Progress 01/03/14 to 09/30/18
Outputs
Target Audience:Target audience were scientists working with neurodegenerative diseases, including both those working with animals and those focused on human disease; and more generally scientists working on animal and plant genomes. Information was deseminated as published papers and at the annual Plant and animal Genome Conference. Changes/Problems:
Nothing Reported
What opportunities for training and professional development has the project provided?Work on this project was principally carried out by a Ph.D. student as their dissertation project. How have the results been disseminated to communities of interest?Yes, in the form of a PAG presentations, a Departmental seminar, andpublications referenced above. What do you plan to do during the next reporting period to accomplish the goals?
Nothing Reported
Impacts
What was accomplished under these goals?
During this period we completed the whole transcriptome sequencing of cerebellum samples from twelve horses, six age-matched controls and six Cerebellar Abiotrophy affected animals, obtaining approximately 34 million reads per horse, with approximately 84% of these reads having a Phred quality score of 30 or higher.Complete MUTYH isoform expression patterns remain unknown, but with further annotation, we were able to expand and annotate additional exons and isoforms of MUTYH in the horse.Our RNA-Se data set was addedto seven other RNA-seq datasets and used to generate a new annotation of genes expressed in the horse, with our lab being a significant site conducting bioinformatics work in the horse. Additionally we developed the first long non-coding RNA (lncRNA) database for the horse from these same RNA-seq datasets. We identified a unique set of differentially expressed genes between the control and CA samples and currently carrying out pathway analysis to identified differentially expressed pathways associated with CA and Pukinje neuron loss. We were able to significantly add to the information concerning cerebellar expression of both TOE-I and MutYH, incuding adding significantly to the understanding of the expression of MutYH, including the acquisition of a new transcription factor binding site associated with the CA SNP and an alteration in gene expression associated with changes in DNA methylation patterns. It is now clear that the CA SNP associated with Cerebellar Abiotrophy in the Arabian horse is associated with significant changes in isoform expression patterns of MutYH.
Publications
- Type:
Journal Articles
Status:
Published
Year Published:
2018
Citation:
Scott, E.Y., Woolard, K.D., Finno, C.J., Penedo, M.C.T. and Murray, J.D. (2018).
Variation in MUTYH Expression in Arabian Horses with Cerebellar Abiotrophy. Brain Research 1678:330-336.
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Progress 10/01/16 to 09/30/17
Outputs
Target Audience:Target audience were scientists working with neurodegenerative diseases, including both those working with animals and those focused on human disease; and more generally scientists working on animal and plant genomes. Changes/Problems:
Nothing Reported
What opportunities for training and professional development has the project provided?Work on this project was principally carried out by a Ph.D. student as their dissertation project. How have the results been disseminated to communities of interest?Yes, in the form of a PAG presentation, a Departmental seminar, and the publications referenced above. What do you plan to do during the next reporting period to accomplish the goals?We will complete the work on the expression and functionality of the two candidate loci we currently think are responsible for Cerebellar Abiotrophy in the Arabian horse. We will continue to work on the functionality of long non-coding RNA in the horse based on the eight tissues samples for which we have RNA-seq data.
Impacts
What was accomplished under these goals?
Our RNA-seq data was added to seven other RNA-seq data sets to generate a new annotation of genes expressed in the horse, with our lab being one of the significant sites conducting the bioinformatics work. Additionally, we also developed a long non-coding RNA database for the horse from these same RNA-seq datasets. Work was continued to characterize the involvement of candidate genes MutYH and TOE-1 causative to the development of cerebellar abiotrophy in Arabian horses.
Publications
- Type:
Journal Articles
Status:
Published
Year Published:
2017
Citation:
Mansour, T.A., Scott, E.Y., Finno, C.J., Bellone, R.R., Mienaltowski, M.J., Penedo, M.C.T., Ross, P.J., Valberg, S.J., Murray, J.D. and Brown, C.T. (2017). Tissue Resolved, Gene Structure Refined Equine Transcriptome. BMC Genomics 18:103. doi: 10.1186/s12864-016-3451-2.
- Type:
Journal Articles
Status:
Published
Year Published:
2017
Citation:
Scott, E.Y.,�Mansour, T., Bellone, R.R., Brown, C.T., Mienaltowski, M.J., Penedo, M.C., Ross, P.J., Valberg, S.J.,�Murray, J.D. and Finno, C.J. (2017). Identification of long non-coding RNA in the horse transcriptome. BMC Genomics 18:511. DOI 10.1186/s12864-017-3884-2.
