Genome-Wide Identification and Analysis of Cell Cycle Genes in Betula pendula

Research Highlights: This study identified the cell cycle genes in birch that likely play important roles during plant growth and development. This provides a basis for understanding the regulatory mechanism of various cell cycles in Betula pendula. Background and Objectives: The cell cycle factors not only influence cell cycle progression together, but also regulate accretion, division and differentiation of cells, and then regulate growth and development of plant. In this study, we identified the putative cell cycle genes in B. pendula genome, based on the annotated cell cycle genes in A. thaliana. It could serve as a foundation for further functional studies. Materials and Methods: The transcript abundance was determined for all the cell cycle genes in xylem, root, leaf and flower tissues using RNA-seq technology. Results: We identified 59cell cycle gene models in the genome of B. pendula, 17 highly expression genes among them. These genes were BpCDKA.1, BpCDKB1.1, BpCDKB2.1, BpCKS1.2, BpCYCB1.1, BpCYCB1.2, BpCYCB2.1, BpCYCD3.1, BpCYCD3.5, BpDEL1, BpDpa2, BpE2Fa, BpE2Fb, BpKRP1, BpKRP2, BpRb1 and BpWEE1. Conclusions: We identified 17 core cell cycle genes in the genome of birch by combining phylogenetic analysis and tissue specific expression data.

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Genome-Wide Identification and Analysis of Cell Cycle Genes in Betula pendula

10.20944/preprints202112.0149.v2 ◽

2021 ◽

Author(s):

Yijie Li ◽

Song Chen ◽

Yuhang Liu ◽

Haijiao Huang

Keyword(s):

Cell Cycle ◽

Growth And Development ◽

Betula Pendula ◽

Cell Cycle Progression ◽

Transcript Abundance ◽

Cell Cycle Gene ◽

Specific Expression ◽

Cell Cycles ◽

Cell Cycle Genes ◽

Functional Studies

Research Highlights: This study identified the cell cycle genes in birch that likely play important roles during plant growth and development. This analysis provides a basis for understanding the regulatory mechanism of various cell cycles in Betula pendula. Background and Objectives: The cell cycle factors not only influence cell cycle progression together, but also regulate accretion, division and differentiation of cells, and then regulate growth and development of plant. In this study, we identified the putative cell cycle genes in B. pendula genome, based on the annotated cell cycle genes in A. thaliana. It could serve as a foundation for further functional studies. Materials and Methods: The transcript abundance was determined for all the cell cycle genes in xylem, root, leaf and flower tissues using RNA-seq technology. Results: We identified 59 cell cycle gene models in the genome of B. pendula, 17 highly expression genes among them. These genes were BpCDKA.1, BpCDKB1.1, BpCDKB2.1, BpCKS1.2, BpCYCB1.1, BpCYCB1.2, BpCYCB2.1, BpCYCD3.1, BpCYCD3.5, BpDEL1, BpDpa2, BpE2Fa, BpE2Fb, BpKRP1, BpKRP2, BpRb1 and BpWEE1. Conclusions: We identified 17 core cell cycle genes in the genome of birch by combining phylogenetic analysis and tissue specific expression data.

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Genome-Wide Identification and Analysis of Cell Cycle Genes in Birch

Forests ◽

10.3390/f13010120 ◽

2022 ◽

Vol 13 (1) ◽

pp. 120

Author(s):

Yijie Li ◽

Song Chen ◽

Yuhang Liu ◽

Haijiao Huang

Keyword(s):

Cell Cycle ◽

Growth And Development ◽

Betula Pendula ◽

Cell Cycle Gene ◽

Expression Data ◽

Rna Seq ◽

Specific Expression ◽

Cell Cycles ◽

Cell Cycle Genes ◽

Genome Wide

Research Highlights: This study identified the cell cycle genes in birch that likely play important roles during the plant’s growth and development. This analysis provides a basis for understanding the regulatory mechanism of various cell cycles in Betula pendula Roth. Background and Objectives: The cell cycle factors not only influence cell cycles progression together, but also regulate accretion, division, and differentiation of cells, and then regulate growth and development of the plant. In this study, we identified the putative cell cycle genes in the B. pendula genome, based on the annotated cell cycle genes in Arabidopsis thaliana (L.) Heynh. It can be used as a basis for further functional research. Materials and Methods: RNA-seq technology was used to determine the transcription abundance of all cell cycle genes in xylem, roots, leaves, and floral tissues. Results: We identified 59 cell cycle gene models in the genome of B. pendula, with 17 highly expression genes among them. These genes were BpCDKA.1, BpCDKB1.1, BpCDKB2.1, BpCKS1.2, BpCYCB1.1, BpCYCB1.2, BpCYCB2.1, BpCYCD3.1, BpCYCD3.5, BpDEL1, BpDpa2, BpE2Fa, BpE2Fb, BpKRP1, BpKRP2, BpRb1, and BpWEE1. Conclusions: By combining phylogenetic analysis and tissue-specific expression data, we identified 17 core cell cycle genes in the Betulapendula genome.

