Ontology highlight
ABSTRACT:
PROVIDER: PRJNA504496 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Nanopore consensus error correction of ribosomal RNA operons
| PRJNA540296 | ENA
Project description:To protect against aneuploidy, chromosomes must attach to microtubules from opposite poles (“biorientation”) prior to their segregation during mitosis. Biorientation relies on the correction of erroneous attachments by the aurora B kinase, which destabilizes kinetochore-microtubule attachments that lack tension. Incorrect attachments are also avoided because sister kinetochores are intrinsically biased towards capture by microtubules from opposite poles. Here we show that shugoshin acts as a pericentromeric adaptor that plays dual roles in biorientation in budding yeast. Shugoshin maintains the aurora B kinase at kinetochores that lack tension, thereby engaging the error correction machinery. Shugoshin also recruits the chromosome-organising complex, condensin, to the pericentromere. Pericentromeric condensin biases sister kinetochores towards capture by microtubules from opposite poles. Overall, shugoshin integrates a bias to sister kinetochore capture with error correction to enable chromosome biorientation. Our findings uncover the molecular basis of the bias to sister kinetochore capture and expose shugoshin as a pericentromeric hub controlling chromosome biorientation.
2014-01-08 | GSE53856 | GEO
Project description:NoDe: a fast error-correction algorithm for pyrosequencing reads
| PRJNA257992 | ENA
Project description:To protect against aneuploidy, chromosomes must attach to microtubules from opposite poles (“biorientation”) prior to their segregation during mitosis. Biorientation relies on the correction of erroneous attachments by the aurora B kinase, which destabilizes kinetochore-microtubule attachments that lack tension. Incorrect attachments are also avoided because sister kinetochores are intrinsically biased towards capture by microtubules from opposite poles. Here we show that shugoshin acts as a pericentromeric adaptor that plays dual roles in biorientation in budding yeast. Shugoshin maintains the aurora B kinase at kinetochores that lack tension, thereby engaging the error correction machinery. Shugoshin also recruits the chromosome-organising complex, condensin, to the pericentromere. Pericentromeric condensin biases sister kinetochores towards capture by microtubules from opposite poles. Overall, shugoshin integrates a bias to sister kinetochore capture with error correction to enable chromosome biorientation. Our findings uncover the molecular basis of the bias to sister kinetochore capture and expose shugoshin as a pericentromeric hub controlling chromosome biorientation. Two experiments: Experiment A: Sgo1 is required for condensin localization in the pericentromere. Sample 1: Wild type input DNA Sample 2: Wild type Brn1-6HA ChIP DNA, Sample 3 sgo1D input DNA, Sample 4 sgo1D Brn1-6HA ChIP DNA; Experiment B: Sgo1 is not required for cohesin localization in the periecentromere: Sample 5: wild type input DNA, Sample 6 Wild type Scc1-6HA ChIP DNA, Sample 7, sgo1D input DNA, Sample 8 sgo1D Scc1-6HA ChIP DNA. 1 replicate of each repeat
2014-01-08 | E-GEOD-53856 | biostudies-arrayexpress
Project description:Kinetochore protein phosphorylation promotes the correction of erroneous microtubule attachments to ensure faithful chromosome segregation during cell division. Determining how phosphorylation executes error correction requires an understanding of whether kinetochore substrates are completely (i.e. all-or-none) or only fractionally phosphorylated. Using quantitative mass spectrometry (MS), we measured phospho-occupancy on the conserved kinetochore protein Hec1 (NDC80) that directly binds microtubules. None of the positions measured exceeded ~50% phospho-occupancy, and the cumulative phospho-occupancy changed by only ~20% in response to changes in microtubule attachment status. The narrow dynamic range of phospho-occupancy is maintained, in part, by ongoing phosphatase activity. Further, both Cdk1-Cyclin B1 and Aurora kinases phosphorylate Hec1 to enhance error correction in response to different types of microtubule attachment errors. The low inherent phospho-occupancy promotes microtubule attachment to kinetochores while the high sensitivity of kinetochore-microtubule attachments to small changes in phospho-occupancy drives error correction and ensures high mitotic fidelity.
2022-06-27 | MSV000089738 | MassIVE
Project description:Quantifying sequencing error and effective sequencing depth of liquid biopsy NGS with unique molecular identifier error correction
| PRJEB39899 | ENA
Project description:The conserved Mps1 kinase corrects improper kinetochore-microtubule attachments, thereby ensuring chromosome biorientation. Yet, its critical targets in this process remain elusive. Mps1 is also involved in the spindle assembly checkpoint (SAC), the surveillance mechanism halting chromosome segregation until biorientation is attained. Its role in SAC activation is antagonized by the PP1 phosphatase and involves phosphorylation of Knl1/Spc105, which recruits Bub1 to kinetochores to promote assembly of SAC effector complexes. A crucial question is whether error correction and SAC activation are part of a single device or separable pathways. Here we characterise a novel yeast mutant, mps1-3, defective in chromosome biorientation and SAC activation. Through an unbiased screen for suppressors, we found that mutations lowering PP1 levels at Spc105 or forced association of Bub1 with Spc105 reinstate both chromosome biorientation and SAC signalling in mps1-3 cells. Our data strongly argue that Mps1-dependent phosphorylation of the Knl1/Spc105 kinetochore scaffold is critical for Mps1 function in both chromosome biorientation and SAC activation, thus supporting the idea that a common sensory apparatus simultaneously elicits error correction and SAC signalling.
2020-02-05 | GSE144741 | GEO
Project description:Microarray data analysis Intensity of 21,939 gene features per array was extracted from scanned microarray images using Feature Extraction 5.1.1 software (Agilent Technologies), which performs background subtractions and dye normalization. This normalization method is targeted at detecting changes in relative expression of individual genes rather than global expression. Global expression change would require external normalization controls (van de Peppel et al., 2003). Text output was processed using an application developed in-house to perform ANOVA analysis (http://lgsun.grc.nia.nih.gov/ANOVA/). Intensity of features measured with a >50% error were replaced with missing values except features with very low intensity. Surrogate values equal to mean error were inserted for values that were negative or less than the probe error. Data were analyzed using ANOVA with embryonic stage as a factor. The small number of biological replications typical in expression profiling experiments results in a highly variable error variance, and this problem is usually addressed by log-ratio thresholds (Schena et al., 1995) that require subjective decisions about biological significance, or by Bayesian adjustment of error variance (Baldi and Long, 2001), which may still underestimate error variance and result in false positive results. To reduce false-positives, we opted for a very conservative error model in which error variance that is used for estimating F-statistics is the maximum of the actual error variance for this gene and the average error variance in 500 genes with similar average intensity. Statistical significance was determined using the False Discovery Rate (FDR = 10%) method (Benjamini and Hochberg, 1995). Pair-wise mean comparison was done with t-statistics and FDR=10%. Further data processing including scatter plots, hierarchical clustering, and principal component analysis (PCA) were also performed through NIA microarray analysis tool (http://lgsun.grc.nia.nih.gov/ANOVA/). The input file for NIA microarray analysis tool is available at http://lgsun.grc.nia.nih.gov/microarray/data.html
2004-01-30 | E-MEXP-73 | biostudies-arrayexpress
Project description:DNA replication-mediated error correction of ectopic CENP-A deposition maintains centromere identity
| PRJNA436748 | ENA