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Table of contents
I Introduction
1. Non coding RNAs: from junk to utility
1.1 A large diversity of transcripts
1.1.1 Cooperation of non-coding and coding transcripts for protein synthesis
1.1.2 The small non-coding regulatory transcripts
1.1.2.1 The siRNAs
1.1.2.2 The miRNAs
1.1.2.3 The phasiRNA and tasiRNAs
1.2 Discovery of the Long Non-Coding RNAs world
1.2.1 LncRNAs features
1.2.2 Are lncRNAs really non-coding?
1.2.3 Conservation of lncRNAs
2. Regulation of gene transcription
2.1 First dimension: Cis-regulatory motifs
2.2 Second dimension: Epigenetic marks
2.2.1 DNA methylation
2.2.2 Chemical modifications of histones
2.3 Third dimension: chromatin conformation
2.3.1 General configuration of genome within the nucleus
2.3.2 Long range interactions
2.3.3 Short-range interaction
2.3.3.1 Looping within a gene locus
2.3.3.2 Enhancer loop
3 Regulation of gene expression by lncRNAs
3.1 Modulation of the transcriptional activity by lncRNAs
3.2 LncRNAs-mediated modification of the epigenetic landscape
3.3 Chromatin architecture changes through lncRNAs activity
3.4 LncRNAs mediating post-transcriptional regulation of gene expression
3.5 Review: Regulatory long non-coding RNAs in root growth and development
4. Aim of the thesis
II Results
5. The non-coding transcriptome from two Arabidopsis ecotypes
5.1 Publication: Landscape of the Noncoding Transcriptome Response of Two Arabidopsis Ecotypes to Phosphate Starvation
6. Exploring transcriptomes to find new cis-regulatory root-related lncRNAs
6.1 LATERALINC, new regulator of lateral root growth in Arabidopsis
6.1.1 Introduction
6.1.2 Results and discussion
6.1.2.1 LATERALINC is positively correlated with IAA14 during plant development
6.1.2.2 Lateral root growth is impaired in LATERALINC downregulated lines
6.1.2.3 LATERALINC expression is correlated with the one of IAA1 but its downregulation does not affect IAA14 and IAA1 genes expression
6.1.3 Methods
6.1.4 Conclusion and perspectives
6.2 MARS, a lncRNA implicated in the transcriptional regulation of an embedded gene cluster
6.2.1 Introduction
6.2.2 Identification of the MARS lncRNA
6.2.3 Preprint: The lncRNA MARS modulates the epigenetic reprogramming of the marneral cluster in response to ABA
6.2.4 Additional results and discussion
6.2.4.1 Deregulation of genes involved in the Carbon/Nitrogen equilibrium and cell oxidation status in the RNAi MARS line
6.2.4.2 MARS physically interact with the marneral cluster genomic region to titrate LHP1 binding
6.2.5 Methods
6.2.6 Conclusion and perspectives of complementary results
III Conclusions and perspectives
7. The non-coding transcriptome, signature of the plant local environment
7.1 Conservation of non-coding genes
7.2 The lncRNA features: an advantage for a quick adaptation to environmental changes?
7.3 Two ecotype-associated lncRNAs in the environmental control of plant growth and development
7.4 An RdDM-acting lincRNA regulates the root system architecture
8. The MARS lncRNA, a novel actor in the plant response to environment
8.1 MARS-mediated marneral genes expression changes is involved in the plant response to its environment
8.2 ABA as precursor or signaling molecule for the marneral biosynthesis and metabolization
8.3 MARS: an enhancer lncRNA located within a Super Enhancer region?
8.4 MARS act in cis or in trans for the control of marneral cluster gene expression?
References
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