Progress 01/01/16 to 12/31/19
Outputs
Target Audience:The primary target audiences reached by our efforts are plant scientists and plant breeders. Our efforts have provided knowledge about the sources of variation that could provide important traits in crops such as maize. We are developing tools to induce, and track, these types of variation. This information will be of interest for plant biotechnology and plant breeding audiences. Changes/Problems:
Nothing Reported
What opportunities for training and professional development has the project provided?A post-doctoral researcher, Sarah Anderson, has worked full-time on this project during the past year. She has had several opportunities to present her work at conferences in the past year and has been a lead author and a co-author on publications. We have provided active mentoring to Sarah and worked with her to develop skills necessary for obtaining, and succeeding in, an academic position. At the end of this project she transitioned to a tenure track faculty position at Iowa State University.In addition, two undergraduate students have worked on this project and have developed basic molecular biology and computational biology skills. How have the results been disseminated to communities of interest?There have been four publications that have resulted from this work in the past year and nine total publications from the project. We are currently preparing two additional manuscripts that we expect to submit within the coming three months. In addition, we have made presentations at Plant and Animal Genome conference, Maize Genetics conference, a Gordon research conference and at ASPB on the research associated with this project. What do you plan to do during the next reporting period to accomplish the goals?
Nothing Reported
Impacts
What was accomplished under these goals?
We have made significant accomplishments related toall three goals of the project. The release of an improved assembly of the B73v4 along with a structural annotation of transposable elements provided valuable resources for this project. In order to address the first goal of documenting the role of transposons in responses of gene expression to abiotic stress we developed an imformatics approach to document the level of expression for each transposon family in the maize genome that incorporates both unique and multiple-matching sequence reads. We have used these resources to reanalyze >150 RNAseq datasets to assess transposon expression. These include samples that had been subjected to abiotic stress as well as numerous developmental stages or tissues. Amanuscript reporting on this approach and the findings was published this year in G3.In addition, we have generated additional samples that have been subjected to abiotic stress and have collected multiple tissues that are being used for expression profiling. These datasets allowed for the identification of genes that have expression changes associated with similar expression changes for nearby transposons. In particular, the availability of consistent TE annotations for four de novo assemblies of maize provides the opportunity to detect whether the presence/absence of a TE is required for changes to nearby genes. We are planning to submit a manuscript related to this project describing these findings. To address the second goal of documenting the mechanism we have been looking at specific isoforms produced in different environmental conditions and looking more closely at the transcripts produced by transposons. We have also been documenting potential regulatory sites and TF binding sites within transposons. We collaborated with Maike Stam's group to assess the putative enhancer regions found within maize transposons resulting in a shared publication in Genome Biology. In addition, we have collaborated with Bob Schmitz's group to use highly detailed chromatin maps for maize to identify regulatory sites within TEs and to link them to specific genes. A manuscript describing these results is currently in preparation. The recent release of de novo genome assemblies for Mo17, PH207 and W22 provide opportunities that relate to the third goal. We are documenting shared and polymorphic transposon insertions among these genomes. We have completed a genome-wide analysis comparing TE insertions in these lines (Anderson et al 2019 Plant Journal). In the course of this analysis we identified a set of TE families that have likely had recent tranpositional activity. Access to the TE polymorphisms data will provide chances to assess the similarities or differences in gene expression responses in these lines to associate variability of transposon insertions with altered expression responses. We have also completed an analysis of transposon expression in several mutant backgrounds. This has highlighted transposons with the potential for expression and movement in these genotypes and this information was included in a recently published manuscript (Anderson et al., G3 2018)
Publications
- Type:
Journal Articles
Status:
Published
Year Published:
2019
Citation:
Anderson SN, Stitzer MC, Zhou P, Ross-Ibarra J, Hirsch CD, Springer NM. (2019) Dynamic Patterns of Transcript Abundance of Transposable Element Families in Maize. G3 (Bethesda). 2019 Nov 5;9(11):3673-3682. doi: 10.1534/g3.119.400431.
- Type:
Journal Articles
Status:
Published
Year Published:
2019
Citation:
Noshay JM, Anderson SN, Zhou P, Ji L, Ricci W, Lu Z, Stitzer MC, Crisp PA, Hirsch CN, Zhang X, Schmitz RJ, Springer NM. (2019) Monitoring the interplay between transposable element families and DNA methylation in maize. PLoS Genet. 2019 Sep 9;15(9):e1008291. doi: 10.1371/journal.pgen.1008291.
