This page was published for Genetics 564 at the University of Wisconsin-Madison
Sotos syndrome is a rare genetic developmental disorder characterized by excessive physical growth in early childhood, obscured facial features and impaired learning development [1]. These physical and neurological defects result from a loss-of-function mutation in one copy of the nuclear receptor SET-domain containing protein 1 (NSD1) gene. NSD1 codes for a protein that contains several highly conserved domains that regulate transcription through histone methylation [2]. The most notable domain is that for which NSD1 was named, the SET domain, which actually facilitates the methylation process. Mutations in NSD1 can vary from microdeletions and frameshifts to insertions and truncations, which could contribute to the spectrum of developmental impairments [2]. One of the most notable variations in phenotype resides in learning disabilities, with patient IQs ranging from average intelligence to severe intellectual disability [3]. Exactly how these mutations contribute to learning is unknown, specifically, the roles of the domains.
To understand how the conserved domains function in learning, I plan to use the Drosophila melanogaster homolog, Mes-4. Mes-4 mutants are comparable to the Sotos phenotypes [4][5]. Assays that measure conditioned behavior memory in Drosophila have been used to assess learning abilities in flies [6]. Thus, similar assays can be utilized to ultimately determine severity of learning disabilities from various mutations in humans. It has been noted that there exists a link between histone methylation and learning, and considering the SET domain's function in this process, I hypothesize that the SET domain has the biggest role in learning in both flies and humans [7].
The primary goal of this study is to examine the conserved domains in Mes-4 and their contribution to learning in Drosophila. Determining how the individual domains of NSD1 affect learning would help further characterize both the protein and the disease. The secondary goal of this study is to determine crucial genes and proteins involved in learning and determine their interaction with NSD1 to help develop future diagnostic tools or potential therapies.
Specific Aim 1: To determine which domains in NSD1/Mes-4 contribute to learning.
Approach: Structure function analysis in Mes-4 will be measured with olfactory learning assays conditioning flies to avoid a particular odorant by electric shock.
Hypothesis: Mutation in the SET domain will have the most profound effect on learning impairment.
Specific Aim 2: To determine which genes and proteins are necessary for learning.
Approach: I will create a STRING protein interaction network to identify proteins involved in learning with Gene Ontology. I will then take my findings run them through SMART to identify similar domains. I will then use RNA-Seq to discover genes in wild type and SET mutant Drosophila models and organize expression profiles based on Gene Ontology terms associated with learning. To confirm the learning associated genes, I will knock these out in Drosophila and run them through the olfactory learning assay to assess the effect on learning.
Hypothesis: There are a wide variety of other genes and proteins associated with learning, most exhibit SET domains.
Specific Aim 3: To identify the conserved amino acids important for learning in mammals.
Approach: Clustal Omega will be used to compare the NSD1 homologs across a number of model organisms. Organization of the results will be based on species type: mammals or non-mammals.
Hypothesis: Mammals will express a different set of residues in the SET domain, suggesting importance in learning.
To understand how the conserved domains function in learning, I plan to use the Drosophila melanogaster homolog, Mes-4. Mes-4 mutants are comparable to the Sotos phenotypes [4][5]. Assays that measure conditioned behavior memory in Drosophila have been used to assess learning abilities in flies [6]. Thus, similar assays can be utilized to ultimately determine severity of learning disabilities from various mutations in humans. It has been noted that there exists a link between histone methylation and learning, and considering the SET domain's function in this process, I hypothesize that the SET domain has the biggest role in learning in both flies and humans [7].
The primary goal of this study is to examine the conserved domains in Mes-4 and their contribution to learning in Drosophila. Determining how the individual domains of NSD1 affect learning would help further characterize both the protein and the disease. The secondary goal of this study is to determine crucial genes and proteins involved in learning and determine their interaction with NSD1 to help develop future diagnostic tools or potential therapies.
Specific Aim 1: To determine which domains in NSD1/Mes-4 contribute to learning.
Approach: Structure function analysis in Mes-4 will be measured with olfactory learning assays conditioning flies to avoid a particular odorant by electric shock.
