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

Forests ◽  
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.

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

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.

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

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 ◽  
Specific Expression ◽  
Cell Cycles ◽  
Cell Cycle Genes ◽  
Functional Studies ◽  
Genome Wide

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.

scholarly journals Unbiased Boolean analysis of public gene expression data for cell cycle gene identification

2019 ◽  
Vol 30 (14) ◽  
pp. 1770-1779 ◽  
Author(s):  
Sarah A. Dabydeen ◽  
Arshad Desai ◽  
Debashis Sahoo
Keyword(s):  
Gene Expression ◽  
Cell Cycle ◽  
Gene Expression Data ◽  
Boolean Logic ◽  
Cell Cycle Gene ◽  
Data Sets ◽  
Expression Data ◽  
Cell Cycle Genes ◽  
Logic Approach ◽  
Definition Of

Cell proliferation is essential for the development and maintenance of all organisms and is dysregulated in cancer. Using synchronized cells progressing through the cell cycle, pioneering microarray studies defined cell cycle genes based on cyclic variation in their expression. However, the concordance of the small number of synchronized cell studies has been limited, leading to discrepancies in definition of the transcriptionally regulated set of cell cycle genes within and between species. Here we present an informatics approach based on Boolean logic to identify cell cycle genes. This approach used the vast array of publicly available gene expression data sets to query similarity to CCNB1, which encodes the cyclin subunit of the Cdk1-cyclin B complex that triggers the G2-to-M transition. In addition to highlighting conservation of cell cycle genes across large evolutionary distances, this approach identified contexts where well-studied genes known to act during the cell cycle are expressed and potentially acting in nondivision contexts. An accessible web platform enables a detailed exploration of the cell cycle gene lists generated using the Boolean logic approach. The methods employed are straightforward to extend to processes other than the cell cycle.

scholarly journals Phosphate transporter genes: genome-wide identification and characterization in Camelina sativa

2021 ◽  
Author(s):  
Soosan Hasanzadeh ◽  
Sahar Faraji ◽  
Abdullah ◽  
Parviz Heidari
Keyword(s):  
Phosphate Transporter ◽  
Rna Seq ◽  
Specific Expression ◽  
Cis Acting ◽  
Genome Wide ◽  
Sodium Dependent ◽  
Intron Number ◽  
Response To Stress ◽  
Growth Energy ◽  
Root Tissues

Phosphorus is known as a key element associated with growth, energy, and cell signaling. In plants, phosphate transporters (PHTs) are responsible for moving and distributing phosphorus in cells and organs. PHT genes have been genome-wide identified and characterized in various plant species, however, these genes have not been widely identified based on available genomic data in Camellia sativa, which is an important oil seed plant. In the present study, we found 66 PHT genes involved in phosphate transporter/translocate in C. sativa. The recognized genes belonged to PHTs1, PHTs2, PHTs4, PHOs1, PHO1 homologs, glycerol-3-PHTs, sodium dependent PHTs, inorganic PHTs, xylulose 5-PHTs, glucose-6-phosphate translocators, and phosphoenolpyruvate translocators. Our finding revealed that PHT proteins are divers based on their physicochemical properties such as Isoelectric point (pI), molecular weight, GRAVY value, and exon-intron number(s). Besides, the expression profile of PHT genes in C. sativa based on RNA-seq data indicate that PHTs are involved in response to abiotic stresses such as cold, drought, salt, and cadmium. The tissue specific expression high expression of PHO1 genes in root tissues of C. sativa. In additions, four PHTs, including a PHT4;5 gene, a sodium dependent PHT gene, and two PHO1 homolog 3 genes were found with an upregulation in response to aforementioned studied stresses. In the current study, we found that PHO1 proteins and their homologs have high potential to post-translation modifications such as N-glycosylation and phosphorylation. Besides, different cis-acting elements associated with response to stress and phytohormone were found in the promoter region of PHT genes. Overall, our results show that PHT genes play various functions in C. Sativa and regulate Camellia responses to external and intracellular stimuli. The results can be used in future studies related to the functional genomics of C. sativa.

