Beyond Trees: Regulons and Regulatory Motif Characterization
Trees and their seeds regulate their germination, growth, and reproduction in response to environmental stimuli. These stimuli, through signal transduction, trigger transcription factors that alter the expression of various genes leading to the unfolding of the genetic program. A regulon is conceptu...
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| Format: | Article |
| Language: | English |
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MDPI AG
2020-08-01
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| Series: | Genes |
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| Online Access: | https://www.mdpi.com/2073-4425/11/9/995 |
| _version_ | 1797555663721725952 |
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| author | Xuhua Xia |
| author_facet | Xuhua Xia |
| author_sort | Xuhua Xia |
| collection | DOAJ |
| description | Trees and their seeds regulate their germination, growth, and reproduction in response to environmental stimuli. These stimuli, through signal transduction, trigger transcription factors that alter the expression of various genes leading to the unfolding of the genetic program. A regulon is conceptually defined as a set of target genes regulated by a transcription factor by physically binding to regulatory motifs to accomplish a specific biological function, such as the CO-FT regulon for flowering timing and fall growth cessation in trees. Only with a clear characterization of regulatory motifs, can candidate target genes be experimentally validated, but motif characterization represents the weakest feature of regulon research, especially in tree genetics. I review here relevant experimental and bioinformatics approaches in characterizing transcription factors and their binding sites, outline problems in tree regulon research, and demonstrate how transcription factor databases can be effectively used to aid the characterization of tree regulons. |
| first_indexed | 2024-03-10T16:50:43Z |
| format | Article |
| id | doaj.art-56fa8ae29472414c9aa0a5e180421ee7 |
| institution | Directory Open Access Journal |
| issn | 2073-4425 |
| language | English |
| last_indexed | 2024-03-10T16:50:43Z |
| publishDate | 2020-08-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Genes |
| spelling | doaj.art-56fa8ae29472414c9aa0a5e180421ee72023-11-20T11:19:24ZengMDPI AGGenes2073-44252020-08-0111999510.3390/genes11090995Beyond Trees: Regulons and Regulatory Motif CharacterizationXuhua Xia0Department of Biology, University of Ottawa, Ottawa, ON K1N 6N5, CanadaTrees and their seeds regulate their germination, growth, and reproduction in response to environmental stimuli. These stimuli, through signal transduction, trigger transcription factors that alter the expression of various genes leading to the unfolding of the genetic program. A regulon is conceptually defined as a set of target genes regulated by a transcription factor by physically binding to regulatory motifs to accomplish a specific biological function, such as the CO-FT regulon for flowering timing and fall growth cessation in trees. Only with a clear characterization of regulatory motifs, can candidate target genes be experimentally validated, but motif characterization represents the weakest feature of regulon research, especially in tree genetics. I review here relevant experimental and bioinformatics approaches in characterizing transcription factors and their binding sites, outline problems in tree regulon research, and demonstrate how transcription factor databases can be effectively used to aid the characterization of tree regulons.https://www.mdpi.com/2073-4425/11/9/995gene expressiontranscription factorregulonregulatory motifscomparative genomicsGibbs sampler |
| spellingShingle | Xuhua Xia Beyond Trees: Regulons and Regulatory Motif Characterization Genes gene expression transcription factor regulon regulatory motifs comparative genomics Gibbs sampler |
| title | Beyond Trees: Regulons and Regulatory Motif Characterization |
| title_full | Beyond Trees: Regulons and Regulatory Motif Characterization |
| title_fullStr | Beyond Trees: Regulons and Regulatory Motif Characterization |
| title_full_unstemmed | Beyond Trees: Regulons and Regulatory Motif Characterization |
| title_short | Beyond Trees: Regulons and Regulatory Motif Characterization |
| title_sort | beyond trees regulons and regulatory motif characterization |
| topic | gene expression transcription factor regulon regulatory motifs comparative genomics Gibbs sampler |
| url | https://www.mdpi.com/2073-4425/11/9/995 |
| work_keys_str_mv | AT xuhuaxia beyondtreesregulonsandregulatorymotifcharacterization |