Hypothesis: Mutation in the SET domain will have the most profound effect on learning impairment.
Specific Aim 2: To determine which genes and proteins are necessary for learning.
Approach: I will create a STRING protein interaction network to identify proteins involved in learning with Gene Ontology. I will then take my findings run them through SMART to identify similar domains. I will then use RNA-Seq to discover genes in wild type and SET mutant Drosophila models and organize expression profiles based on Gene Ontology terms associated with learning. To confirm the learning associated genes, I will knock these out in Drosophila and run them through the olfactory learning assay to assess the effect on learning.
Hypothesis: There are a wide variety of other genes and proteins associated with learning, most exhibit SET domains.
Specific Aim 3: To identify the conserved amino acids important for learning in mammals.
Approach: Clustal Omega will be used to compare the NSD1 homologs across a number of model organisms. Organization of the results will be based on species type: mammals or non-mammals.
Hypothesis: Mammals will express a different set of residues in the SET domain, suggesting importance in learning.
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References:
[1] Sotos Syndrome 1;SOTOS1. (2013). OMIM Database. Retrieved March 21, 2014, from http://www.omim.org/entry/117550
[2] Tatton-Brown, K., Douglas, J., et.al. (2005). Genotype-Phenotype Associations in Sotos Syndrome: An Analysis of 266 Individuals with NSD1 Aberrations. The American Journal of Human Genetics, 77(2), 193-204. doi: http://dx.doi.org/10.1086/432082
[3] Sarimski, K. (2003). Behavioural and emotional characteristics in children with Sotos syndrome and learning disabilities. Developmental Medicine and Child Neurology. 45. 172-178. doi: 10.1017/S0012162203000331
[4] Wagner, E. J. and Carpenter, P. B. (2012). Understanding the language of Lys36 methylation at histone H3. Molec Cell Biol. 13. 115-126. doi: 10.1038/nrm3274
[5] St. Pierre SE, Ponting L, Stefancsik R, McQuilton P, and the FlyBase Consortium (2014). FlyBase 102 - advanced approaches to interrogating FlyBase. Nucleic Acids Res. 42(D1):D780-D788. doi: 10.1093/nar/gkt1092 [FBrf0223749]
[6] Quinn, W. G., Harris, W. A., & Benzer, S. (1974). Conditioned Behavior in Drosophila melanogaster. Proceedings of the National Academy of Sciences, 71(3), 708-712.
[7] Gupta, S., Kim, S. Y., et.al. (2010). Histone methylation regulates memory formation. The Journal of Neuroscience. 30(10). 3589-3599.
[1] Sotos Syndrome 1;SOTOS1. (2013). OMIM Database. Retrieved March 21, 2014, from http://www.omim.org/entry/117550
[2] Tatton-Brown, K., Douglas, J., et.al. (2005). Genotype-Phenotype Associations in Sotos Syndrome: An Analysis of 266 Individuals with NSD1 Aberrations. The American Journal of Human Genetics, 77(2), 193-204. doi: http://dx.doi.org/10.1086/432082
[3] Sarimski, K. (2003). Behavioural and emotional characteristics in children with Sotos syndrome and learning disabilities. Developmental Medicine and Child Neurology. 45. 172-178. doi: 10.1017/S0012162203000331
[4] Wagner, E. J. and Carpenter, P. B. (2012). Understanding the language of Lys36 methylation at histone H3. Molec Cell Biol. 13. 115-126. doi: 10.1038/nrm3274
[5] St. Pierre SE, Ponting L, Stefancsik R, McQuilton P, and the FlyBase Consortium (2014). FlyBase 102 - advanced approaches to interrogating FlyBase. Nucleic Acids Res. 42(D1):D780-D788. doi: 10.1093/nar/gkt1092 [FBrf0223749]
[6] Quinn, W. G., Harris, W. A., & Benzer, S. (1974). Conditioned Behavior in Drosophila melanogaster. Proceedings of the National Academy of Sciences, 71(3), 708-712.
[7] Gupta, S., Kim, S. Y., et.al. (2010). Histone methylation regulates memory formation. The Journal of Neuroscience. 30(10). 3589-3599.