The main objective of this thesis was to investigate the role of eukaryotic transcription in the regulation of gene expression. We contributed to advance our understanding of transcription regulation of genes isoforms. We used the plant model organisms Arabidopsis thaliana and defined the landscape of gene isoform and found widespread promoter proximal termination. We reviewed the chromatin landscape during transcription in plants and investigated the role of chromatin in transcription initiation. This thesis is organized in four main chapters with two published articles, one unpublished manuscript, and one project.
Chapter I is a published article reviewing our current knowledge of histone post translation modifications (PTM) during the main phases of plant genes transcription. We focused on histone PTMs marking active transcription of coding-genes. Using published ChIP-seq datasets we characterized altogether the histone positional system during transcription. We reviewed the current knowledge of factors involved in the regulation of histone PTM throughout transcription phases and reflected upon plant specificities. We also described the known consequences on gene expression through dysregulation of the histone PTM patterns.
Chapter II is a published research article where we defined the isoform landscape in Arabidopsis seedlings and found a new class of RNAs associated with promoter-proximal transcription termination at plant coding genes. We used a powerful transcription profiling technique, Transcript isoform Sequencing to investigate the boundaries of RNAPII transcription. We characterized RNAPII transcripts boundaries genome-wide in wild type and mutants affecting transcription initiation and degradation and identified that 15% of expressed genes produce cryptic short promoter proximal RNAs (sppRNAs) initiating at the canonical TSS and terminating prematurely few nucleotides downstream. The regulation of sppRNAs correlated with mRNA regulation and known factors of transcription attenuation.
Chapter III is an unpublished research article investigating the co-transcriptional mechanism for a TFIID subunit homolog on transcription initiation. We identified HAF2 a TAF1 homolog, as a repressor of transcription initiation in plants. We found that HAF2 is a strong regulator of circadian rhythm associated genes (i.e ELF4) with opposite effect to the chromatin remodeler FACT. We found that HAF2 govern the histone PTM environment (e.g H3K4me3) around the TSS and prevents cryptic anti-sense initiation and maintain accurate sense initiation.
Chapter VI Documents the research approaches and preliminary data to identify endogenous events of gene expression repression through the act of transcription interference in Arabidopsis thaliana.
Appendix II Documents the preliminary data of a possible role for the transcription factor FLD in transcription interference.