- Type:
Journal Articles
Status:
Published
Year Published:
2019
Citation:
Anderson SN, Stitzer MC, Brohammer AB, Zhou P, Noshay JM, O'Connor CH, Hirsch CD, Ross-Ibarra J, Hirsch CN, Springer NM. (2019) Transposable elements contribute to dynamic genome content in maize. Plant J. 2019 Dec;100(5):1052-1065. doi: 10.1111/tpj.14489. Epub 2019 Sep 18.
- Type:
Journal Articles
Status:
Published
Year Published:
2019
Citation:
Xue W, Anderson SN, Wang X, Yang L, Crisp PA, Li Q, Noshay J, Albert PS, Birchler JA, Bilinski P, Stitzer MC, Ross-Ibarra J, Flint-Garcia S, Chen X, Springer NM, Doebley JF. (2019) Hybrid Decay: A Transgenerational Epigenetic Decline in Vigor and Viability Triggered in Backcross Populations of Teosinte with Maize. Genetics. 2019 Sep;213(1):143-160. doi: 10.1534/genetics.119.302378.
|
Progress 01/01/18 to 12/31/18
Outputs
Target Audience:The primary target audiences reached by our efforts are plant scientists and plant breeders. Our efforts have provided knowledge about the sources of variation that could provide important traits in crops such as maize. We are developing tools to induce, and track, these types of variation. This information will be of interest for plant biotechnology and plant breeding audiences. Changes/Problems:There is nothing major to report. The only change was a requested no-cost extension to finalize the research and publications associated with this project. What opportunities for training and professional development has the project provided?A post-doctoral researcher, Sarah Anderson, has worked full-time on this project during the past year. She has had several opportunities to present her work at conferences in the past year and has been a lead author and a co-author on publications. We have provided active mentoring to Sarah and worked with her to develop skills necessary for obtaining, and succeeding in, an academic position. In addition, two undergraduate students have worked on this project and have developed basic molecular biology and computational biology skills. How have the results been disseminated to communities of interest?There have been four publications that have resulted from this work in the past year. We are currently preparing four additional manuscripts that are already submitted (2) or that we expect tosubmit within the coming three months (2). In addition, we have made presentations at Plant and Animal Genome conference, Maize Genetics conference, a Gordon research conference andat ASPB on the research associated with this project. What do you plan to do during the next reporting period to accomplish the goals?We are finalizing several analyses during the no-cost extension of this project. These will provide a landmark paper that provides a comprehensive view of TE expression in response to abiotic stress and the potential for these changes to affect nearby genes. In addition, these publications will provide careful analyses of the presence of enhancers or cis-regulatory regions within maize TEs. The other remaining work is focused on documenting potential examples of recent TE movement.
Impacts
What was accomplished under these goals?
We have made strong progress towards all three goalsof the project. The release of an improved assembly of the B73v4 along with a structural annotation of transposable elements provided valuable resources for this project. In order to address the first goal of documenting the role of transposons in responses of gene expression to abiotic stress we developed an imformatics approach to document the level of expression for each transposon family in the maize genome that incorporates both unique and multiple-matching sequence reads. We have used these resources to reanalyze >150 RNAseq datasets to assess transposon expression.These include samples that had been subjected to abiotic stress as well as numerous developmental stages or tissues. We are currently finalizing a manuscript that will report on this pipeline for per-family analysis of TE expression and the biology of TE expression. We also have assessed gene expression in each of these samples. In addition, we have generated additional samples that have been subjected to abiotic stress and have collected multiple tissues that are being used for expression profiling. These datasets will allow for the identification of genes that have expression changes associated with similar expression changes for nearby transposons. A detailed analysis of the coordinate changes for TE expression and changes in nearby genes is a focus of the current work on this project as all necessary datasets are now available. In particular, the availability of consistent TE annotations for four de novo assemblies of maize provides the opportunity to detect whether the presence/absence of a TE is required for changes to nearby genes. To address the second goal of documenting the mechanism we have been looking at specific isoforms produced in different environmental conditions and looking more closely at the transcripts produced by transposons. We have also been documenting potential regulatory sites and TF binding sites within transposons. We collaborated with Maike Stam's group to assess the putative enhancer regions found within maize transposons resulting in a shared publication in Genome Biology. In addition, we have collaborated with other groups that are assessing chromatin patterns in the maize genome. This is providing opportunities to find regulatory sites within TEs and to link them to specific genes. The recent release of de novo genome assemblies for Mo17, PH207 and W22 provide opportunities that relate to the third goal. We are documenting shared and polymorphic transposon insertions among these genomes. We have completed a genome-wide analysis comparing TE insertions in these lines that is currently under review (and available through bioRxiv - Anderson et al). In the course of this analysis we identified a set of TE families that have likely had recent tranpositional activity. Access to the TE polymorphisms data will provide chances to assess the similarities or differences in gene expression responses in these lines to associate variability of transposon insertions with altered expression responses. We have also completed an analysis of transposon expression in several mutant backgrounds. This has highlighted transposons with the potential for expression and movement in these genotypes and this information was included in a recently published manuscript (Anderson et al., G3 2018).
