scholarly journals Genome-Wide Identification and Functional Characterization of the PheE2F/DP Gene Family in Moso Bamboo

2020 ◽  
Author(s):  
Long Li ◽  
Qianqian Shi ◽  
Jian Gao
Keyword(s):  
Cell Cycle ◽  
Regulatory Element ◽  
Cell Cycle Control ◽  
Expression Patterns ◽  
Functional Characterization ◽  
Divergence Time ◽  
Duplication Event ◽  
Moso Bamboo ◽  
Functional Verification ◽  
Genome Duplication Event

Abstract BackgroundE2F/DP proteins have been shown to regulate genes implicated in cell cycle control and DNA repair. However, to date, research into the potential role of Moso bamboo E2F/DP family has been limited.ResultsHere, we identified 24 E2F/DPs in the Moso bamboo genome including nine E2F, six DP, eight DEL and one gene with partial E2F domain. Estimation of the divergence time of paralogous gene pairs suggested that E2F/DP family expansion was mainly contributed by whole-genome duplication event. The regulatory element and coexpression network analysis indicated that E2F/DP regulated the expression of cell cycle-related genes. Yeast two hybrid assay and expression analysis based on transcriptome data and in situ hybridization indicated that PheE2F-PheDP complex played important roles in winter moso bamboo shoot growth. qRT-PCR results showed that PheE2F/DPs performed diverse expression patterns in response to drought and salt treatment and diurnal cycles. ConclusionOur findings provide novel insights into the Moso bamboo E2F/DP family and partial experimental evidence for further functional verification of the PheE2F/DPs.

scholarly journals Genome-Wide Identification and Functional Characterization of the PheE2F/DP Gene Family in Moso Bamboo

2020 ◽  
Author(s):  
Long Li ◽  
Qianqian Shi ◽  
Zhouqi Li ◽  
Jian Gao
Keyword(s):  
Cell Cycle ◽  
Regulatory Element ◽  
Cell Cycle Control ◽  
Expression Patterns ◽  
Functional Characterization ◽  
Divergence Time ◽  
Duplication Event ◽  
Moso Bamboo ◽  
Functional Verification ◽  
Genome Duplication Event

Abstract Background E2F/DP proteins have been shown to regulate genes implicated in cell cycle control and DNA repair. However, to date, research into the potential role of the Moso bamboo E2F/DP family has been limited.Results Here, we identified 23 E2F/DPs in the Moso bamboo genome, including nine E2F genes, six DP genes, eight DEL genes and one gene with a partial E2F domain. An estimation of the divergence time of the paralogous gene pairs suggested that the E2F/DP family expansion primarily occurred through a whole-genome duplication event. A regulatory element and coexpression network analysis indicated that E2F/DP regulated the expression of cell cycle-related genes. A yeast two-hybrid assay and expression analysis based on transcriptome data and in situ hybridization indicated that the PheE2F-PheDP complex played important roles in winter Moso bamboo shoot growth. The qRT-PCR results showed that the PheE2F/DPs exhibited diverse expression patterns in response to drought and salt treatment and diurnal cycles. Conclusion Our findings provide novel insights into the Moso bamboo E2F/DP family and partial experimental evidence for further functional verification of the PheE2F/DPs.

scholarly journals Genome-wide identification and functional characterization of the PheE2F/DP gene family in Moso bamboo

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Long Li ◽  
Qianqian Shi ◽  
Zhouqi Li ◽  
Jian Gao
Keyword(s):  
Cell Cycle ◽  
Regulatory Element ◽  
Cell Cycle Control ◽  
Expression Patterns ◽  
Functional Characterization ◽  
Divergence Time ◽  
Duplication Event ◽  
Moso Bamboo ◽  
Functional Verification ◽  
Genome Duplication Event

Abstract Background E2F/DP proteins have been shown to regulate genes implicated in cell cycle control and DNA repair. However, to date, research into the potential role of the Moso bamboo E2F/DP family has been limited. Results Here, we identified 23 E2F/DPs in the Moso bamboo genome, including nine E2F genes, six DP genes, eight DEL genes and one gene with a partial E2F domain. An estimation of the divergence time of the paralogous gene pairs suggested that the E2F/DP family expansion primarily occurred through a whole-genome duplication event. A regulatory element and coexpression network analysis indicated that E2F/DP regulated the expression of cell cycle-related genes. A yeast two-hybrid assay and expression analysis based on transcriptome data and in situ hybridization indicated that the PheE2F-PheDP complex played important roles in winter Moso bamboo shoot growth. The qRT-PCR results showed that the PheE2F/DPs exhibited diverse expression patterns in response to drought and salt treatment and diurnal cycles. Conclusion Our findings provide novel insights into the Moso bamboo E2F/DP family and partial experimental evidence for further functional verification of the PheE2F/DPs.

