombination Rate ◽  
Genomic Organization ◽  
Reproductive Mode ◽  
Repetitive Elements ◽  
Repeat Content ◽  
Genomic Landscape ◽  
Chromosome Position ◽  
Caenorhabditis Species ◽  
Evolutionary Simulations

Abstract The abundance, diversity, and genomic distribution of repetitive elements is highly variable among species. These patterns are thought to be driven in part by reproductive mode and the interaction of selection and recombination, and recombination rates typically vary by chromosomal position. In the nematode Caenorhabditis elegans, repetitive elements are enriched at chromosome arms and depleted on centers, and this mirrors the chromosomal distributions of other genomic features such as recombination rate. How conserved is this genomic landscape of repeats, and what evolutionary forces maintain it? To address this, we compared the genomic organization of repetitive elements across five Caenorhabditis species with chromosome-level assemblies. As previously reported, repeat content is enriched on chromosome arms in most Caenorhabditis species, and no obvious patterns of repeat content associated with reproductive mode were observed. However, the fig-associated C. inopinata has experienced repetitive element expansion and reveals no association of global repeat density with chromosome position. Patterns of repeat superfamily specific distributions reveal this global pattern is driven largely by a few repeat superfamilies that in C. inopinata have expanded in number and have weak associations with chromosome position. Additionally, 15% of predicted protein-coding genes in C. inopinata align to transposon-related proteins. When these are excluded, C. inopinata has no enrichment of genes in chromosome centers, in contrast to its close relatives who all have such clusters. Forward evolutionary simulations reveal that chromosomal heterogeneity in recombination rate alone can generate structured repetitive genomic landscapes when insertions are weakly deleterious, whereas chromosomal heterogeneity in the fitness effects of transposon insertion can promote such landscapes across a variety of evolutionary scenarios. Thus, patterns of gene density along chromosomes likely contribute to global repetitive landscapes in this group, although other historical or genomic factors are needed to explain the idiosyncrasy of genomic organization of various transposable element taxa within C. inopinata. Taken together, these results highlight the power of comparative genomics and evolutionary simulations in testing hypotheses regarding the causes of genome organization.

scholarly journals Genetic Dissection of Grain Yield and Agronomic Traits in Maize under Optimum and Low-Nitrogen Stressed Environments

2020 ◽  
Vol 21 (2) ◽  
pp. 543 ◽  
Author(s):  
Berhanu Tadesse Ertiro ◽  
Michael Olsen ◽  
Biswanath Das ◽  
Manje Gowda ◽  
Maryke Labuschagne
Keyword(s):  
Grain Yield ◽  
Agronomic Traits ◽  
Genotyping By Sequencing ◽  
Genetic Dissection ◽  
Common Qtl ◽  
Chromosome Position ◽  
Maize Varieties ◽  
Dh Lines ◽  
Genomic Regions ◽  
Low Nitrogen

Understanding the genetic basis of maize grain yield and other traits under low-nitrogen (N) stressed environments could improve selection efficiency. In this study, five doubled haploid (DH) populations were evaluated under optimum and N-stressed conditions, during the main rainy season and off-season in Kenya and Rwanda, from 2014 to 2015. Identifying the genomic regions associated with grain yield (GY), anthesis date (AD), anthesis-silking interval (ASI), plant height (PH), ear height (EH), ear position (EPO), and leaf senescence (SEN) under optimum and N-stressed environments could facilitate the use of marker-assisted selection to develop N-use-efficient maize varieties. DH lines were genotyped with genotyping by sequencing. A total of 13, 43, 13, 25, 30, 21, and 10 QTL were identified for GY, AD ASI, PH, EH, EPO, and SEN, respectively. For GY, PH, EH, and SEN, the highest number of QTL was found under low-N environments. No common QTL between optimum and low-N stressed conditions were identified for GY and ASI. For secondary traits, there were some common QTL for optimum and low-N conditions. Most QTL conferring tolerance to N stress was on a different chromosome position under optimum conditions.

Chromosome distribution between two restitution nuclei in a cell following colchicine treatment

1983 ◽  
Vol 25 (5) ◽  
pp. 437-445 ◽  
Author(s):  
D. Davidson ◽  
E. Pertens ◽  
J.-P. Zhao
Keyword(s):  
Colchicine Treatment ◽  
Hordeum Vulgare L ◽  
Chromosome Distribution ◽  
Chromatid Segregation ◽  
Chromosome Position ◽  
Allium Cepa L ◽  
Secale Cereale L ◽  
Prophase Nucleus ◽  
A Cell ◽  
Group Chromosome

Roots of Zea mays L., Secale cereale L., Vicia faba, L., Allium cepa L., and Hordeum vulgare L. were treated with colchicine. C-metaphases were observed in cells which had chromosomes present in two distinct groups, not the typical single group. Chromosome distribution into two groups was not followed by chromatid segregation: instead, the chromosomes underwent restitution and binucleate-interphase cells were formed. The distribution of chromosomes into two groups is functionally equivalent to chromosome nondisjunction. In some cases, the two groups contained different numbers of chromosomes; these gave rise to aneuploid nuclei. The results support the view that the pattern of chromosome distribution into two groups is not random; it may reflect chromosome position in the interphase or prophase nucleus. The results are related to (i) the formation of genotypic and phenotypic mosaics produced by treatment with other microtubule inhibiting drugs or in response to cell division mutants and (ii) the spatial distribution of chromosomes within the nucleus.

