scholarly journals Depletion of KNL2 Results in Altered Expression of Genes Involved in Regulation of the Cell Cycle, Transcription, and Development in Arabidopsis

2019 ◽  
Vol 20 (22) ◽  
pp. 5726 ◽  
Author(s):  
Anastassia Boudichevskaia ◽  
Andreas Houben ◽  
Anne Fiebig ◽  
Klara Prochazkova ◽  
Ales Pecinka ◽  
...  
Keyword(s):  
Cell Cycle ◽  
Critical Role ◽  
Histone H3 ◽  
Global Gene Expression ◽  
Proper Function ◽  
Knockout Mutant ◽  
Flower Bud ◽  
Altered Expression ◽  
Expression Of Genes ◽  
Histone H3 Variant

Centromeres contain specialized nucleosomes at which histone H3 is partially replaced by the centromeric histone H3 variant cenH3 that is required for the assembly, maintenance, and proper function of kinetochores during mitotic and meiotic divisions. Previously, we identified a KINETOCHORE NULL 2 (KNL2) of Arabidopsis thaliana that is involved in the licensing of centromeres for the cenH3 recruitment. We also demonstrated that a knockout mutant for KNL2 shows mitotic and meiotic defects, slower development, reduced growth rate, and fertility. To analyze an effect of KNL2 mutation on global gene transcription of Arabidopsis, we performed RNA-sequencing experiments using seedling and flower bud tissues of knl2 and wild-type plants. The transcriptome data analysis revealed a high number of differentially expressed genes (DEGs) in knl2 plants. The set was enriched in genes involved in the regulation of the cell cycle, transcription, development, and DNA damage repair. In addition to comprehensive information regarding the effects of KNL2 mutation on the global gene expression, physiological changes in plants are also presented, which provides an integrated understanding of the critical role played by KNL2 in plant growth and development.

scholarly journals Imaging the fate of histone Cse4 reveals de novo replacement in S phase and subsequent stable residence at centromeres

eLife ◽  
2014 ◽  
Vol 3 ◽  
Author(s):  
Jan Wisniewski ◽  
Bassam Hajj ◽  
Jiji Chen ◽  
Gaku Mizuguchi ◽  
Hua Xiao ◽  
...  
Keyword(s):  
Cell Cycle ◽  
Elevated Temperatures ◽  
De Novo ◽  
Histone H3 ◽  
S Phase ◽  
Nuclear Accumulation ◽  
Histone H3 Variant ◽  
Functionally Impaired ◽  
Cell Cycle Dynamics ◽  
Cell Lethality

The budding yeast centromere contains Cse4, a specialized histone H3 variant. Fluorescence pulse-chase analysis of an internally tagged Cse4 reveals that it is replaced with newly synthesized molecules in S phase, remaining stably associated with centromeres thereafter. In contrast, C-terminally-tagged Cse4 is functionally impaired, showing slow cell growth, cell lethality at elevated temperatures, and extra-centromeric nuclear accumulation. Recent studies using such strains gave conflicting findings regarding the centromeric abundance and cell cycle dynamics of Cse4. Our findings indicate that internally tagged Cse4 is a better reporter of the biology of this histone variant. Furthermore, the size of centromeric Cse4 clusters was precisely mapped with a new 3D-PALM method, revealing substantial compaction during anaphase. Cse4-specific chaperone Scm3 displays steady-state, stoichiometric co-localization with Cse4 at centromeres throughout the cell cycle, while undergoing exchange with a nuclear pool. These findings suggest that a stable Cse4 nucleosome is maintained by dynamic chaperone-in-residence Scm3.

scholarly journals Ser68 phosphoregulation is essential for CENP-A deposition, centromere function and viability in mice

2021 ◽  
Author(s):  
Yuting Liu ◽  
Kehui Wang ◽  
Li Huang ◽  
Jicheng Zhao ◽  
Xinpeng Chen ◽  
...  
Keyword(s):  
Cell Cycle ◽  
Cell Viability ◽  
Histone H3 ◽  
Dependent Manner ◽  
Centromere Function ◽  
Histone H3 Variant ◽  
A Cell ◽  
Cycle Dependent ◽  
Spatiotemporal Control

