This web page was produced as an assignment for Genetics 677, an undergraduate course in UW Madison
GATA transcription factor family
Based on the observations that GATA transcription factors seemed to appear several times during my research I decided to investigate what is known for these proteins and what pathways are they involved in. The data I retrieved from GeneCards and SMART gave me the following summary:
GATA family are zinc finger transcription factors (they have two tandem zinc finger domains) and mediate cell differentiation in a diverse range of tissues. Normally they function as transcription activators. There are six classes of GATA transcription factors all of which recognize and bind to the GATA motif in the DNA sequence.
GATA4 -regulate genes involved in embryogenesis and in myocardial differentiation and function. Mutations in this gene have been associated with cardiac septal defects.
GATA3 - Transcriptional activator which binds to the enhancer of the T-cell receptor alpha and delta genes.
GATA2 - expressed in hematopoietic progenitors, promotes proliferation at the expense of differentiation
GATA1 - erythroid development by regulating the switch of fetal hemoglobin to adult hemoglobin
The alignment of their protein domains revealed high level of homology and the presence of zinc finger tandem in all four mentioned above. In a future parts of my research I will try to identify homologues of these protein in the model organisms I have been investigating and determine how are these proteins conserved in the evolution and what kind of experimental data is published for these proteins.
GATA family are zinc finger transcription factors (they have two tandem zinc finger domains) and mediate cell differentiation in a diverse range of tissues. Normally they function as transcription activators. There are six classes of GATA transcription factors all of which recognize and bind to the GATA motif in the DNA sequence.
GATA4 -regulate genes involved in embryogenesis and in myocardial differentiation and function. Mutations in this gene have been associated with cardiac septal defects.
GATA3 - Transcriptional activator which binds to the enhancer of the T-cell receptor alpha and delta genes.
GATA2 - expressed in hematopoietic progenitors, promotes proliferation at the expense of differentiation
GATA1 - erythroid development by regulating the switch of fetal hemoglobin to adult hemoglobin
The alignment of their protein domains revealed high level of homology and the presence of zinc finger tandem in all four mentioned above. In a future parts of my research I will try to identify homologues of these protein in the model organisms I have been investigating and determine how are these proteins conserved in the evolution and what kind of experimental data is published for these proteins.
Future approaches.
1. RNAi experiments
In summary I would like to discuss what possible experiments and research can be conducted to establish the exact role of GSK3B in heart development. As we can see from the phenotypes and the research done in mice (Kerkela, 2008) and zebrafish (et al Lee 2007) the authors finding seem to be contradictory to each other.
One possible explanation that had not been discussed by them have to do with the fact that zebrafish GSK3B was silenced very early in the development by injection of morpholino oligonucleotides. This treatment was able to suppress not only the zygotic expressed genes but also the maternally deposited mRNA for GSK3B. I would like to admit that my knowledge in maternal effect genes in mice is highly insufficient but considering how highly conserved the protein is in the different species it is possible that its deposition in the mature oocyte might also be conserved. In order to establish the maternal effect (if any) of the protein we can develop experiments where double stranded RNAs can be used and injected shortly after fertilization in mice embryos, the results can be compared again with the GSK3B experiments in zebrafish for a more thorough analysis.
2. Knockout and knockdown of GATA4 and Microarray tests.
It is apparent that GATA4 transcription factor is crucial for proper heart development therefore mouse and zebrafish organisms can be used to test the effects of the gene silencing and compare the results with the already published data from GSK3B. I realize that some of these data might be already available but in addition to the knockout experiments it will be also necessary to provide a microarray expression comparison to determine the level of GSK3B expression in the studies – as I previously mentioned expression profiles were not available from the used databases.
3. Specific protein-protein interactions.
Last but not least it will be helpful to determine the proteins with which GSK3B was proposed to have direct interactions but results for which do not seem to be published based on experimental procedures. Such molecules include NF-ATc, GATA4, cyclin D1 and c-Myc. Yeast 2 hybrid system might be especially useful – it is relatively cheap and it can allow the researchers to create truncated forms of the protein to determine more specific amino acids that will participate in the interactions. In addition TAP –tag tests might give information for protein complexes that have not been previously identified especially if it combined with subsequent Mass spectrometry analysis.
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In summary I would like to discuss what possible experiments and research can be conducted to establish the exact role of GSK3B in heart development. As we can see from the phenotypes and the research done in mice (Kerkela, 2008) and zebrafish (et al Lee 2007) the authors finding seem to be contradictory to each other.
One possible explanation that had not been discussed by them have to do with the fact that zebrafish GSK3B was silenced very early in the development by injection of morpholino oligonucleotides. This treatment was able to suppress not only the zygotic expressed genes but also the maternally deposited mRNA for GSK3B. I would like to admit that my knowledge in maternal effect genes in mice is highly insufficient but considering how highly conserved the protein is in the different species it is possible that its deposition in the mature oocyte might also be conserved. In order to establish the maternal effect (if any) of the protein we can develop experiments where double stranded RNAs can be used and injected shortly after fertilization in mice embryos, the results can be compared again with the GSK3B experiments in zebrafish for a more thorough analysis.
2. Knockout and knockdown of GATA4 and Microarray tests.
It is apparent that GATA4 transcription factor is crucial for proper heart development therefore mouse and zebrafish organisms can be used to test the effects of the gene silencing and compare the results with the already published data from GSK3B. I realize that some of these data might be already available but in addition to the knockout experiments it will be also necessary to provide a microarray expression comparison to determine the level of GSK3B expression in the studies – as I previously mentioned expression profiles were not available from the used databases.
3. Specific protein-protein interactions.
Last but not least it will be helpful to determine the proteins with which GSK3B was proposed to have direct interactions but results for which do not seem to be published based on experimental procedures. Such molecules include NF-ATc, GATA4, cyclin D1 and c-Myc. Yeast 2 hybrid system might be especially useful – it is relatively cheap and it can allow the researchers to create truncated forms of the protein to determine more specific amino acids that will participate in the interactions. In addition TAP –tag tests might give information for protein complexes that have not been previously identified especially if it combined with subsequent Mass spectrometry analysis.
Back to Home page
References
1. Kerkela, R. (2008). Deletion of GSK-3 beta in mice leads to hypertrophic cardiomyopathy secondary to cardiomyoblast hyperproliferation. The journal of clinical investigation, 118, iss:11, 3609 -3618
2. Lee et al. BMC Developmental Biology 2007 7:93 doi:10.1186/1471-213X-7-93
3. SMART: http://smart.embl-heidelberg.de
4.GeneCards: http://www.genecards.org
2. Lee et al. BMC Developmental Biology 2007 7:93 doi:10.1186/1471-213X-7-93
3. SMART: http://smart.embl-heidelberg.de
4.GeneCards: http://www.genecards.org