Publications
- Type:
Journal Articles
Status:
Published
Year Published:
2018
Citation:
Anderson SN, Springer NM. Potential roles for transposable elements in creating imprinted expression. Curr Opin Genet Dev. 2018 Apr;49:8-14. doi: 10.1016/j.gde.2018.01.008.
- Type:
Journal Articles
Status:
Published
Year Published:
2018
Citation:
Anderson SN, Zynda GJ, Song J, Han Z, Vaughn MW, Li Q, Springer NM. Subtle Perturbations of the Maize Methylome Reveal Genes and Transposons Silenced by Chromomethylase or RNA-Directed DNA Methylation Pathways. G3 (Bethesda). 2018 May 31;8(6):1921-1932. doi: 10.1534/g3.118.200284.
- Type:
Journal Articles
Status:
Published
Year Published:
2018
Citation:
Springer NM, Anderson SN, Andorf CM, Ahern KR, Bai F, Barad O, Barbazuk WB, Bass HW, Baruch K, Ben-Zvi G, Buckler ES, Bukowski R, Campbell MS, Cannon EKS, Chomet P, Dawe RK, Davenport R, Dooner HK, Du LH, Du C, Easterling KA, Gault C, Guan JC, Hunter CT, Jander G, Jiao Y, Koch KE, Kol G, K�llner TG, Kudo T, Li Q, Lu F, Mayfield-Jones D, Mei W, McCarty DR, Noshay JM, Portwood JL 2nd, Ronen G, Settles AM, Shem-Tov D, Shi J, Soifer I, Stein JC, Stitzer MC, Suzuki M, Vera DL, Vollbrecht E, Vrebalov JT, Ware D, Wei S, Wimalanathan K, Woodhouse MR, Xiong W, Brutnell TP. The maize W22 genome provides a foundation for functional genomics and transposon biology. Nat Genet. 2018 Sep;50(9):1282-1288. doi: 10.1038/s41588-018-0158-0.
- Type:
Journal Articles
Status:
Published
Year Published:
2019
Citation:
Crisp PA, Noshay JM, Anderson SN, Springer NM. Opportunities to Use DNA Methylation to Distil Functional Elements in Large Crop Genomes. Mol Plant. 2019 Feb 22. pii: S1674-2052(19)30060-7. doi: 10.1016/j.molp.2019.02.006
|
Progress 01/01/17 to 12/31/17
Outputs
Target Audience:The primary target audiences reached by our efforts are plant scientists and plant breeders. Our efforts have provided knowledge about the sources of variation that could provide important traits in crops such as maize. We are developing tools to induce, and track, these types of variation. This information will be of interest for plant biotechnology and plant breeding audiences. Changes/Problems:
Nothing Reported
What opportunities for training and professional development has the project provided?A post-doctoral researcher, Sarah Anderson, has worked full-time on this project during the past year. She has had several opportunities to present her work at conferences in the past year and has been a lead author and a co-author on publications. We have provided active mentoring to Sarah and worked with her to develop skills necessary for obtaining, and succeeding in, an academic position. In addition, two undergraduate students have worked on this project and have developed basic molecular biology and computational biology skills. How have the results been disseminated to communities of interest?Two publications have resulted from this work in the past year. We are currently preparing additional manuscripts as well. In addition, we have made presentations at Plant and Animal Genome conference, Maize Genetics conference, a Gordon research conference and a Plant Genome workshop at New York University on the research associated with this project. What do you plan to do during the next reporting period to accomplish the goals?We plan to finalize the analyses associated with the first and second goal in the coming year. This should provide a comprehensive analysis of changes in transposon expression associated with nearby changes in gene expression. We will also perform a more in-depth analysis of transposon polymorphisms in order to document potential roles of transposons in the observed expression responses.
Impacts
What was accomplished under these goals?