scholarly journals Genome-Wide Identification and Functional Characterization of the PheE2F/DP Gene Family in Moso Bamboo

2020 ◽  
Author(s):  
Long Li ◽  
Qianqian Shi ◽  
Jian Gao
Keyword(s):  
Cell Cycle ◽  
Regulatory Element ◽  
Cell Cycle Control ◽  
Expression Patterns ◽  
Functional Characterization ◽  
Divergence Time ◽  
Moso Bamboo ◽  
Functional Verification ◽  
Diurnal Cycles ◽  
Abiotic Stimuli

Abstract Background E2F/DP proteins have been shown to regulate genes implicated in cell cycle control and DNA repair. However, to date, research into the E2F/DP family and its functional role in Moso bamboo has been limited. Results Here, we identified 24 E2F/DP genes in the Moso bamboo genome, including nine E2F, six DP, and eight DEL genes. Simulation of the divergence time of paralogous gene pairs revealed an important role of whole-genome duplication in the expansion of the E2F/DP family. The regulatory element and coexpression network analysis indicated that E2F/DP regulated the expression of cell cycle-related genes. Yeast two hybrid assay and expression analysis based on transcriptome data and in situ hybridization indicated that PheE2F-PheDP complex play important roles in winter moso bamboo shoot growth. Expressional analysis based on qRT-PCR performed diverse expression patterns of PheE2F/DPs in response to both various abiotic stimuli and diurnal cycles. Conclusion These findings provide insights into the E2F/DP family members in Moso bamboo and experimental evidence for further functional verification of the E2F/DP family.

scholarly journals The Gene Targeting Approach of Small Fragment Homologous Replacement (SFHR) Alters the Expression Patterns of DNA Repair and Cell Cycle Control Genes

2016 ◽  
Vol 5 ◽  
pp. e304 ◽  
Author(s):  
Silvia Pierandrei ◽  
Andrea Luchetti ◽  
Massimo Sanchez ◽  
Giuseppe Novelli ◽  
Federica Sangiuolo ◽  
...  
Keyword(s):  
Cell Cycle ◽  
Dna Repair ◽  
Gene Targeting ◽  
Cell Cycle Control ◽  
Expression Patterns ◽  
Small Fragment

Gene expression changes during mouse skeletal myoblast differentiation revealed by transcriptional profiling

2002 ◽  
Vol 10 (2) ◽  
pp. 103-111 ◽  
Author(s):  
Jennifer L. Moran ◽  
Yizheng Li ◽  
Andrew A. Hill ◽  
William M. Mounts ◽  
Christopher P. Miller
Keyword(s):  
Cell Cycle ◽  
Transcriptional Profiling ◽  
Cell Cycle Control ◽  
Expression Patterns ◽  
Muscle Growth ◽  
Myoblast Differentiation ◽  
Functional Categories ◽  
Self Organizing Maps ◽  
Oligonucleotide Arrays ◽  
Significant Enrichment

Studies described here utilize high-density oligonucleotide arrays to characterize changes in global mRNA expression patterns during proliferation, cell cycle withdrawal, and terminal differentiation in mouse C2C12 myoblasts. Statistical analyses revealed 629 sequences differentially regulated between proliferating and differentiating myoblasts. These genes were clustered using self-organizing maps to identify sets of coregulated genes and were assigned to functional categories that were analyzed for distribution across expression clusters. Clusters were identified with statistically significant enrichment of functional categories including muscle contraction, cell adhesion, extracellular matrix function, cellular metabolism, mitochondrial transport, DNA replication, cell cycle control, mRNA transcription, and unexpectedly, immune regulation. In addition, functional category enrichment data can be used to predict gene function for numerous differentially regulated expressed sequence tags. The results provide new insight into how genes involved in these cellular processes may play a role in skeletal muscle growth and differentiation.

scholarly journals Consequences of Hox gene duplication in the vertebrates: an investigation of the zebrafish Hox paralogue group 1 genes