scholarly journals CENP-E Is Essential for Reliable Bioriented Spindle Attachment, but Chromosome Alignment Can Be Achieved via Redundant Mechanisms in Mammalian Cells

2001 ◽  
Vol 12 (9) ◽  
pp. 2776-2789 ◽  
Author(s):  
Bruce F. McEwen ◽  
Gordon K.T. Chan ◽  
Beata Zubrowski ◽  
Matthew S. Savoian ◽  
Matthew T. Sauer ◽  
...  
Keyword(s):  
Mammalian Cells ◽  
Protein Localization ◽  
Mitotic Arrest ◽  
Spindle Pole ◽  
Critical Determinant ◽  
Microtubule Binding ◽  
Checkpoint Protein ◽  
Spindle Poles ◽  
Chromosome Position ◽  
Chromosome Alignment

CENP-E is a kinesin-like protein that when depleted from mammalian kinetochores leads to mitotic arrest with a mixture of aligned and unaligned chromosomes. In the present study, we used immunofluorescence, video, and electron microscopy to demonstrate that depletion of CENP-E from kinetochores via antibody microinjection reduces kinetochore microtubule binding by 23% at aligned chromosomes, and severely reduces microtubule binding at unaligned chromosomes. Disruption of CENP-E function also reduces tension across the centromere, increases the incidence of spindle pole fragmentation, and results in monooriented chromosomes approaching abnormally close to the spindle pole. Nevertheless, chromosomes show typical patterns of congression, fast poleward motion, and oscillatory motions. Furthermore, kinetochores of aligned and unaligned chromosomes exhibit normal patterns of checkpoint protein localization. These data are explained by a model in which redundant mechanisms enable kinetochore microtubule binding and checkpoint monitoring in the absence of CENP-E at kinetochores, but where reduced microtubule-binding efficiency, exacerbated by poor positioning at the spindle poles, results in chronically monooriented chromosomes and mitotic arrest. Chromosome position within the spindle appears to be a critical determinant of CENP-E function at kinetochores.

scholarly journals Chromosome position determines the success of double-strand break repair

2015 ◽  
Vol 113 (2) ◽  
pp. E146-E154 ◽  
Author(s):  
Cheng-Sheng Lee ◽  
Ruoxi W. Wang ◽  
Hsiao-Han Chang ◽  
Daniel Capurso ◽  
Mark R. Segal ◽  
...  
Keyword(s):  
Donor Site ◽  
Strand Break ◽  
Double Strand Break ◽  
Target Sequence ◽  
Dsb Repair ◽  
Enhancer Element ◽  
Protein Factor ◽  
Repair Efficiency ◽  
Chromosome Position ◽  
Donor Locus

Repair of a chromosomal double-strand break (DSB) by gene conversion depends on the ability of the broken ends to encounter a donor sequence. To understand how chromosomal location of a target sequence affects DSB repair, we took advantage of genome-wide Hi-C analysis of yeast chromosomes to create a series of strains in which an induced site-specific DSB in budding yeast is repaired by a 2-kb donor sequence inserted at different locations. The efficiency of repair, measured by cell viability or competition between each donor and a reference site, showed a strong correlation (r = 0.85 and 0.79) with the contact frequencies of each donor with the DSB repair site. Repair efficiency depends on the distance between donor and recipient rather than any intrinsic limitation of a particular donor site. These results further demonstrate that the search for homology is the rate-limiting step in DSB repair and suggest that cells often fail to repair a DSB because they cannot locate a donor before other, apparently lethal, processes arise. The repair efficiency of a donor locus can be improved by four factors: slower 5′ to 3′ resection of the DSB ends, increased abundance of replication protein factor A (RPA), longer shared homology, or presence of a recombination enhancer element adjacent to a donor.

scholarly journals Versatile multi-transgene expression using improved BAC TG-EMBED toolkit, novel BAC episomes, and BAC-MAGIC

2019 ◽  
Author(s):  
Binhui Zhao ◽  
Pankaj Chaturvedi ◽  
David L. Zimmerman ◽  
Andrew S. Belmont
Keyword(s):  
Mammalian Cells ◽  
Transgene Expression ◽  
Large Fraction ◽  
Fine Tuning ◽  
Cmv Promoter ◽  
Chromosome Position ◽  
High Level ◽  
Genomic Regions ◽  
Expression In Mammalian Cells

ABSTRACTAchieving reproducible, stable, and high-level transgene expression in mammalian cells remains problematic. Previously, we attained copy-number-dependent, chromosome-position-independent expression of reporter minigenes by embedding them within a BAC containing the mouseMsh3-Dhfrlocus (DHFR BAC). Here we extend this “BAC TG-EMBED” approach. First, we report a toolkit of endogenous promoters capable of driving transgene expression over a 0.01-5 fold expression range relative to the CMV promoter, allowing fine-tuning of relative expression levels of multiple reporter genes expressed on a single BAC. Second, we show small variability in both the expression level and long-term expression stability of a reporter gene embedded in BACs containing either transcriptionally active or inactive genomic regions, making choice of BACs more flexible. Third, we describe an intriguing phenomenon in which BAC transgenes are maintained as episomes in a large fraction of stably selected clones. Finally, we demonstrate the utility of BAC TG-EMBED by simultaneously labeling three nuclear compartments in 94% of stable clones using a multi-reporter DHFR BAC, constructed with a combination of synthetic biology and BAC recombineering tools. Our extended BAC TG-EMBED method provides a versatile platform for achieving reproducible, stable simultaneous expression of multiple transgenes maintained either as episomes or stably integrated copies.

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