Delineation of condition specific Cis- and Trans-acting elements in plant promoters under various Endo- and exogenous stimuli
Abstract Background Transcription factors (TFs) play essential roles during plant development and response to environmental stresses. However, the relationships among transcription factors, cis-acting elements and target gene expression under endo- and exogenous stimuli have not been systematically...
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BMC
2018-05-01
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| Series: | BMC Genomics |
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| Online Access: | http://link.springer.com/article/10.1186/s12864-018-4469-4 |
| _version_ | 1811265115968765952 |
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| author | Chi-Nga Chow Yi-Fan Chiang-Hsieh Chia-Hung Chien Han-Qin Zheng Tzong-Yi Lee Nai-Yun Wu Kuan-Chieh Tseng Ping-Fu Hou Wen-Chi Chang |
| author_facet | Chi-Nga Chow Yi-Fan Chiang-Hsieh Chia-Hung Chien Han-Qin Zheng Tzong-Yi Lee Nai-Yun Wu Kuan-Chieh Tseng Ping-Fu Hou Wen-Chi Chang |
| author_sort | Chi-Nga Chow |
| collection | DOAJ |
| description | Abstract Background Transcription factors (TFs) play essential roles during plant development and response to environmental stresses. However, the relationships among transcription factors, cis-acting elements and target gene expression under endo- and exogenous stimuli have not been systematically characterized. Results Here, we developed a series of bioinformatics analysis methods to infer transcriptional regulation by using numerous gene expression data from abiotic stresses and hormones treatments. After filtering the expression profiles of TF-encoding genes, 291 condition specific transcription factors (CsTFs) were obtained. Differentially expressed genes were then classified into various co-expressed gene groups based on each CsTFs. In the case studies of heat stress and ABA treatment, several known and novel cis-acting elements were identified following our bioinformatics approach. Significantly, a palindromic sequence of heat-responsive elements is recognized, and also obtained from a 3D protein structure of heat-shock protein-DNA complex. Notably, overrepresented 3- and 4-mer motifs in an enriched 8-mer motif could be a core cis-element for a CsTF. In addition, the results suggest DNA binding preferences of the same CsTFs are different according to various conditions. Conclusions The overall results illustrate this study may be useful in identifying condition specific cis- and trans- regulatory elements and facilitate our understanding of the relationships among TFs, cis-acting elements and target gene expression. |
| first_indexed | 2024-04-12T20:16:46Z |
| format | Article |
| id | doaj.art-199751e2c0ee4ce1a198c2e13ef5424d |
| institution | Directory Open Access Journal |
| issn | 1471-2164 |
| language | English |
| last_indexed | 2024-04-12T20:16:46Z |
| publishDate | 2018-05-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Genomics |
| spelling | doaj.art-199751e2c0ee4ce1a198c2e13ef5424d2022-12-22T03:18:05ZengBMCBMC Genomics1471-21642018-05-0119S210912110.1186/s12864-018-4469-4Delineation of condition specific Cis- and Trans-acting elements in plant promoters under various Endo- and exogenous stimuliChi-Nga Chow0Yi-Fan Chiang-Hsieh1Chia-Hung Chien2Han-Qin Zheng3Tzong-Yi Lee4Nai-Yun Wu5Kuan-Chieh Tseng6Ping-Fu Hou7Wen-Chi Chang8College of Biosciences and Biotechnology, Institute of Tropical Plant Sciences, National Cheng Kung UniversityCollege of Biosciences and Biotechnology, Institute of Tropical Plant Sciences, National Cheng Kung UniversityCollege of Biosciences and Biotechnology, Institute of Tropical Plant Sciences, National Cheng Kung UniversityCollege of Biosciences and Biotechnology, Institute of Tropical Plant Sciences, National Cheng Kung UniversitySchool of Science and Engineering, The Chinese University of Hong KongCollege of Biosciences and Biotechnology, Institute of Tropical Plant Sciences, National Cheng Kung UniversityCollege of Biosciences and Biotechnology, Institute of Tropical Plant Sciences, National Cheng Kung UniversityCollege of Biosciences and Biotechnology, Institute of Tropical Plant Sciences, National Cheng Kung UniversityCollege of Biosciences and Biotechnology, Institute of Tropical Plant Sciences, National Cheng Kung UniversityAbstract Background Transcription factors (TFs) play essential roles during plant development and response to environmental stresses. However, the relationships among transcription factors, cis-acting elements and target gene expression under endo- and exogenous stimuli have not been systematically characterized. Results Here, we developed a series of bioinformatics analysis methods to infer transcriptional regulation by using numerous gene expression data from abiotic stresses and hormones treatments. After filtering the expression profiles of TF-encoding genes, 291 condition specific transcription factors (CsTFs) were obtained. Differentially expressed genes were then classified into various co-expressed gene groups based on each CsTFs. In the case studies of heat stress and ABA treatment, several known and novel cis-acting elements were identified following our bioinformatics approach. Significantly, a palindromic sequence of heat-responsive elements is recognized, and also obtained from a 3D protein structure of heat-shock protein-DNA complex. Notably, overrepresented 3- and 4-mer motifs in an enriched 8-mer motif could be a core cis-element for a CsTF. In addition, the results suggest DNA binding preferences of the same CsTFs are different according to various conditions. Conclusions The overall results illustrate this study may be useful in identifying condition specific cis- and trans- regulatory elements and facilitate our understanding of the relationships among TFs, cis-acting elements and target gene expression.http://link.springer.com/article/10.1186/s12864-018-4469-4Abiotic stressCis-acting elementsCo-expressionHormoneMicroarrayTranscription factors |
| spellingShingle | Chi-Nga Chow Yi-Fan Chiang-Hsieh Chia-Hung Chien Han-Qin Zheng Tzong-Yi Lee Nai-Yun Wu Kuan-Chieh Tseng Ping-Fu Hou Wen-Chi Chang Delineation of condition specific Cis- and Trans-acting elements in plant promoters under various Endo- and exogenous stimuli BMC Genomics Abiotic stress Cis-acting elements Co-expression Hormone Microarray Transcription factors |
| title | Delineation of condition specific Cis- and Trans-acting elements in plant promoters under various Endo- and exogenous stimuli |
| title_full | Delineation of condition specific Cis- and Trans-acting elements in plant promoters under various Endo- and exogenous stimuli |
| title_fullStr | Delineation of condition specific Cis- and Trans-acting elements in plant promoters under various Endo- and exogenous stimuli |
| title_full_unstemmed | Delineation of condition specific Cis- and Trans-acting elements in plant promoters under various Endo- and exogenous stimuli |
| title_short | Delineation of condition specific Cis- and Trans-acting elements in plant promoters under various Endo- and exogenous stimuli |
| title_sort | delineation of condition specific cis and trans acting elements in plant promoters under various endo and exogenous stimuli |
| topic | Abiotic stress Cis-acting elements Co-expression Hormone Microarray Transcription factors |
| url | http://link.springer.com/article/10.1186/s12864-018-4469-4 |
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