Development ◽  
2001 ◽  
Vol 128 (13) ◽  
pp. 2471-2484 ◽  
Author(s):  
James M. McClintock ◽  
Robin Carlson ◽  
Devon M. Mann ◽  
Victoria E. Prince
Keyword(s):  
Hox Genes ◽  
Genome Duplication ◽  
Expression Patterns ◽  
Detailed Comparison ◽  
Duplication Event ◽  
Amino Acid Sequences ◽  
Functional Domains ◽  
Genome Duplication Event ◽  
Basic Functions ◽  
Functional Capacities

As a result of a whole genome duplication event in the lineage leading to teleosts, the zebrafish has seven clusters of Hox patterning genes, rather than four, as described for tetrapod vertebrates. To investigate the consequences of this genome duplication, we have carried out a detailed comparison of genes from a single Hox paralogue group, paralogue group (PG) 1. We have analyzed the sequences, expression patterns and potential functions of all four of the zebrafish PG1 Hox genes, and compared our data with that available for the three mouse genes. As the basic functions of Hox genes appear to be tightly constrained, comparison with mouse data has allowed us to identify specific changes in the developmental roles of Hox genes that have occurred during vertebrate evolution. We have found variation in expression patterns, amino acid sequences within functional domains, and potential gene functions both within the PG1 genes of zebrafish, and in comparison to mouse PG1 genes. We observed novel expression patterns in the midbrain, such that zebrafish hoxa1a and hoxc1a are expressed anterior to the domain traditionally thought to be under Hox patterning control. The hoxc1a gene shows significant coding sequence changes in known functional domains, which correlate with a reduced capacity to cause posteriorizing transformations. Moreover, the hoxb1 duplicate genes have differing functional capacities, suggesting divergence after duplication. We also find that an intriguing function ‘shuffling’ between paralogues has occurred, such that one of the zebrafish hoxb1 duplicates, hoxb1b, performs the role in hindbrain patterning played in mouse by the non-orthologous Hoxa1 gene.

scholarly journals SREBP-1c as a molecular bridge between lipogenesis and cell cycle progression of clear cell renal carcinoma

2017 ◽  
Vol 37 (6) ◽  
Author(s):  
Gautam Sethi ◽  
Muthu K. Shanmugam ◽  
Alan Prem Kumar
Keyword(s):  
Cell Cycle ◽  
Lipid Metabolism ◽  
Cell Cycle Progression ◽  
Clear Cell ◽  
Regulatory Element ◽  
Cell Cycle Control ◽  
Ring Finger ◽  
Cell Renal Cell Carcinoma ◽  
Cycle Progression ◽  
Molecular Bridge

Sterol regulatory element binding protein 1c (SREBP-1c) promotes lipogenesis and tumor growth in various cancers. It is well known that clear cell renal cell carcinoma (ccRCC), a major subtype of the kidney cancers, exhibits elevated lipid accumulation. However, it has not been fully understood how lipid metabolism might be associated with cell cycle regulation in ccRCC. In a recent issue, Lee et al. (Molecular and Cellular Biology (2017) pii: MCB.00265-17) demonstrate that SREBP-1c is up-regulated in ccRCC by ring finger protein 20 (RNF20) down-regulation, leading to aberrant lipid storage and pituitary tumor transforming gene 1 (PTTG1)-dependent cell cycle progression. These findings suggest that SREBP-1c serves as a molecular bridge between lipid metabolism and cell cycle control in ccRCC tumorigenesis.

scholarly journals Symbiosis maintenance in the facultative coral, Oculina arbuscula, relies on nitrogen cycling, cell cycle modulation, and immunity

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
H. E. Rivera ◽  
S. W. Davies
Keyword(s):  
Gene Expression ◽  
Cell Cycle ◽  
Nitrogen Cycling ◽  
Physiological Stress ◽  
Cell Cycle Control ◽  
Expression Patterns ◽  
Cycling Cell ◽  
Unicellular Algae ◽  
Oculina Arbuscula ◽  
Baseline Conditions

AbstractSymbiosis with unicellular algae in the family Symbiodiniaceae is common across tropical marine invertebrates. Reef-building corals offer a clear example of cellular dysfunction leading to a dysbiosis that disrupts entire ecosystems in a process termed coral bleaching. Due to their obligate symbiotic relationship, understanding the molecular underpinnings that sustain this symbiosis in tropical reef-building corals is challenging, as any aposymbiotic state is inherently coupled with severe physiological stress. Here, we leverage the subtropical, facultatively symbiotic and calcifying coral Oculina arbuscula to investigate gene expression differences between aposymbiotic and symbiotic branches within the same colonies under baseline conditions. We further compare gene ontology (GO) and KOG enrichment in gene expression patterns from O. arbuscula with prior work in the sea anemone Exaiptasia pallida (Aiptasia) and the salamander Ambystoma maculatum—both of which exhibit endophotosymbiosis with unicellular algae. We identify nitrogen cycling, cell cycle control, and immune responses as key pathways involved in the maintenance of symbiosis under baseline conditions. Understanding the mechanisms that sustain a healthy symbiosis between corals and Symbiodiniaceae algae is of urgent importance given the vulnerability of these partnerships to changing environmental conditions and their role in the continued functioning of critical and highly diverse marine ecosystems.

