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Transcription factors KANADI 1, MYB DOMAIN PROTEIN 44, and PHYTOCHROME INTERACTING FACTOR 4 regulate long intergenic noncoding RNAs expressed in Arabidopsis roots

Li Liu (UGent) , Michel Heidecker, Thomas Depuydt, Nicolás Manosalva Pérez (UGent) , Martin Crespi, Thomas Blein and Klaas Vandepoele (UGent)
(2023) PLANT PHYSIOLOGY. 193(3). p.1933-1953
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Abstract
Thousands of long intergenic noncoding RNAs (lincRNAs) have been identified in plant genomes. While some lincRNAs have been characterized as important regulators in different biological processes, little is known about the transcriptional regulation for most plant lincRNAs. Through the integration of 8 annotation resources, we defined 6,599 high-confidence lincRNA loci in Arabidopsis (Arabidopsis thaliana). For lincRNAs belonging to different evolutionary age categories, we identified major differences in sequence and chromatin features, as well as in the level of conservation and purifying selection acting during evolution. Spatiotemporal gene expression profiles combined with transcription factor (TF) chromatin immunoprecipitation (ChIP) data were used to construct a TF-lincRNA regulatory network containing 2,659 lincRNAs and 15,686 interactions. We found that properties characterizing lincRNA expression, conservation, and regulation differ between plants and animals. Experimental validation confirmed the role of 3 TFs, KANADI 1, MYB DOMAIN PROTEIN 44, and PHYTOCHROME INTERACTING FACTOR 4, as key regulators controlling root-specific lincRNA expression, demonstrating the predictive power of our network. Furthermore, we identified 58 lincRNAs, regulated by these TFs, showing strong root cell type-specific expression or chromatin accessibility, which are linked with genome-wide association studies genetic associations related to root system development and growth. The multilevel genome-wide characterization covering chromatin state information, promoter conservation, and chromatin immunoprecipitation-based TF binding, for all detectable lincRNAs across 769 expression samples, permits rapidly defining the biological context and relevance of Arabidopsis lincRNAs through regulatory networks.
Keywords
Plant Science, Genetics, Physiology, COMPARATIVE GENOMICS, FACTOR-BINDING, ANNOTATION, REVEALS, DISCOVERY, EVOLUTION, DROUGHT, LNCRNAS, STRESS, ROLES

