UCLA

How multicellular organisms modulate transcription in response to internal and external cues is a fundamental question in plant and animal development and growth. In Arabidopsis, TOPLESS(TPL), a Groucho/Tup1 like co-repressor, is involved in the transcriptional response to multiple plant hormones and plays a crucial role in a range of major developmental processes, such as embryonic apical-basal patterning and post-embryonic floral patterning. This dissertation describes the advances made toward the elucidation of the molecular mechanisms underlying transcriptional regulation by TPL.

As a co-repressor, TPL lacks intrinsic DNA binding activity and has been shown to be recruited by transcription factors with repressive motifs. To date, a range of transcription factors have been reported to interact with TPL, yet the functionality of most of these interactions is not known. We found that the members of the Class III Homedomain-Leucine Zipper (HD- ZIPIII) transcription factor family co-localize with TPL to form complexes at the promoters of thousands of genes in the genome. HD-ZIPIIIs both antagonistically and cooperatively regulate entire pathways at multiple steps in a cell or tissue specific manner. The five members in the family form homo- and hetero-dimers and act both as activators and repressors. The association with TPL confers the repressive function of HD-ZIPIIIs.

Just like its counterparts in animals and fungi, TPL also associates with histone deacetylases(HDACs) to repress transcription. We characterized the binding profiles of TPL and HDA19, a class I histone deacetylase that interacts with TPL, and found they tend to bind to the promoters of dynamically expressed genes. Almost all HDA19 peaks have an overlapping TPL peak, while about half of the TPL peaks are in common with HDA19, suggesting HDA19 is involved only at a subset of TPL targets. Specifically, we found the three members of the evolutionarily conserved NAM/CUC (for NO APICAL MERISTEM and CUP-SHAPED COTYLEDON) transcription factors, CUC1, CUC2 and CUC3, are regulated by TPL and HDA19 to control boundary specification during floral development.

Finally, we showed that TPL interacts with lysine 27-trimethylated histone H3(H3K27me3) and binds to a significant number of genomic regions with this modification, suggesting a novel layer of regulation which has not been reported in animals. A decrease in TPL binding was observed in plants that have a mutation in the Polycomb Repressive Complexes 2 (PRC2), which mediates the deposition of H3K27me3. TPL itself affects H3K27me3 levels and interacts with a component of the PRC1 complex, which recognizes H3K27me3 and further contributes to chromatin compaction. Genes potentially regulated by both TPL and PRCs are involved in multiple developmental processes and stress responses. These data suggest that upon the recruitment of TPL, binding affinity is enhanced by H3K27me3 marked nucleosomes and TPL may further contributes to the repressive transcriptional state via the association with Polycomb group (PcG) proteins.

Overall, we propose a model of transcriptional regulation by TPL that consists of three steps: TPL first is recruited by specific transcription factors; the association of TPL at some target genes is enhanced by the presence of H3K27me3; and TPL forms co-repressor complexes with HDA19 and possibly PcGs to repress gene expression.