Centromere identity is defined by nucleosomes containing CENP-A, a histone H3 variant. The deposition of CENP-A at centromeres is tightly regulated in a cell-cycle-dependent manner. We previously reported that the spatiotemporal control of centromeric CENP-A incorporation is mediated by the phosphorylation of CENP-A Ser68. However, a recent report argued that Ser68 phosphoregulation is dispensable for accurate CENP-A loading. Here, we report that the substitution of Ser68 of endogenous CENP-A with either Gln68 or Glu68 severely impairs CENP-A deposition and cell viability. We also find that mice harboring the corresponding mutations are lethal. Together, these results indicate that the dynamic phosphorylation of Ser68 ensures cell-cycle-dependent CENP-A deposition and cell viability.

scholarly journals Subunit interactions and arrangements in the fission yeast Mis16–Mis18–Mis19 complex

2019 ◽  
Vol 2 (4) ◽  
pp. e201900408 ◽  
Author(s):  
Melanie Korntner-Vetter ◽  
Stéphane Lefèvre ◽  
Xiao-Wen Hu ◽  
Roger George ◽  
Martin R Singleton
Keyword(s):  
Cell Cycle ◽  
Binding Site ◽  
Fission Yeast ◽  
Histone H3 ◽  
Histone H4 ◽  
Subunit Interactions ◽  
Centromeric Chromatin ◽  
Partner Protein ◽  
Histone H3 Variant

Centromeric chromatin in fission yeast is distinguished by the presence of nucleosomes containing the histone H3 variant Cnp1CENP-A. Cell cycle–specific deposition of Cnp1 requires the Mis16–Mis18–Mis19 complex, which is thought to direct recruitment of Scm3-chaperoned Cnp1/histone H4 dimers to DNA. Here, we present the structure of the essential Mis18 partner protein Mis19 and describe its interaction with Mis16, revealing a bipartite-binding site. We provide data on the stoichiometry and overall architecture of the complex and provide detailed insights into the Mis18–Mis19 interface.

Inheritance of chromatin modifications through the cell cycle

2019 ◽  
pp. 184-190
Author(s):  
John C. Lucchesi
Keyword(s):  
Cell Cycle ◽  
Histone H3 ◽  
Parent Cell ◽  
Dna Repeats ◽  
Cpg Dinucleotides ◽  
Daughter Cells ◽  
Histone H3 Variant ◽  
Dna Strands ◽  
Non Coding Rnas ◽  
Transcriptional Landscape

Following mitosis, the particular transcriptional landscape of the parent cell must be faithfully transmitted to daughter cells. Although transcription ceases, not all transcription factors are displaced. DNA methylation has been implicated in the inheritance of chromatin characteristics because maintenance DNA methyl transferases methylate CpG dinucleotides on the newly replicated strand if the corresponding GpC on the parent strand is methylated. Nucleosomes that are deposited on the newly synthesized DNA strands are made up of old and new histones, and some marks present on the old histones are maintained. The proper distribution of nucleosomes and the topological organization of the genome into topologically associating domains (TADs) must be transmitted to daughter cells. Following DNA replication, centromeres must be specified on the daughter chromatids. In most eukaryotes, centromeres are identified by the presence of nucleosomes bearing the histone H3 variant CENP-A. An additional number of proteins and non-coding RNAs originating from centric and pericentromeric DNA repeats associate with centromeres and appear to play a role in centromere function.

scholarly journals SUMO-targeted ubiquitin ligase (STUbL) Slx5 regulates proteolysis of centromeric histone H3 variant Cse4 and prevents its mislocalization to euchromatin

2016 ◽  
Vol 27 (9) ◽  
pp. 1500-1510 ◽  
Author(s):  
Kentaro Ohkuni ◽  
Yoshimitsu Takahashi ◽  
Alyona Fulp ◽  
Josh Lawrimore ◽  
Wei-Chun Au ◽  
...  
Keyword(s):  
Ubiquitin Ligase ◽  
Genome Stability ◽  
Critical Role ◽  
Histone H3 ◽  
E3 Ligases ◽  
Physiological Conditions ◽  
Histone H3 Variant ◽  
Maintain Genome Stability

