scholarly journals Studying the effect of cell division on expression patterns of the segment polarity genes

2008 ◽  
Vol 5 (suppl_1) ◽  
Author(s):  
Madalena Chaves ◽  
Réka Albert
Keyword(s):  
Cell Division ◽  
Expression Patterns ◽  
Gene Expression Pattern ◽  
Specific Gene ◽  
Biological Processes ◽  
Segment Polarity Genes ◽  
Genes Expression ◽  
Its Gene ◽  
Segment Polarity ◽  
Segment Polarity Gene

The segment polarity gene family, and its gene regulatory network, is at the basis of Drosophila embryonic development. The network's capacity for generating and robustly maintaining a specific gene expression pattern has been investigated through mathematical modelling. The models have provided several useful insights by suggesting essential network links, or uncovering the importance of the relative time scales of different biological processes in the formation of the segment polarity genes' expression patterns. But the developmental pattern formation process raises many other questions. Two of these questions are analysed here: the dependence of the signalling protein sloppy paired on the segment polarity genes and the effect of cell division on the segment polarity genes' expression patterns. This study suggests that cell division increases the robustness of the segment polarity network with respect to perturbations in biological processes.

scholarly journals Genome-wide analysis and expression profile of the bZIP gene family in poplar

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Kai Zhao ◽  
Song Chen ◽  
Wenjing Yao ◽  
Zihan Cheng ◽  
Boru Zhou ◽  
...  
Keyword(s):  
Salt Stress ◽  
Systems Biology ◽  
Gene Family ◽  
Stress Responses ◽  
Metal Ion ◽  
Gene Networks ◽  
Expression Patterns ◽  
Gene Set Enrichment Analysis ◽  
Specific Gene ◽  
Biological Processes

Abstract Background The bZIP gene family, which is widely present in plants, participates in varied biological processes including growth and development and stress responses. How do the genes regulate such biological processes? Systems biology is powerful for mechanistic understanding of gene functions. However, such studies have not yet been reported in poplar. Results In this study, we identified 86 poplar bZIP transcription factors and described their conserved domains. According to the results of phylogenetic tree, we divided these members into 12 groups with specific gene structures and motif compositions. The corresponding genes that harbor a large number of segmental duplication events are unevenly distributed on the 17 poplar chromosomes. In addition, we further examined collinearity between these genes and the related genes from six other species. Evidence from transcriptomic data indicated that the bZIP genes in poplar displayed different expression patterns in roots, stems, and leaves. Furthermore, we identified 45 bZIP genes that respond to salt stress in the three tissues. We performed co-expression analysis on the representative genes, followed by gene set enrichment analysis. The results demonstrated that tissue differentially expressed genes, especially the co-expressing genes, are mainly involved in secondary metabolic and secondary metabolite biosynthetic processes. However, salt stress responsive genes and their co-expressing genes mainly participate in the regulation of metal ion transport, and methionine biosynthetic. Conclusions Using comparative genomics and systems biology approaches, we, for the first time, systematically explore the structures and functions of the bZIP gene family in poplar. It appears that the bZIP gene family plays significant roles in regulation of poplar development and growth and salt stress responses through differential gene networks or biological processes. These findings provide the foundation for genetic breeding by engineering target regulators and corresponding gene networks into poplar lines.

The segment polarity gene armadillo interacts with the wingless signaling pathway in both embryonic and adult pattern formation

Development ◽  
1991 ◽  
Vol 111 (4) ◽  
pp. 1029-1043 ◽  
Author(s):  
M. Peifer ◽  
C. Rauskolb ◽  
M. Williams ◽  
B. Riggleman ◽  
E. Wieschaus
Keyword(s):  
Pattern Formation ◽  
Imaginal Discs ◽  
Protein Accumulation ◽  
Segment Polarity Genes ◽  
Adult Pattern ◽  
Segment Polarity ◽  
Lethal Allele ◽  
Segment Polarity Gene ◽  
Polarity Gene

The segment polarity genes of Drosophila were initially defined as genes required for pattern formation within each embryonic segment. Some of these genes also function to establish the pattern of the adult cuticle. We have examined the role of the armadillo (arm) gene in this latter process. We confirmed and extended earlier findings that arm and the segment polarity gene wingless are very similar in their effects on embryonic development. We next discuss the role of arm in pattern formation in the imaginal discs, as determined by using a pupal lethal allele, by analyzing clones of arm mutant tissue in imaginal discs, and by using a transposon carrying arm to produce adults with a reduced level of arm. Together, these experiments established that arm is required for the development of all imaginal discs. The requirement for arm varies along the dorsal-ventral and proximal-distal axes. Cells that require the highest levels of arm are those that express the wingless gene. Further, animals with reduced arm levels have phenotypes that resemble those of weak alleles of wingless. We present a description of the patterns of arm protein accumulation in imaginal discs. Finally, we discuss the implications of these results for the role of arm and wingless in pattern formation.