scholarly journals Oxyresveratrol Modulates Gene Expression of Apoptosis, Cell Cycle Control and DNA Repair in MCF7 Cells

2021 ◽  
Vol 12 ◽  
Author(s):  
Sarayut Radapong ◽  
Kelvin Chan ◽  
Satyajit D. Sarker ◽  
Kenneth J. Ritchie
Keyword(s):  
Gene Expression ◽  
Cell Cycle ◽  
Dna Repair ◽  
Biological Activities ◽  
Chromatin Condensation ◽  
Cell Cycle Control ◽  
Expression Patterns ◽  
Treated Group ◽  
Pcr Analysis ◽  
Mcf7 Cells

Oxyresveratrol (OXY) is a small molecule of phytochemical known as hydroxystilbenoids, which have been reported significantly important biological activities. The aim of this study was to elucidate the gene expression and biological pathways altered in MCF7, breast cancer cells. The cytotoxicity to different cancer cell lines was screened using MTT assay and then whole gene expression was elucidated using microarray. The pathways selected also validated by quantitative PCR analysis, fluorometric and western blot assay. A total of 686 genes were found to have altered mRNA expression levels of two-fold or more in the 50 μM OXY-treated group, while 2,338 genes were differentially expressed in the 100 µM-treated group. The relevant visualized global expression patterns of genes and pathways were generated. Apoptosis was activated through mitochondria-lost membrane potential, caspase-3 expression and chromatin condensation without DNA damage. G0/G1 and S phases of the cell cycle control were inhibited dose-dependently by the compound. Rad51 gene (DNA repair pathway) was significantly down-regulated (p < 0.0001). These results indicated that OXY moderated the key genes and pathways in MCF7 cells that could be developed as chemotherapy or chemo-sensitizing agent.

scholarly journals Global assessment of organ specific basal gene expression over a diurnal cycle with analyses of gene copies exhibiting cyclic expression patterns

BMC Genomics ◽  
2020 ◽  
Vol 21 (1) ◽  
Author(s):  
Yuan Lu ◽  
Mikki Boswell ◽  
William Boswell ◽  
Raquel Ybanez Salinas ◽  
Markita Savage ◽  
...  
Keyword(s):  
Gene Expression ◽  
Expression Pattern ◽  
Genome Duplication ◽  
Functional Divergence ◽  
Expression Patterns ◽  
Duplication Event ◽  
Global Scale ◽  
Genome Duplication Event ◽  
Gene Copies ◽  
Cyclic Expression

Abstract Background Studying functional divergences between paralogs that originated from genome duplication is a significant topic in investigating molecular evolution. Genes that exhibit basal level cyclic expression patterns including circadian and light responsive genes are important physiological regulators. Temporal shifts in basal gene expression patterns are important factors to be considered when studying genetic functions. However, adequate efforts have not been applied to studying basal gene expression variation on a global scale to establish transcriptional activity baselines for each organ. Furthermore, the investigation of cyclic expression pattern comparisons between genome duplication created paralogs, and potential functional divergence between them has been neglected. To address these questions, we utilized a teleost fish species, Xiphophorus maculatus, and profiled gene expression within 9 organs at 3-h intervals throughout a 24-h diurnal period. Results Our results showed 1.3–21.9% of genes in different organs exhibited cyclic expression patterns, with eye showing the highest fraction of cycling genes while gonads yielded the lowest. A majority of the duplicated gene pairs exhibited divergences in their basal level expression patterns wherein only one paralog exhibited an oscillating expression pattern, or both paralogs exhibit oscillating expression patterns, but each gene duplicate showed a different peak expression time, and/or in different organs. Conclusions These observations suggest cyclic genes experienced significant sub-, neo-, or non-functionalization following the teleost genome duplication event. In addition, we developed a customized, web-accessible, gene expression browser to facilitate data mining and data visualization for the scientific community.

Sign in / Sign up

Export Citation Format

Share Document