scholarly journals Genome-wide analysis of gene expression reveals gene regulatory networks that regulate chasmogamous and cleistogamous flowering in Pseudostellaria heterophylla (Caryophyllaceae)

BMC Genomics ◽  
2016 ◽  
Vol 17 (1) ◽  
Author(s):  
Yan Luo ◽  
Jin-Yong Hu ◽  
Lu Li ◽  
Yin-Ling Luo ◽  
Peng-Fei Wang ◽  
...  
Keyword(s):  
Gene Expression ◽  
Gene Regulatory Networks ◽  
Regulatory Networks ◽  
Genome Wide Analysis ◽  
Pseudostellaria Heterophylla ◽  
Genome Wide ◽  
Gene Regulatory

scholarly journals Genome-Wide Analysis of Gene Regulatory Networks of the FVE-HDA6-FLD Complex in Arabidopsis

2016 ◽  
Vol 7 ◽  
Author(s):  
Chun-Wei Yu ◽  
Kao-Yuan Chang ◽  
Keqiang Wu
Keyword(s):  
Gene Regulatory Networks ◽  
Regulatory Networks ◽  
Genome Wide Analysis ◽  
Genome Wide ◽  
Gene Regulatory

scholarly journals In vivo genome-wide analysis of multiple tissues identifies gene regulatory networks, novel functions and downstream regulatory genes for Bapx1 and its co-regulation with Sox9 in the mammalian vertebral column

BMC Genomics ◽  
2014 ◽  
Vol 15 (1) ◽  
pp. 1072 ◽  
Author(s):  
Sumantra Chatterjee ◽  
V Sivakamasundari ◽  
Sook Yap ◽  
Petra Kraus ◽  
Vibhor Kumar ◽  
...  
Keyword(s):  
Gene Regulatory Networks ◽  
Vertebral Column ◽  
Regulatory Networks ◽  
Regulatory Genes ◽  
Genome Wide Analysis ◽  
Genome Wide ◽  
Gene Regulatory

Current Development and Review of Dynamic Bayesian Network-Based Methods for Inferring Gene Regulatory Networks from Gene Expression Data

2014 ◽  
Vol 9 (5) ◽  
pp. 531-539 ◽  
Author(s):  
Lian Chai ◽  
Mohd Mohamad ◽  
Safaai Deris ◽  
Chuii Chong ◽  
Yee Choon ◽  
...  
Keyword(s):  
Gene Expression ◽  
Bayesian Network ◽  
Gene Expression Data ◽  
Gene Regulatory Networks ◽  
Regulatory Networks ◽  
Dynamic Bayesian Network ◽  
Expression Data ◽  
Current Development ◽  
Gene Regulatory

scholarly journals GATA-targeted compounds modulate cardiac subtype cell differentiation in dual reporter stem cell line

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Mika J. Välimäki ◽  
Robert S. Leigh ◽  
Sini M. Kinnunen ◽  
Alexander R. March ◽  
Ana Hernández de Sande ◽  
...  
Keyword(s):  
Gene Expression ◽  
Progenitor Cells ◽  
Cell Fate ◽  
Reporter Gene ◽  
Gene Regulatory Networks ◽  
Regulatory Networks ◽  
Cell Fate Decisions ◽  
Dual Reporter ◽  
Gene Regulatory ◽  
Reporter Gene Assays

AbstractBackgroundPharmacological modulation of cell fate decisions and developmental gene regulatory networks holds promise for the treatment of heart failure. Compounds that target tissue-specific transcription factors could overcome non-specific effects of small molecules and lead to the regeneration of heart muscle following myocardial infarction. Due to cellular heterogeneity in the heart, the activation of gene programs representing specific atrial and ventricular cardiomyocyte subtypes would be highly desirable. Chemical compounds that modulate atrial and ventricular cell fate could be used to improve subtype-specific differentiation of endogenous or exogenously delivered progenitor cells in order to promote cardiac regeneration.MethodsTranscription factor GATA4-targeted compounds that have previously shown in vivo efficacy in cardiac injury models were tested for stage-specific activation of atrial and ventricular reporter genes in differentiating pluripotent stem cells using a dual reporter assay. Chemically induced gene expression changes were characterized by qRT-PCR, global run-on sequencing (GRO-seq) and immunoblotting, and the network of cooperative proteins of GATA4 and NKX2-5 were further explored by the examination of the GATA4 and NKX2-5 interactome by BioID. Reporter gene assays were conducted to examine combinatorial effects of GATA-targeted compounds and bromodomain and extraterminal domain (BET) inhibition on chamber-specific gene expression.ResultsGATA4-targeted compounds 3i-1000 and 3i-1103 were identified as differential modulators of atrial and ventricular gene expression. More detailed structure-function analysis revealed a distinct subclass of GATA4/NKX2-5 inhibitory compounds with an acetyl lysine-like domain that contributed to ventricular cells (%Myl2-eGFP+). Additionally, BioID analysis indicated broad interaction between GATA4 and BET family of proteins, such as BRD4. This indicated the involvement of epigenetic modulators in the regulation of GATA-dependent transcription. In this line, reporter gene assays with combinatorial treatment of 3i-1000 and the BET bromodomain inhibitor (+)-JQ1 demonstrated the cooperative role of GATA4 and BRD4 in the modulation of chamber-specific cardiac gene expression.ConclusionsCollectively, these results indicate the potential for therapeutic alteration of cell fate decisions and pathological gene regulatory networks by GATA4-targeted compounds modulating chamber-specific transcriptional programs in multipotent cardiac progenitor cells and cardiomyocytes. The compound scaffolds described within this study could be used to develop regenerative strategies for myocardial regeneration.

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