FOXA1 in breast cancer

2009 ◽  
Vol 11 ◽  
Author(s):  
Harikrishna Nakshatri ◽  
Sunil Badve
Keyword(s):  
Breast Cancer ◽  
Gene Expression ◽  
Transcription Factor ◽  
Expression Patterns ◽  
Gene Expression Pattern ◽  
Gene Expression Signature ◽  
Specific Gene ◽  
Breast Cancers ◽  
Transcription Factor Network ◽  
Histopathological Classification

Breast cancer is a heterogeneous disease and classification is important for clinical management. At least five subtypes can be identified based on unique gene expression patterns; this subtype classification is distinct from the histopathological classification. The transcription factor network(s) required for the specific gene expression signature in each of these subtypes is currently being elucidated. The transcription factor network composed of the oestrogen (estrogen) receptor α (ERα), FOXA1 and GATA3 may control the gene expression pattern in luminal subtype A breast cancers. Breast cancers that are dependent on this network correspond to well-differentiated and hormone-therapy-responsive tumours with good prognosis. In this review, we discuss the interplay between these transcription factors with a particular emphasis on FOXA1 structure and function, and its ability to control ERα function. Additionally, we discuss modulators of FOXA1 function, ERα–FOXA1–GATA3 downstream targets, and potential therapeutic agents that may increase differentiation through FOXA1.

Molecular Phenotype of Malignant CD34+ Hematopoietic Stem and Progenitor Cells in Chronic Myelogenous Leukemia.

Blood ◽  
2005 ◽  
Vol 106 (11) ◽  
pp. 2863-2863
Author(s):  
Ralf Kronenwett ◽  
Elena Diaz-Blanco ◽  
Thorsten Graef ◽  
Ulrich Steidl ◽  
Slawomir Kliszewski ◽  
...  
Keyword(s):  
Gene Expression ◽  
Fatty Acid ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Gene Expression Pattern ◽  
Leukemic Cell ◽  
Differentially Expressed ◽  
Specific Gene ◽  
Hematopoietic Stem ◽  
Cd34 Cells

Abstract In this study, we examined gene expression profiles of immunomagnetically enriched CD34+ cells from bone marrow (BM) of 9 patients with untreated CML in chronic phase and from 8 healthy volunteers using Affymetrix GeneChips. Additionally, in 3 patients CD34+ from peripheral blood (PB) were compared with those from BM. Differential expression of 12 candidate genes was corroborated by quantitative real-time RT-PCR. Following hybridization of labelled cRNA to Affymetrix GeneChips covering 8793 genes we used the statistical scripting language “R” for data analysis. For normalization a method of variance stabilization transformations was used. To identify significantly differentially expressed genes we used the Significance Analysis of Microarrays (SAM) algorithm. The intraindividual comparison of CD34+ cells from BM and PB in CML showed no differentially expressed genes which is different to normal CD34+ cells which had distinct gene expression patterns comparing circulating and sedentary CD34+ cells (Steidl et al., Blood, 2002). Comparing malignant BM CD34+ cells from CML with normal BM CD34+ cells 792 genes were significantly differentially expressed (fold change: >1.3; q-value: <0.03). 735 genes had a higher and 57 genes a lower expression in CML. Gene expression patterns reflected BCR-ABL-induced functional alterations such as increased cell-cycle and proteasome activity as well as decreased apoptosis. Downregulation of several genes involved in DNA repair and detoxification in CML might be the basis for DNA instability and progression to blast crisis. An interesting finding was an upregulation of fetal hemoglobin (Hb) components such as Hb gamma A and G in leukemic progenitor cells whereas no difference in adult Hb expression was observed suggesting an induction of fetal Hb synthesis in CML. Looking at genes involved in stem cell maintenance we found an upregulation of GATA2 and a reduced expression of proteins from the Wnt signalling pathway suggesting an increased self-renewal of CML hematopoietic stem cells compared to the normal counterpart. Moreover, several genes playing a role in ubiquitin-dependent protein catabolism and in fatty acid biosynthesis such as fatty acid synthase (FAS) were stronger expressed in CML. The functional role of FAS for leukemic cell growth was assessed in cell culture experiments. Incubation of the leukemic cell line K562 with the FAS inhibitor cerulenin (10 μg/ml) for 3 days resulted in death of 99% of cells suggesting that survival of leukemic cells depends upon endogenous fatty acid synthesis. In an attempt to find a specific gene expression pattern associated with response to imatinib therapy we divided the patients included in this study into two groups: maximal reduction of BCR-ABL transcript level <3-log vs. >3-log (major molecular remission) during therapy. Comparing pretherapeutic gene expression profiles of both groups we could not identify a pattern predictive for major molecular response. In conclusion, malignant CD34+ cells in CML have a specific gene expression pattern which seems not to be predictive for response to imatinib therapy.