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Alu RNA Modulates the Expression of Cell Cycle Genes in Human Fibroblasts

International Journal of Molecular Sciences ◽

10.3390/ijms20133315 ◽

2019 ◽

Vol 20 (13) ◽

pp. 3315 ◽

Cited By ~ 3

Author(s):

Simona Cantarella ◽

Davide Carnevali ◽

Marco Morselli ◽

Anastasia Conti ◽

Matteo Pellegrini ◽

...

Keyword(s):

Cell Cycle ◽

Cell Cycle Progression ◽

Human Fibroblasts ◽

Rna Polymerase Iii ◽

Protein Coding ◽

Non Coding Rna ◽

Genome Wide ◽

Hela Cell Lines ◽

Significant Enrichment ◽

Alu Rna

Alu retroelements, whose retrotransposition requires prior transcription by RNA polymerase III to generate Alu RNAs, represent the most numerous non-coding RNA (ncRNA) gene family in the human genome. Alu transcription is generally kept to extremely low levels by tight epigenetic silencing, but it has been reported to increase under different types of cell perturbation, such as viral infection and cancer. Alu RNAs, being able to act as gene expression modulators, may be directly involved in the mechanisms determining cellular behavior in such perturbed states. To directly address the regulatory potential of Alu RNAs, we generated IMR90 fibroblasts and HeLa cell lines stably overexpressing two slightly different Alu RNAs, and analyzed genome-wide the expression changes of protein-coding genes through RNA-sequencing. Among the genes that were upregulated or downregulated in response to Alu overexpression in IMR90, but not in HeLa cells, we found a highly significant enrichment of pathways involved in cell cycle progression and mitotic entry. Accordingly, Alu overexpression was found to promote transition from G1 to S phase, as revealed by flow cytometry. Therefore, increased Alu RNA may contribute to sustained cell proliferation, which is an important factor of cancer development and progression.

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A Genetic Screen for Suppressors and Enhancers of the Drosophila Cdk1-Cyclin B Identifies Maternal Factors That Regulate Microtubule and Microfilament Stability

Genetics ◽

10.1093/genetics/162.3.1179 ◽

2002 ◽

Vol 162 (3) ◽

pp. 1179-1195 ◽

Cited By ~ 3

Author(s):

Jun-Yuan Ji ◽

Marjan Haghnia ◽

Cory Trusty ◽

Lawrence S B Goldstein ◽

Gerold Schubiger

Keyword(s):

Cell Cycle ◽

Cell Cycle Progression ◽

Genetic Screen ◽

Cyclin B ◽

Gene Products ◽

Nuclear Movement ◽

Cell Cycles ◽

Major Mechanism ◽

Cytoskeletal Dynamics ◽

Chromosome Bridges

Abstract Coordination between cell-cycle progression and cytoskeletal dynamics is important for faithful transmission of genetic information. In early Drosophila embryos, increasing maternal cyclin B leads to higher Cdk1-CycB activity, shorter microtubules, and slower nuclear movement during cycles 5-7 and delays in nuclear migration to the cortex at cycle 10. Later during cycle 14 interphase of six cycB embryos, we observed patches of mitotic nuclei, chromosome bridges, abnormal nuclear distribution, and small and large nuclei. These phenotypes indicate disrupted coordination between the cell-cycle machinery and cytoskeletal function. Using these sensitized phenotypes, we performed a dosage-sensitive genetic screen to identify maternal proteins involved in this process. We identified 10 suppressors classified into three groups: (1) gene products regulating Cdk1 activities, cdk1 and cyclin A; (2) gene products interacting with both microtubules and microfilaments, Actin-related protein 87C; and (3) gene products interacting with microfilaments, chickadee, diaphanous, Cdc42, quail, spaghetti-squash, zipper, and scrambled. Interestingly, most of the suppressors that rescue the astral microtubule phenotype also reduce Cdk1-CycB activities and are microfilament-related genes. This suggests that the major mechanism of suppression relies on the interactions among Cdk1-CycB, microtubule, and microfilament networks. Our results indicate that the balance among these different components is vital for normal early cell cycles and for embryonic development. Our observations also indicate that microtubules and cortical microfilaments antagonize each other during the preblastoderm stage.