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Progress 10/01/15 to 09/30/16
Outputs
Target Audience:Target audience were scientists working with neurodegenerative diseases, including both those working with animals and those focused on human disease; and more generally scientists working on animal and plant genomes. Changes/Problems:
Nothing Reported
What opportunities for training and professional development has the project provided?Work on this project is principally being carried out by a Ph.D. student as their dissertation project. How have the results been disseminated to communities of interest?Yes, in the form of a PAG presentation, a Departmental seminar, and the publication referenced above. What do you plan to do during the next reporting period to accomplish the goals?We will complete the work on the expression and functionality of the candidate loci we currently think are responsible for Cerebellar Abiotrophy in the Arabian horse. We will publish papers on the new equine transcriptome and the annotation of long non-coding RNA in the horse based on the eight tissues samples for which we have RNA-seq data.
Impacts
What was accomplished under these goals?
RNA-seq data from the cerebellum was annotated, with special reference to the genes of interest; MutYH and TOE-1. Our RNA-seq data was added to seven other RNA-seq data sets to generate a new annotation of genes expressed in the horse, with our lab being one of the significant sites conducting the bioinformatics work. Additionally, we have also began developing a lon non-coding RNA database for the horse from these same RNA-seq datasets.
Publications
- Type:
Journal Articles
Status:
Published
Year Published:
2016
Citation:
Scott, E.Y., Penedo, M.C.T., Murray, J.D. and Finno, C.J. (2016). Defining Trends in Global Gene Expression in Arabian Horses with Cerebellar Abiotrophy. Cerebellum : DOI 10.1007/s12311-016-0823-8
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Progress 10/01/14 to 09/30/15
Outputs
Target Audience:As we were staring new analysis there was nothing reported during this period, but we have begun submitting abstracts and papers on our new work. Changes/Problems:
Nothing Reported
What opportunities for training and professional development has the project provided?A Ph.D. student is being trained on this project. How have the results been disseminated to communities of interest?
Nothing Reported
What do you plan to do during the next reporting period to accomplish the goals?By completing the analysis of the sequence data we should be able to address outstanding issues relevant to the genetic lesion responsible for CA and contribute to the annotation of the cerebellar transcriptome of the horse. During the coming year, in addition to publishing our current results, we will begin experiments to confirm the role of differentially expressed pathways in the CA phenotype.
Impacts
What was accomplished under these goals?
During this period we have completed the whole transcriptome sequencing of cerebellum samples from twelve horses, six age-matched controls and six Cerebellar Abiotrophy affected animals, obtaining approximately 34 million reads per horse, with approximately 84% of these reads having a Phred quality score of 30 or higher. Complete MUTYH isoform expression patterns remains unknown, further annotation, which hopefully will be provided by the RNAseq data, is needed to determine sequences of horse MUTYH isoforms. We have worked to develop a new annotation pipeline using our dataset as well as datasets contributed by other laboratories. We identified a unique set of differentially expressed genes between the control and CA samples and currently carrying out pathway analysis to identified differentially expressed pathways associated with CA and Pukinje neuron loss.
Publications
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Progress 01/03/14 to 09/30/14
Outputs
Target Audience:
Nothing Reported
Changes/Problems:
Nothing Reported
What opportunities for training and professional development has the project provided? A Ph.D. student is being trained on this project. How have the results been disseminated to communities of interest?
Nothing Reported
What do you plan to do during the next reporting period to accomplish the goals? By completing the analysis of the sequence data we shoudl be able to address outstanding issues relevant to the genetic lesion responsible for CA and contribute to the annotation of the cerebellar transcriptome of the horse.
Impacts
What was accomplished under these goals?
During this period we have completed the whole transcriptome sequencing of twelve horses, six age-matched controls and six Cerebellar Abiotrophy affected animals, obtaining approximately 34 million reads per horse, with approximately 84% of these reads having a quality score of 30 or higher. Complete MUTYH isoform expression patterns remains unknown, further annotation, which hopefully will be provided by the RNAseq data, is needed to determine sequences of horse MUTYH isoforms. TOE1 expression levels remain undetectable, but RNAseq data as well as TOE1 activity assays hope to elucidate how TOE1 expression and activity may be impacted by the CA SNP.
Publications
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