scholarly journals Genome-wide Characterization of GRAS Transcription Factors and Their Potential Roles in Development and Drought Resilience in Rose (Rosa chinensis)

2021 ◽  
Author(s):  
Priya Kumari ◽  
Vijay Gahlaut ◽  
Ekjot Kaur ◽  
Sanatsujat Singh ◽  
Sanjay Kumar ◽  
...  
Keyword(s):  
Transcription Factors ◽  
Stress Responses ◽  
Phylogenetic Analyses ◽  
Expression Patterns ◽  
Specific Gene ◽  
Biological Processes ◽  
Rosa Chinensis ◽  
Genome Wide ◽  
Am Symbiosis ◽  
Hormone Responses

Abstract In the past few years, plant-specific GRAS transcription factors (TFs) were reported to play an essential role in regulating several biological processes, such as plant growth and development, phytochrome signal, arbuscular mycorrhiza (AM) symbiosis, environmental stress responses. GRAS genes have been thoroughly studied in several plant species, but unexplored in Rosa chinensis (rose). In this study, 59 rose GRAS genes (RcGRAS) were identified. Phylogenetic analyses grouped RcGRAS genes into 17 subfamilies, of which subfamily Rc2 was Rosaceae family-specific. Gene structure analyses showed that most of the RcGRAS genes were intronless and were relatively conserved. Cis-element analyses suggested that RcGRAS genes may involve in distinct biological processes and responsive to diverse abiotic stresses. Most of the genes were localized in the nucleus, except for a few in the cytoplasm. Gene expression analysis was also performed in various tissues, during gibberellin (GA) and drought stress treatment. The expression patterns of RcGRAS genes during GA treatment and in response to drought stresses suggested the potential functions of these genes in regulating stress and hormone responses. In summary, a comprehensive exploration of the rose GRAS gene family was performed, and the generated information can be utilized for further functional-based studies on this family.

scholarly journals The consequences of ubiquitous expression of the wingless gene in the Drosophila embryo

Development ◽  
1992 ◽  
Vol 116 (3) ◽  
pp. 711-719 ◽  
Author(s):  
J. Noordermeer ◽  
P. Johnston ◽  
F. Rijsewijk ◽  
R. Nusse ◽  
P.A. Lawrence
Keyword(s):  
Expression Patterns ◽  
Cell Communication ◽  
Drosophila Embryo ◽  
Cubitus Interruptus ◽  
Segment Polarity ◽  
Type Pattern ◽  
Essential Function ◽  
Segment Polarity Gene ◽  
Local Accumulation ◽  
Made In

The segment polarity gene wingless has an essential function in cell-to-cell communication during various stages of Drosophila development. The wingless gene encodes a secreted protein that affects gene expression in surrounding cells but does not spread far from the cells where it is made. In larvae, wingless is necessary to generate naked cuticle in a restricted part of each segment. To test whether the local accumulation of wingless is essential for its function, we made transgenic flies that express wingless under the control of a hsp70 promoter (HS-wg flies). Uniform wingless expression results in a complete naked cuticle, uniform armadillo accumulation and broadening of the engrailed domain. The expression patterns of patched, cubitus interruptus Dominant and Ultrabithorax follow the change in engrailed. The phenotype of heatshocked HS-wg embryos resembles the segment polarity mutant naked, suggesting that embryos that overexpress wingless or lack the naked gene enter similar developmental pathways. The ubiquitous effects of ectopic wingless expression may indicate that most cells in the embryo can receive and interpret the wingless signal. For the development of the wild-type pattern, it is required that wingless is expressed in a subset of these cells.

scholarly journals MODA: MOdule Differential Analysis for weighted gene co-expression network

2016 ◽  
Author(s):  
Dong Li ◽  
James B. Brown ◽  
Luisa Orsini ◽  
Zhisong Pan ◽  
Guyu Hu ◽  
...  
Keyword(s):  
Gene Expression ◽  
Expression Patterns ◽  
Synthetic Data ◽  
R Package ◽  
Gene Expression Patterns ◽  
Specific Gene ◽  
Biological Processes ◽  
Expression Data ◽  
Differential Analysis ◽  
Transcriptomic Data

