Data Sheet 2_Transcriptome-wide prediction of heat-sensitive RNA structures in Zea mays.pdf
Introduction<p>As global temperatures rise, understanding the potential effects on agriculture and food security is critical. Plant heat stress responses are finely controlled at transcriptional and post-transcriptional levels, with RNA secondary structure now recognized as an important regula...
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2025
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| _version_ | 1849927623710343168 |
|---|---|
| author | Mason W. Eisenhauer (22687085) |
| author2 | Abdelraouf O. Dapour (22687088) Warren B. Rouse (12153010) Walter N. Moss (159608) |
| author2_role | author author author |
| author_facet | Mason W. Eisenhauer (22687085) Abdelraouf O. Dapour (22687088) Warren B. Rouse (12153010) Walter N. Moss (159608) |
| author_role | author |
| dc.creator.none.fl_str_mv | Mason W. Eisenhauer (22687085) Abdelraouf O. Dapour (22687088) Warren B. Rouse (12153010) Walter N. Moss (159608) |
| dc.date.none.fl_str_mv | 2025-11-26T06:27:07Z |
| dc.identifier.none.fl_str_mv | 10.3389/fpls.2025.1688991.s001 |
| dc.relation.none.fl_str_mv | https://figshare.com/articles/dataset/Data_Sheet_2_Transcriptome-wide_prediction_of_heat-sensitive_RNA_structures_in_Zea_mays_pdf/30718358 |
| dc.rights.none.fl_str_mv | CC BY 4.0 info:eu-repo/semantics/openAccess |
| dc.subject.none.fl_str_mv | Plant Biology heat stress heat shock factors covariation ScanFold RNA structure Zea mays |
| dc.title.none.fl_str_mv | Data Sheet 2_Transcriptome-wide prediction of heat-sensitive RNA structures in Zea mays.pdf |
| dc.type.none.fl_str_mv | Dataset info:eu-repo/semantics/publishedVersion dataset |
| description | Introduction<p>As global temperatures rise, understanding the potential effects on agriculture and food security is critical. Plant heat stress responses are finely controlled at transcriptional and post-transcriptional levels, with RNA secondary structure now recognized as an important regulator in this process.</p>Methods<p>To characterize and identify structure-function relationships in Zea mays, we applied the computational approach ScanFold to construct a transcriptome-wide database of RNA secondary structures and associated metrics. This database was analyzed at temperatures ranging from moderate 28°C to extreme 42°C. We performed an in-depth analysis of two heat shock factors, ZmHsf04 and ZmHsf17, as a case study for analyzing thermotolerance in maize.</p>Results<p>Using the database, we identified evolutionarily conserved RNA structures across the transcriptome that are sensitive to temperature-induced conformational switching. Our analysis of ZmHsf04 and ZmHsf17 yielded two key findings: many predicted structures are supported by significant sequence covariation, indicating evolutionary selection and likely functionality; and several structures of interest also exhibited extreme changes in conformation upon temperature increases.</p>Discussion<p>These identified structures in ZmHsf04 and ZmHsf17 may regulate gene expression through dynamic changes influencing processes like mRNA maturation, localization, expression, or alternative splicing, providing a rubric for understanding and approaching future studies of the transcriptome-wide dataset. The dataset and methodology presented here provide a rapid and robust approach to facilitate research into plant abiotic stress response, offering a crucial first step in understanding the role of RNA structure in Z. mays heat response.</p> |
| eu_rights_str_mv | openAccess |
| id | Manara_146740b8219b5fb4e39983a80b4e66ce |
| identifier_str_mv | 10.3389/fpls.2025.1688991.s001 |
| network_acronym_str | Manara |
| network_name_str | ManaraRepo |
| oai_identifier_str | oai:figshare.com:article/30718358 |
| publishDate | 2025 |
| repository.mail.fl_str_mv | |
| repository.name.fl_str_mv | |
| repository_id_str | |
| rights_invalid_str_mv | CC BY 4.0 |
| spelling | Data Sheet 2_Transcriptome-wide prediction of heat-sensitive RNA structures in Zea mays.pdfMason W. Eisenhauer (22687085)Abdelraouf O. Dapour (22687088)Warren B. Rouse (12153010)Walter N. Moss (159608)Plant Biologyheat stressheat shock factorscovariationScanFoldRNA structureZea maysIntroduction<p>As global temperatures rise, understanding the potential effects on agriculture and food security is critical. Plant heat stress responses are finely controlled at transcriptional and post-transcriptional levels, with RNA secondary structure now recognized as an important regulator in this process.</p>Methods<p>To characterize and identify structure-function relationships in Zea mays, we applied the computational approach ScanFold to construct a transcriptome-wide database of RNA secondary structures and associated metrics. This database was analyzed at temperatures ranging from moderate 28°C to extreme 42°C. We performed an in-depth analysis of two heat shock factors, ZmHsf04 and ZmHsf17, as a case study for analyzing thermotolerance in maize.</p>Results<p>Using the database, we identified evolutionarily conserved RNA structures across the transcriptome that are sensitive to temperature-induced conformational switching. Our analysis of ZmHsf04 and ZmHsf17 yielded two key findings: many predicted structures are supported by significant sequence covariation, indicating evolutionary selection and likely functionality; and several structures of interest also exhibited extreme changes in conformation upon temperature increases.</p>Discussion<p>These identified structures in ZmHsf04 and ZmHsf17 may regulate gene expression through dynamic changes influencing processes like mRNA maturation, localization, expression, or alternative splicing, providing a rubric for understanding and approaching future studies of the transcriptome-wide dataset. The dataset and methodology presented here provide a rapid and robust approach to facilitate research into plant abiotic stress response, offering a crucial first step in understanding the role of RNA structure in Z. mays heat response.</p>2025-11-26T06:27:07ZDatasetinfo:eu-repo/semantics/publishedVersiondataset10.3389/fpls.2025.1688991.s001https://figshare.com/articles/dataset/Data_Sheet_2_Transcriptome-wide_prediction_of_heat-sensitive_RNA_structures_in_Zea_mays_pdf/30718358CC BY 4.0info:eu-repo/semantics/openAccessoai:figshare.com:article/307183582025-11-26T06:27:07Z |
| spellingShingle | Data Sheet 2_Transcriptome-wide prediction of heat-sensitive RNA structures in Zea mays.pdf Mason W. Eisenhauer (22687085) Plant Biology heat stress heat shock factors covariation ScanFold RNA structure Zea mays |
| status_str | publishedVersion |
| title | Data Sheet 2_Transcriptome-wide prediction of heat-sensitive RNA structures in Zea mays.pdf |
| title_full | Data Sheet 2_Transcriptome-wide prediction of heat-sensitive RNA structures in Zea mays.pdf |
| title_fullStr | Data Sheet 2_Transcriptome-wide prediction of heat-sensitive RNA structures in Zea mays.pdf |
| title_full_unstemmed | Data Sheet 2_Transcriptome-wide prediction of heat-sensitive RNA structures in Zea mays.pdf |
| title_short | Data Sheet 2_Transcriptome-wide prediction of heat-sensitive RNA structures in Zea mays.pdf |
| title_sort | Data Sheet 2_Transcriptome-wide prediction of heat-sensitive RNA structures in Zea mays.pdf |
| topic | Plant Biology heat stress heat shock factors covariation ScanFold RNA structure Zea mays |