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Citation

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MLA
Liu, Li, et al. “Transcription Factors KANADI 1, MYB DOMAIN PROTEIN 44, and PHYTOCHROME INTERACTING FACTOR 4 Regulate Long Intergenic Noncoding RNAs Expressed in Arabidopsis Roots.” PLANT PHYSIOLOGY, vol. 193, no. 3, 2023, pp. 1933–53, doi:10.1093/plphys/kiad360.
APA
Liu, L., Heidecker, M., Depuydt, T., Manosalva Pérez, N., Crespi, M., Blein, T., & Vandepoele, K. (2023). Transcription factors KANADI 1, MYB DOMAIN PROTEIN 44, and PHYTOCHROME INTERACTING FACTOR 4 regulate long intergenic noncoding RNAs expressed in Arabidopsis roots. PLANT PHYSIOLOGY, 193(3), 1933–1953. https://doi.org/10.1093/plphys/kiad360
Chicago author-date
Liu, Li, Michel Heidecker, Thomas Depuydt, Nicolás Manosalva Pérez, Martin Crespi, Thomas Blein, and Klaas Vandepoele. 2023. “Transcription Factors KANADI 1, MYB DOMAIN PROTEIN 44, and PHYTOCHROME INTERACTING FACTOR 4 Regulate Long Intergenic Noncoding RNAs Expressed in Arabidopsis Roots.” PLANT PHYSIOLOGY 193 (3): 1933–53. https://doi.org/10.1093/plphys/kiad360.
Chicago author-date (all authors)
Liu, Li, Michel Heidecker, Thomas Depuydt, Nicolás Manosalva Pérez, Martin Crespi, Thomas Blein, and Klaas Vandepoele. 2023. “Transcription Factors KANADI 1, MYB DOMAIN PROTEIN 44, and PHYTOCHROME INTERACTING FACTOR 4 Regulate Long Intergenic Noncoding RNAs Expressed in Arabidopsis Roots.” PLANT PHYSIOLOGY 193 (3): 1933–1953. doi:10.1093/plphys/kiad360.
Vancouver
1.
Liu L, Heidecker M, Depuydt T, Manosalva Pérez N, Crespi M, Blein T, et al. Transcription factors KANADI 1, MYB DOMAIN PROTEIN 44, and PHYTOCHROME INTERACTING FACTOR 4 regulate long intergenic noncoding RNAs expressed in Arabidopsis roots. PLANT PHYSIOLOGY. 2023;193(3):1933–53.
IEEE
[1]
L. Liu et al., “Transcription factors KANADI 1, MYB DOMAIN PROTEIN 44, and PHYTOCHROME INTERACTING FACTOR 4 regulate long intergenic noncoding RNAs expressed in Arabidopsis roots,” PLANT PHYSIOLOGY, vol. 193, no. 3, pp. 1933–1953, 2023.
@article{01H5HPQZEAS4E2WCCEXGXXD0Y2,
  abstract     = {{Thousands of long intergenic noncoding RNAs (lincRNAs) have been identified in plant genomes. While some lincRNAs have been characterized as important regulators in different biological processes, little is known about the transcriptional regulation for most plant lincRNAs. Through the integration of 8 annotation resources, we defined 6,599 high-confidence lincRNA loci in Arabidopsis (Arabidopsis thaliana). For lincRNAs belonging to different evolutionary age categories, we identified major differences in sequence and chromatin features, as well as in the level of conservation and purifying selection acting during evolution. Spatiotemporal gene expression profiles combined with transcription factor (TF) chromatin immunoprecipitation (ChIP) data were used to construct a TF-lincRNA regulatory network containing 2,659 lincRNAs and 15,686 interactions. We found that properties characterizing lincRNA expression, conservation, and regulation differ between plants and animals. Experimental validation confirmed the role of 3 TFs, KANADI 1, MYB DOMAIN PROTEIN 44, and PHYTOCHROME INTERACTING FACTOR 4, as key regulators controlling root-specific lincRNA expression, demonstrating the predictive power of our network. Furthermore, we identified 58 lincRNAs, regulated by these TFs, showing strong root cell type-specific expression or chromatin accessibility, which are linked with genome-wide association studies genetic associations related to root system development and growth. The multilevel genome-wide characterization covering chromatin state information, promoter conservation, and chromatin immunoprecipitation-based TF binding, for all detectable lincRNAs across 769 expression samples, permits rapidly defining the biological context and relevance of Arabidopsis lincRNAs through regulatory networks.}},
  author       = {{Liu, Li and Heidecker, Michel and Depuydt, Thomas and Manosalva Pérez, Nicolás and Crespi, Martin and Blein, Thomas and Vandepoele, Klaas}},
  issn         = {{0032-0889}},
  journal      = {{PLANT PHYSIOLOGY}},
  keywords     = {{Plant Science,Genetics,Physiology,COMPARATIVE GENOMICS,FACTOR-BINDING,ANNOTATION,REVEALS,DISCOVERY,EVOLUTION,DROUGHT,LNCRNAS,STRESS,ROLES}},
  language     = {{eng}},
  number       = {{3}},
  pages        = {{1933--1953}},
  title        = {{Transcription factors KANADI 1, MYB DOMAIN PROTEIN 44, and PHYTOCHROME INTERACTING FACTOR 4 regulate long intergenic noncoding RNAs expressed in Arabidopsis roots}},
  url          = {{http://doi.org/10.1093/plphys/kiad360}},
  volume       = {{193}},
  year         = {{2023}},
}
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