scholarly journals Cell Cycle Programs of Gene Expression Control Morphogenetic Protein Localization

2000 ◽  
Vol 151 (7) ◽  
pp. 1501-1512 ◽  
Author(s):  
Matthew Lord ◽  
Melody C. Yang ◽  
Michelle Mischke ◽  
John Chant
Keyword(s):  
Gene Expression ◽  
Cell Cycle ◽  
Protein Localization ◽  
Expression Profiles ◽  
Direct Role ◽  
Periodic Gene ◽  
Gene Expression Control ◽  
Genomic Studies ◽  
And Function ◽  
Periodic Gene Expression

Genomic studies in yeast have revealed that one eighth of genes are cell cycle regulated in their expression. Almost without exception, the significance of cell cycle periodic gene expression has not been tested. Given that many such genes are critical to cellular morphogenesis, we wanted to examine the importance of periodic gene expression to this process. The expression profiles of two genes required for the axial pattern of cell division, BUD3 and BUD10/AXL2/SRO4, are strongly cell cycle regulated. BUD3 is expressed close to the onset of mitosis. BUD10 is expressed in late G1. Through promotor-swap experiments, the expression profile of each gene was altered and the consequences examined. We found that an S/G2 pulse of BUD3 expression controls the timing of Bud3p localization, but that this timing is not critical to Bud3p function. In contrast, a G1 pulse of BUD10 expression plays a direct role in Bud10p localization and function. Bud10p, a membrane protein, relies on the polarized secretory machinery specific to G1 to be delivered to its proper location. Such a secretion-based targeting mechanism for membrane proteins provides cells with flexibility in remodeling their architecture or evolving new forms.

scholarly journals Live-cell monitoring of periodic gene expression in synchronous human cells identifies Forkhead genes involved in cell cycle control

2012 ◽  
Vol 23 (16) ◽  
pp. 3079-3093 ◽  
Author(s):  
Gavin D. Grant ◽  
Joshua Gamsby ◽  
Viktor Martyanov ◽  
Lionel Brooks ◽  
Lacy K. George ◽  
...  
Keyword(s):  
Gene Expression ◽  
Cell Cycle ◽  
Dna Binding ◽  
Luciferase Activity ◽  
Binding Motif ◽  
Sequencing Analysis ◽  
Peak Expression ◽  
Periodic Gene ◽  
Regulated Gene Expression ◽  
Periodic Gene Expression

We developed a system to monitor periodic luciferase activity from cell cycle–regulated promoters in synchronous cells. Reporters were driven by a minimal human E2F1 promoter with peak expression in G1/S or a basal promoter with six Forkhead DNA-binding sites with peak expression at G2/M. After cell cycle synchronization, luciferase activity was measured in live cells at 10-min intervals across three to four synchronous cell cycles, allowing unprecedented resolution of cell cycle–regulated gene expression. We used this assay to screen Forkhead transcription factors for control of periodic gene expression. We confirmed a role for FOXM1 and identified two novel cell cycle regulators, FOXJ3 and FOXK1. Knockdown of FOXJ3 and FOXK1 eliminated cell cycle–dependent oscillations and resulted in decreased cell proliferation rates. Analysis of genes regulated by FOXJ3 and FOXK1 showed that FOXJ3 may regulate a network of zinc finger proteins and that FOXK1 binds to the promoter and regulates DHFR, TYMS, GSDMD, and the E2F binding partner TFDP1. Chromatin immunoprecipitation followed by high-throughput sequencing analysis identified 4329 genomic loci bound by FOXK1, 83% of which contained a FOXK1-binding motif. We verified that a subset of these loci are activated by wild-type FOXK1 but not by a FOXK1 (H355A) DNA-binding mutant.

scholarly journals A Computational Approach to the Functional Clustering of Periodic Gene-Expression Profiles

Genetics ◽  
2008 ◽  
Vol 180 (2) ◽  
pp. 821-834 ◽  
Author(s):  
Bong-Rae Kim ◽  
Li Zhang ◽  
Arthur Berg ◽  
Jianqing Fan ◽  
Rongling Wu
Keyword(s):  
Gene Expression ◽  
Expression Profiles ◽  
Gene Expression Profiles ◽  
Computational Approach ◽  
Functional Clustering ◽  
Periodic Gene ◽  
Periodic Gene Expression

Periodic gene expression program of the fission yeast cell cycle

2004 ◽  
Vol 36 (8) ◽  
pp. 809-817 ◽  
Author(s):  
Gabriella Rustici ◽  
Juan Mata ◽  
Katja Kivinen ◽  
Pietro Lió ◽  
Christopher J Penkett ◽  
...  
Keyword(s):  
Gene Expression ◽  
Cell Cycle ◽  
Yeast Cell ◽  
Fission Yeast ◽  
Gene Expression Program ◽  
Yeast Cell Cycle ◽  
Fission Yeast Cell ◽  
Periodic Gene ◽  
Expression Program ◽  
Periodic Gene Expression

scholarly journals Oscillatory Phosphorylation of Yeast Fus3 MAP Kinase Controls Periodic Gene Expression and Morphogenesis