1SummaryGene co-expression network differential analysis is designed to help biologists understand gene expression patterns under different conditions. We have implemented an R package called MODA (Module Differential Analysis) for gene co-expression network differential analysis. Based on transcriptomic data, MODA can be used to estimate and construct condition-specific gene co-expression networks, and identify differentially expressed subnetworks as conserved or condition specific modules which are potentially associated with relevant biological processes. The usefulness of the method is also demonstrated by synthetic data as well as Daphnia magna gene expression data under different environmental stresses.

scholarly journals Repression precedes the stepwise evolution of a highly specific gene expression pattern

2020 ◽  
Author(s):  
Jian Pu ◽  
Zinan Wang ◽  
Haosu Cong ◽  
Jacqueline S.R. Chin ◽  
Jessa Justen ◽  
...  
Keyword(s):  
Gene Expression ◽  
Expression Pattern ◽  
Expression Patterns ◽  
Gene Expression Pattern ◽  
Regulatory Elements ◽  
Fatty Acyl ◽  
Specific Gene ◽  
Spatial Expression ◽  
Origin And Evolution ◽  
And Function

AbstractWell-controlled gene expression is critical for the proper development and function of many traits. Highly-specific temporal and spatial expression patterns are often due to the overlapping activities of activator and repressor sequences that form cis-regulatory elements called enhancers. While many studies have shown that evolutionary changes in enhancers can result in novel traits, few studies illuminate how enhancers originate, how activator and repressor sequences interact during enhancer evolution, and the order in which they evolve. Here, we traced the evolutionary origin of a recently evolved enhancer that drives the expression of the fatty acyl-CoA elongase, bond, specifically in the semicircular wall epithelium (swe) of the Drosophila male ejaculatory bulb (EB). We show that this enhancer consists of two activator regions that drive bond expression in the entire EB and a repressor region that restricts expression specifically to the EB swe. Interestingly, the repressor region preceded the evolution of the two activator regions. The evolution of the first activator region, consisting of two putative Abdominal-B sites, did not drive expression in the EB due to the action of the repressor region. Expression of bond in the EB swe requires the evolution of the second activator region, which does not drive expression on its own, but synergizes with the first activator region and the repressor region to produce a highly-specific spatial expression pattern. Our results show that the origin and evolution of a novel enhancer require multiple steps and the evolution of repressor sequences can precede the evolution of activator sequences.

scholarly journals Condition-adaptive fused graphical lasso (CFGL): an adaptive procedure for inferring condition-specific gene co-expression network

2018 ◽  
Author(s):  
Yafei Lyu ◽  
Lingzhou Xue ◽  
Feipeng Zhang ◽  
Hillary Koch ◽  
Laura Saba ◽  
...  
Keyword(s):  
Gene Regulation ◽  
Expression Patterns ◽  
Joint Estimation ◽  
Data Driven ◽  
Specific Gene ◽  
Breast Cancer Dataset ◽  
Biological Processes ◽  
Graphical Lasso ◽  
Data Driven Approach ◽  
Multiple Conditions

AbstractCo-expression network analysis provides useful information for studying gene regulation in biological processes. Examining condition-specific patterns of co-expression can provide insights into the underlying cellular processes activated in a particular condition. One challenge in this type of analysis is that the sample sizes in each condition are usually small, making the statistical inference of co-expression patterns highly underpowered. A joint network construction that borrows information from related structures across conditions has the potential to improve the power of the analysis.One possible approach to constructing the co-expression network is to use the Gaussian graphical model. Though several methods are available for joint estimation of multiple graphical models, they do not fully account for the heterogeneity between samples and between co-expression patterns introduced by condition specificity. Here we develop the condition-adaptive fused graphical lasso (CFGL), a data-driven approach to incorporate condition specificity in the estimation of co-expression networks. We show that this method improves the accuracy with which networks are learned. The application of this method on a rat multi-tissue dataset and The Cancer Genome Atlas (TCGA) breast cancer dataset provides interesting biological insights. In both analyses, we identify numerous modules enriched for Gene Ontology functions and observe that the modules that are upregulated in a particular condition are often involved in condition-specific activities. Interestingly, we observe that the genes strongly associated with survival time in the TCGA dataset are less likely to be network hubs, suggesting that genes associated with cancer progression are likely to govern specific functions, rather than regulating a large number of biological processes. Additionally, we observed that the tumor-specific hub genes tend to have few shared edges with normal tissue, revealing tumor-specific regulatory mechanism.Author summaryGene co-expression networks provide insights into the mechanism of cellular activity and gene regulation. Condition-specific mechanisms may be identified by constructing and comparing co-expression networks of multiple conditions. We propose a novel statistical method to jointly construct co-expression networks for gene expression profiles from multiple conditions. By using a data-driven approach to capture condition-specific co-expression patterns, this method is effective in identifying both co-expression patterns that are specific to a condition and that are common across conditions. The application of this method on real datasets reveals interesting biological insights.

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