We have made strong progress towards the first and second goal of the project and are developing materials and approaches for the third primary goal. The release of an improved assembly of the B73v4 along with a structural annotation of transposable elements provided valuable resources for this project. In order to address the first goal of documenting the role of transposons in responses of gene expression to abiotic stress we developed an imformatics approach to document the level of expression for each transposon family in the maize genome that incorporates both unique and multiple-matching sequence reads. In the past year we have used these resources to re-analyze >150 RNAseq datasets to assess transposon expression. These include samples that had been subjected to abiotic stress as well as numerous developmental stages or tissues. We also have assessed gene expression in each of these samples. In addition, we have generated additional samples that have been subjected to abiotic stress and have collected multiple tissues that are being used for expression profiling. These datasets will allow for the identification of genes that have expression changes associated with similar expression changes for nearby transposons. To address the second goal of documenting the mechanism we have been looking at specific isoforms produced in different environmental conditions and looking more closely at the transcripts produced by transposons. We have also been documenting potential regulatory sites and TF binding sites within transposons. We collaborated with Maike Stam's group to assess the putative enhancer regions found within maize transposons resulting in a shared publication in Genome Biology. The recent release of de novo genome assemblies for PH207 and W22 provide opportunities that relate to the third goal. We are documenting shared and polymorphic transposon insertions among these genomes. In addition, we will be able to assess the similarities or differences in gene expression responses in these lines to associate variability of transposon insertions with altered expression responses. We have also completed an analysis of transposon expression in several mutant backgrounds. This has highlighted transposons with the potential for expression and movement in these genotypes and this information was included in a recently submitted manuscript.
Publications
- Type:
Journal Articles
Status:
Published
Year Published:
2017
Citation:
Oka R, Zicola J, Weber B, Anderson SN, Hodgman C, Gent JI, Wesselink JJ, Springer NM, Hoefsloot HCJ, Turck F, Stam M. Genome-wide mapping of transcriptional enhancer candidates using DNA and chromatin features in maize. Genome Biol. 2017 Jul 21;18(1):137. doi: 10.1186/s13059-017-1273-4
- Type:
Journal Articles
Status:
Submitted
Year Published:
2017
Citation:
Anderson S, Zynda G, Song J, Han Z, Vaughn M, Li Q, Springer NM. Subtle perturbations of the maize methylome reveal genes and transposons silenced by DNA methylation. BioRxiv. doi: https://doi.org/10.1101/221580
|
Progress 01/01/16 to 12/31/16
Outputs
Target Audience:The target audiance of the proposed research include scientists studying basic aspects of gene regulation in plants as well as plant breeders. To date, our efforts have centered around development of tools for simoultaneously monitoring transposon and gene expression. We have been working to develop new resources for these studies and are preparing to share these with the community. Changes/Problems:There has not really been a major change in the approach. However, new resources have slightly shifted our approach to the first aim. The release of an improved genome assembly for maize along with a radically improved transposon annotation has allowed for new analyses of transposon and gene expression. In addition, the release of a de novo assembly for another maize genotype (PH207) will improve the analyses we can perform in the third aim. We are utilizing these new resources to improve the outputs in our described experiments. What opportunities for training and professional development has the project provided?A post-doctoral researcher, Sarah Anderson, began full time work on the project in August. She has developed skills for performing bioinformatic analyses. She has spent substantial time working on making critical files for a new maize genome assembly and new TE annotation. These files, combined with a new informatics pipeline she has developed, have now given us the ability to coordinately analyze TE and gene expression using existing RNAseq datasets. In addition, she is mentoring two undergraduates that are working to grow plants and perform abiotic stress treatment. How have the results been disseminated to communities of interest?To date we have published one review article. Sarah is currently working to develop a publication that will describe the methods for analyzing transposon expression. This will be coordinated with a publication on the new TE annotation and will provide tools for studying transposon expression. What do you plan to do during the next reporting period to accomplish the goals?We anticipate the completion of the first goal within the next 6 months. Our efforts will then shift to the experiments described in the second and third goals of the project. Once the transposon families that regulate expression of nearby genes have been identified we will initiate the molecular studies to document the exact mechanisms of this interaction. In addition, we have began several experiments that will seek to activate transposons and will be planting these populations in the summer of 2017 to generate materials for the third goal.
Impacts
What was accomplished under these goals?
One significant change in the past year has been the release of a new version of the maize genome (version 4) along with a vastly improved annotation of transposons. This has provided new resources for studying transposon expression and the relationship with the expression of nearby genes. However, it has also introduced some additional technical difficulties as the improved annotation now allows re-assembly of transposons that have been interrupted by other transposon insertions. We have found solutions to these issues and have now developed robust methods for determining transposon and gene expression. We are currently using these new resources and approaches to analyze RNAseq data from control plants and plants subjected to abiotic stress to complete the analyses for the first goal of the proposal. We have also initiatied activities that will provide resources and datasets for the second and third goals.
Publications
- Type:
Journal Articles
Status:
Published
Year Published:
2016
Citation:
Hirsch CD, Springer NM. 2016. Transposable element influences on gene expression in plants. Biochim Biophys Acta. 2016 May 25. pii: S1874-9399(16)30100-6.
|
|