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

2016 ◽  
Vol 143 ◽  
pp. 1-7 ◽  
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

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

2004 ◽  
Vol 22 (3) ◽  
pp. 589-597 ◽  
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

scholarly journals Genome-wide annotation, expression profiling, and protein interaction studies of the core cell-cycle genes in Phalaenopsis aphrodite

2013 ◽  
Vol 84 (1-2) ◽  
pp. 203-226 ◽  
Author(s):  
Hsiang-Yin Lin ◽  
Jhun-Chen Chen ◽  
Miao-Ju Wei ◽  
Yi-Chen Lien ◽  
Huang-Hsien Li ◽  
...  
Keyword(s):  
Cell Cycle ◽  
Protein Interaction ◽  
Expression Profiling ◽  
Cell Cycle Genes ◽  
The Core ◽  
Interaction Studies ◽  
Genome Wide ◽  
Phalaenopsis Aphrodite

scholarly journals Progesterone Increases Rat Neural Progenitor Cell Cycle Gene Expression and Proliferation Via Extracellularly Regulated Kinase and Progesterone Receptor Membrane Components 1 and 2

Endocrinology ◽  
2009 ◽  
Vol 150 (7) ◽  
pp. 3186-3196 ◽  
Author(s):  
Lifei Liu ◽  
Junming Wang ◽  
Liqin Zhao ◽  
Jon Nilsen ◽  
Kelsey McClure ◽  
...  
Keyword(s):  
Cell Cycle ◽  
Progesterone Receptor ◽  
Progenitor Cell ◽  
Neural Progenitor Cell ◽  
Neural Progenitor ◽  
Mammalian Brain ◽  
Cell Cycle Gene ◽  
Cell Cycle Genes ◽  
Expression Of Genes ◽  
Membrane Components

Progesterone receptor (PR) expression and regulation of neural progenitor cell (NPC) proliferation was investigated using NPC derived from adult rat brain. RT-PCR revealed that PRA mRNA was not detected in rat NPCs, whereas membrane-associated PRs, PR membrane components (PGRMCs) 1 and 2, mRNA were expressed. Progesterone-induced increase in 5-bromo-2-deoxyuridine incorporation was confirmed by fluorescent-activated cell sorting analysis, which indicated that progesterone promoted rat NPC exit of G0/G1 phase at 5 h, followed by an increase in S-phase at 6 h and M-phase at 8 h, respectively. Microarray analysis of cell-cycle genes, real-time PCR, and Western blot validation revealed that progesterone increased expression of genes that promote mitosis and decreased expression of genes that repress cell proliferation. Progesterone-induced proliferation was not dependent on conversion to metabolites and was antagonized by the ERK1/2 inhibitor UO126. Progesterone-induced proliferation was isomer and steroid specific. PGRMC1 small interfering RNA treatment, together with computational structural analysis of progesterone and its isomers, indicated that the proliferative effect of progesterone is mediated by PGRMC1/2. Progesterone mediated NPC proliferation and concomitant regulation of mitotic cell cycle genes via a PGRMC/ERK pathway mechanism is a potential novel therapeutic target for promoting neurogenesis in the mammalian brain.

scholarly journals New insights into virulence mechanisms of rice pathogen Acidovorax avenae subsp. avenae strain RS-1 following exposure to ß-lactam antibiotics

2016 ◽  
Vol 6 (1) ◽  
Author(s):  
Bin Li ◽  
Mengyu Ge ◽  
Yang Zhang ◽  
Li Wang ◽  
Muhammad Ibrahim ◽  
...  
Keyword(s):  
Biofilm Formation ◽  
Extracellular Polymeric Substances ◽  
Expression Data ◽  
Rna Seq ◽  
Quantitative Real Time Pcr ◽  
Type Vi Secretion System ◽  
Pathogen Virulence ◽  
Type Vi Secretion ◽  
Genome Wide ◽  
Knockout Mutants

Abstract Recent research has shown that pathogen virulence can be altered by exposure to antibiotics, even when the growth rate is unaffected. Investigating this phenomenon provides new insights into understanding the virulence mechanisms of bacterial pathogens. This study investigates the phenotypic and transcriptomic responses of the rice pathogenic bacterium Acidovorax avenae subsp. avenae (Aaa) strain RS-1 to ß-lactam antibiotics especially Ampicillin (Amp). Our results indicate that exposure to Amp does not influence bacterial growth and biofilm formation, but alters the virulence, colonization capacity, composition of extracellular polymeric substances and secretion of Type VI secretion system (T6SS) effector Hcp. This attenuation in virulence is linked to unique or differential expression of known virulence-associated genes based on genome-wide transcriptomic analysis. The reliability of expression data generated by RNA-Seq was verified with quantitative real-time PCR of 21 selected T6SS genes, where significant down-regulation in expression of hcp gene, corresponding to the reduction in secretion of Hcp, was observed under exposure to Amp. Hcp is highlighted as a potential target for Amp, with similar changes observed in virulence-associated phenotypes between exposure to Amp and mutation of hcp gene. In addition, Hcp secretion is reduced in knockout mutants of 4 differentially expressed T6SS genes.

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