Centromeric histone H3, CENP-ACse4, is essential for faithful chromosome segregation. Stringent regulation of cellular levels of CENP-ACse4 restricts its localization to centromeres. Mislocalization of CENP-ACse4 is associated with aneuploidy in yeast and flies and tumorigenesis in human cells; thus defining pathways that regulate CENP-A levels is critical for understanding how mislocalization of CENP-A contributes to aneuploidy in human cancers. Previous work in budding yeast shows that ubiquitination of overexpressed Cse4 by Psh1, an E3 ligase, partially contributes to proteolysis of Cse4. Here we provide the first evidence that Cse4 is sumoylated by E3 ligases Siz1 and Siz2 in vivo and in vitro. Ubiquitination of Cse4 by the small ubiquitin-related modifier (SUMO)-targeted ubiquitin ligase (STUbL) Slx5 plays a critical role in proteolysis of Cse4 and prevents mislocalization of Cse4 to euchromatin under normal physiological conditions. Accumulation of sumoylated Cse4 species and increased stability of Cse4 in slx5∆ strains suggest that sumoylation precedes ubiquitin-mediated proteolysis of Cse4. Slx5-mediated Cse4 proteolysis is independent of Psh1, since slx5∆ psh1∆ strains exhibit higher levels of Cse4 stability and mislocalization than either slx5∆ or psh1∆ strains. Our results demonstrate a role for Slx5 in ubiquitin-mediated proteolysis of Cse4 to prevent its mislocalization and maintain genome stability.

scholarly journals Global gene expression and secondary metabolite changes in Arabidopsis thaliana ABI4 over-expression lines

Botany ◽  
2016 ◽  
Vol 94 (8) ◽  
pp. 615-634 ◽  
Author(s):  
Bianyun Yu ◽  
Margaret Y. Gruber ◽  
Shu Wei ◽  
Rong Zhou ◽  
Dwayne Hegedus ◽  
...  
Keyword(s):  
Arabidopsis Thaliana ◽  
Secondary Metabolite ◽  
Plant Development ◽  
Global Gene Expression ◽  
Comprehensive Overview ◽  
Altered Expression ◽  
Transcript Levels ◽  
Over Expression ◽  
Expression Of Genes ◽  
Genes Encoding

Despite numerous studies on ABI4, its role in plant secondary metabolism has not been fully investigated. Here, we used metabolite profiling together with transcriptome analysis to demonstrate that ABI4 transcript levels regulate a host of secondary metabolite pathways and growth modalities in ABI4 over-expression (ABI4_OE) lines of Arabidopsis thaliana. This strategy provided a unique and comprehensive overview of the regulation of metabolic shifts in response to ABI4 transcription. We show that enhancement of ABI4 transcript levels changed seed proanthocyanidin (PA), flavonoid, and carotenoid levels in ABI4_OE seeds and 30-day-old shoots, as well as the expression of genes encoding enzymes involved in the production of these and other secondary metabolites in ABI4_OE shoots. In seeds, PA accumulated in very large uneven patches, which was dramatically different from the even distribution of PA in wild-type seeds. Shoots of ABI4_OE lines also exhibited altered expression of a range of genes involved in several aspects of plant development, including hormone and cell-wall synthesis. Alteration of such disparate secondary metabolite pathways, along with hormone and developmental pathways, suggests that ABI4 is a master regulator integrating these compounds with plant development.

scholarly journals Genetic screening identifies a SUMO protease dynamically maintaining centromeric chromatin and the associated centromere complex

2019 ◽  
Author(s):  
Sreyoshi Mitra ◽  
Dani L. Bodor ◽  
Ana F. David ◽  
João F. Mata ◽  
Beate Neumann ◽  
...  
Keyword(s):  
Cell Cycle ◽  
Genetic Screening ◽  
Chromatin Modification ◽  
Histone H3 ◽  
Centromeric Chromatin ◽  
Sumo Protease ◽  
Chromatin Regulators ◽  
Histone H3 Variant ◽  
Key Factor ◽  
Labeling Approach