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The NIMA-related kinase X-Nek2B is required for efficient assembly of the zygotic centrosome in Xenopus laevis

Journal of Cell Science ◽

10.1242/jcs.113.11.1973 ◽

2000 ◽

Vol 113 (11) ◽

pp. 1973-1984 ◽

Cited By ~ 7

Author(s):

A.M. Fry ◽

P. Descombes ◽

C. Twomey ◽

R. Bacchieri ◽

E.A. Nigg

Keyword(s):

Cell Cycle ◽

Xenopus Laevis ◽

Basal Body ◽

Chromatin Condensation ◽

Embryonic Cells ◽

Serine Threonine Kinase ◽

Cell Cycles ◽

Functional Studies ◽

Mammalian Cell Cycle ◽

Egg Extracts

Nek2 is a mammalian cell cycle-regulated serine/threonine kinase that belongs to the family of proteins related to NIMA of Aspergillus nidulans. Functional studies in diverse species have implicated NIMA-related kinases in G(2)/M progression, chromatin condensation and centrosome regulation. To directly address the requirements for vertebrate Nek2 kinases in these cell cycle processes, we have turned to the biochemically-tractable system provided by Xenopus laevis egg extracts. Following isolation of a Xenopus homologue of Nek2, called X-Nek2B, we found that X-Nek2B abundance and activity remained constant through the first mitotic cycle implying a fundamental difference in Nek2 regulation between embryonic and somatic cell cycles. Removal of X-Nek2B from extracts did not disturb either entry into mitosis or the accompanying condensation of chromosomes providing no support for a requirement for Nek2 in these processes at least in embryonic cells. In contrast, X-Nek2B localized to centrosomes of adult Xenopus cells and was rapidly recruited to the basal body of Xenopus sperm following incubation in egg extracts. Recruitment led to phosphorylation of the X-Nek2B kinase. Most importantly, depletion of X-Nek2B from extracts significantly delayed both the assembly of microtubule asters and the recruitment of gamma-tubulin to the basal body. Hence, these studies demonstrate that X-Nek2B is required for efficient assembly of a functional zygotic centrosome and highlight the possibility of multiple roles for vertebrate Nek2 kinases in the centrosome cycle.

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Stage specific expression of cell cycle genes during in vivo or in vitro development of ovarian follicles in sheep

Small Ruminant Research ◽

10.1016/j.smallrumres.2016.08.011 ◽

2016 ◽

Vol 143 ◽

pp. 1-7 ◽

Cited By ~ 2

Author(s):

V. Praveen Chakravarthi ◽

S.S.R. Kona ◽

A.V.N. Siva Kumar ◽

M. Bhaskara ◽

V.H. Rao

Keyword(s):

Cell Cycle ◽

Ovarian Follicles ◽

Specific Expression ◽

In Vitro Development ◽

Cell Cycle Genes ◽

Vitro Development

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Genome-Wide Analysis of Core Cell Cycle Genes in the Unicellular Green Alga Ostreococcus tauri

Molecular Biology and Evolution ◽

10.1093/molbev/msi044 ◽

2004 ◽

Vol 22 (3) ◽

pp. 589-597 ◽

Cited By ~ 36

Author(s):

Steven Robbens ◽

Basheer Khadaroo ◽

Alain Camasses ◽

Evelyne Derelle ◽

Conchita Ferraz ◽

...

Keyword(s):

Cell Cycle ◽

Green Alga ◽

Genome Wide Analysis ◽

Cell Cycle Genes ◽

Ostreococcus Tauri ◽

Genome Wide ◽

Unicellular Green Alga

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GATA-2 Controls Proliferation of Megakaryocyte Progenitors and Its Expression Contributes to Human DS-AMKL.

Blood ◽

10.1182/blood.v112.11.1380.1380 ◽

2008 ◽

Vol 112 (11) ◽

pp. 1380-1380

Author(s):

Zan Huang ◽

John Crispino

Keyword(s):

Cell Cycle ◽

Cell Cycle Progression ◽

Blast Crisis ◽

Myelogenous Leukemia ◽

Chromosome 21 ◽

Cell Cycle Regulators ◽

Megakaryoblastic Leukemia ◽

Aberrant Gene Expression ◽

Genome Wide ◽

Aberrant Gene

Abstract GATA2 is an essential transcription factor that regulates multiple aspects of hematopoiesis. Mutations in GATA2 are associated with blast crisis phase of chronic myelogenous leukemia (CML) while overexpression of GATA2 is a hallmark of Down syndrome acute megakaryoblastic leukemia (DS-AMKL), a malignancy that is defined by the combination of trisomic chromosome 21 and a GATA1 mutation. Here, we show thatGATA2 is essential for megakaryocyte development from both wild-type and GATA-1mutant hematopoietic progenitors. Furthermore, we reveal that GATA2 is indispensable for cell cycle progression and that its expression cooperates with activated JAK3 to promote TPO-independent expansion of megakaryocytes. Genome-wide microarray analysis revealed that GATA2 regulates a wide set of genes including cell cycle regulators and lineage-specific genes that are essential for terminal differentiation of megakaryocytes. Of note, a subset of genes within the GATA2 signature is contained within human DS-AMKL patient specimens. These observations implicate overexpression of GATA2 in the aberrant gene expression and proliferation of AMKL. Taken together, our data demonstrate thatGATA2 is a critical regulator of normal and malignant megakaryopoiesis.

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