2008 ◽  
Vol 18 (23) ◽  
pp. 1897
Author(s):  
Zoe Hilioti ◽  
Walid Sabbagh ◽  
Saurabh Paliwal ◽  
Adriel Bergmann ◽  
Marcus D. Goncalves ◽  
...  
Keyword(s):  
Gene Expression ◽  
Map Kinase ◽  
Periodic Gene ◽  
Periodic Gene Expression

scholarly journals Analysis of the transcriptome of bovine endometrial cells isolated by laser micro-dissection (1): specific signatures of stromal, glandular and luminal epithelial cells

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Wiruntita Chankeaw ◽  
Sandra Lignier ◽  
Christophe Richard ◽  
Theodoros Ntallaris ◽  
Mariam Raliou ◽  
...  
Keyword(s):  
Gene Expression ◽  
Protein Localization ◽  
Expression Profiles ◽  
Cell Types ◽  
Molecular Signature ◽  
Receptor Protein ◽  
Specific Gene ◽  
Specific Cell ◽  
Biological Processes ◽  
Endometrial Cells

Abstract Background A number of studies have examined mRNA expression profiles of bovine endometrium at estrus and around the peri-implantation period of pregnancy. However, to date, these studies have been performed on the whole endometrium which is a complex tissue. Consequently, the knowledge of cell-specific gene expression, when analysis performed with whole endometrium, is still weak and obviously limits the relevance of the results of gene expression studies. Thus, the aim of this study was to characterize specific transcriptome of the three main cell-types of the bovine endometrium at day-15 of the estrus cycle. Results In the RNA-Seq analysis, the number of expressed genes detected over 10 transcripts per million was 6622, 7814 and 8242 for LE, GE and ST respectively. ST expressed exclusively 1236 genes while only 551 transcripts were specific to the GE and 330 specific to LE. For ST, over-represented biological processes included many regulation processes and response to stimulus, cell communication and cell adhesion, extracellular matrix organization as well as developmental process. For GE, cilium organization, cilium movement, protein localization to cilium and microtubule-based process were the only four main biological processes enriched. For LE, over-represented biological processes were enzyme linked receptor protein signaling pathway, cell-substrate adhesion and circulatory system process. Conclusion The data show that each endometrial cell-type has a distinct molecular signature and provide a significantly improved overview on the biological process supported by specific cell-types. The most interesting result is that stromal cells express more genes than the two epithelial types and are associated with a greater number of pathways and ontology terms.

Neural system-enriched gene expression: relationship to biological pathways and neurological diseases

2004 ◽  
Vol 18 (2) ◽  
pp. 167-183 ◽  
Author(s):  
Jianhua Zhang ◽  
Amy Moseley ◽  
Anil G. Jegga ◽  
Ashima Gupta ◽  
David P. Witte ◽  
...  
Keyword(s):  
Gene Expression ◽  
Nervous System ◽  
Intracellular Signaling ◽  
Large Scale ◽  
Expression Profiles ◽  
Gene List ◽  
Structure And Function ◽  
System Structure ◽  
Psychiatric Disease ◽  
And Function

To understand the commitment of the genome to nervous system differentiation and function, we sought to compare nervous system gene expression to that of a wide variety of other tissues by gene expression database construction and mining. Gene expression profiles of 10 different adult nervous tissues were compared with that of 72 other tissues. Using ANOVA, we identified 1,361 genes whose expression was higher in the nervous system than other organs and, separately, 600 genes whose expression was at least threefold higher in one or more regions of the nervous system compared with their median expression across all organs. Of the 600 genes, 381 overlapped with the 1,361-gene list. Limited in situ gene expression analysis confirmed that identified genes did represent nervous system-enriched gene expression, and we therefore sought to evaluate the validity and significance of these top-ranked nervous system genes using known gene literature and gene ontology categorization criteria. Diverse functional categories were present in the 381 genes, including genes involved in intracellular signaling, cytoskeleton structure and function, enzymes, RNA metabolism and transcription, membrane proteins, as well as cell differentiation, death, proliferation, and division. We searched existing public sites and identified 110 known genes related to mental retardation, neurological disease, and neurodegeneration. Twenty-one of the 381 genes were within the 110-gene list, compared with a random expectation of 5. This suggests that the 381 genes provide a candidate set for further analyses in neurological and psychiatric disease studies and that as a field, we are as yet, far from a large-scale understanding of the genes that are critical for nervous system structure and function. Together, our data indicate the power of profiling an individual biologic system in a multisystem context to gain insight into the genomic basis of its structure and function.

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