AbstractCentromeres are defined by a unique self-propagating chromatin structure featuring nucleosomes containing the histone H3 variant CENP-A. CENP-A turns over slower than general chromatin and a key question is whether this unusual stability is intrinsic to CENP-A nucleosomes or rather imposed by external factors. We designed a specific genetic screen to identify proteins involved in CENP-A stability based on SNAP-tag pulse chase labeling. Using a double pulse-labeling approach we simultaneously assay for factors with selective roles in CENP-A chromatin assembly. We discover a series of new proteins involved in CENP-A propagation, including proteins with known roles in DNA replication, repair and chromatin modification and transcription, revealing that a broad set of chromatin regulators impacts in CENP-A transmission through the cell cycle. The key factor we find to strongly affect CENP-A stability is SENP6. This SUMO-protease controls not only the levels of chromatin bound CENP-A but is required for the maintenance of virtually the entire centromere and kinetochore, with the exception of CENP-B. Acute depletion of SENP6 protein reveals its requirement for maintaining centromeric CENP-A levels throughout the cell cycle, suggesting that a dynamic SUMO cycle underlies a continuous surveillance of the centromere complex.

scholarly journals The structure of the Ctf19c/CCAN from budding yeast

eLife ◽  
2019 ◽  
Vol 8 ◽  
Author(s):  
Stephen M Hinshaw ◽  
Stephen C Harrison
Keyword(s):  
Electron Microscopy ◽  
Cell Cycle ◽  
Budding Yeast ◽  
Histone H3 ◽  
Kinetochore Assembly ◽  
Microtubule Attachment ◽  
Cryo Electron Microscopy ◽  
Histone H3 Variant

Eukaryotic kinetochores connect spindlemicrotubules to chromosomal centromeres. A group of proteins called the Ctf19 complex (Ctf19c) in yeast and the constitutive centromere associated network (CCAN) in other organisms creates the foundation of a kinetochore. The Ctf19c/CCAN influences the timing of kinetochore assembly, sets its location by associating with a specialized nucleosome containing the histone H3 variant Cse4/CENP-A, and determines the organization of the microtubule attachment apparatus. We present here the structure of a reconstituted 13-subunit Ctf19c determined by cryo-electron microscopy at ~4 Å resolution. The structure accounts for known and inferred contacts with the Cse4 nucleosome and for an observed assembly hierarchy. We describe its implications for establishment of kinetochores and for their regulation by kinases throughout the cell cycle.

scholarly journals Quantitative single-molecule microscopy reveals that CENP-A Cnp1 deposition occurs during G2 in fission yeast

Open Biology ◽  
2012 ◽  
Vol 2 (7) ◽  
pp. 120078 ◽  
Author(s):  
David Lando ◽  
Ulrike Endesfelder ◽  
Harald Berger ◽  
Lakxmi Subramanian ◽  
Paul D. Dunne ◽  
...  
Keyword(s):  
Cell Cycle ◽  
Fission Yeast ◽  
Single Molecule ◽  
Cell Biology ◽  
Histone H3 ◽  
Histone Variants ◽  
Epigenetic Mechanism ◽  
Eukaryotic Cells ◽  
Stochastic Variation ◽  
Histone H3 Variant

The inheritance of the histone H3 variant CENP-A in nucleosomes at centromeres following DNA replication is mediated by an epigenetic mechanism. To understand the process of epigenetic inheritance, or propagation of histones and histone variants, as nucleosomes are disassembled and reassembled in living eukaryotic cells, we have explored the feasibility of exploiting photo-activated localization microscopy (PALM). PALM of single molecules in living cells has the potential to reveal new concepts in cell biology, providing insights into stochastic variation in cellular states. However, thus far, its use has been limited to studies in bacteria or to processes occurring near the surface of eukaryotic cells. With PALM, one literally observes and ‘counts’ individual molecules in cells one-by-one and this allows the recording of images with a resolution higher than that determined by the diffraction of light (the so-called super-resolution microscopy). Here, we investigate the use of different fluorophores and develop procedures to count the centromere-specific histone H3 variant CENP-A Cnp1 with single-molecule sensitivity in fission yeast ( Schizosaccharomyces pombe ). The results obtained are validated by and compared with ChIP-seq analyses. Using this approach, CENP-A Cnp1 levels at fission yeast ( S. pombe ) centromeres were followed as they change during the cell cycle. Our measurements show that CENP-A Cnp1 is deposited solely during the G2 phase of the cell cycle.

Sign in / Sign up

Export Citation Format

Share Document