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NODAL/Activin signalling to chromatin: mechanisms of SMAD2-regulated transcription

Coda, Davide Martino; (2018) NODAL/Activin signalling to chromatin: mechanisms of SMAD2-regulated transcription. Doctoral thesis (Ph.D), UCL (University College London). Green open access

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Abstract

NODAL/Activin signalling regulates key processes during embryonic development via SMAD2. How SMAD2 activates programmes of gene expression that are modulated over time, however, is not known. In this thesis, using the P19 embryonic teratoma cell line as a model system, I delineate the sequence of events that occur from SMAD2 binding to transcriptional activation, and the underlying mechanisms. I show that NODAL/Activin signalling induces dramatic changes in the chromatin landscape, and orchestrates a dynamic transcriptional network regulated by SMAD2, which acts via multiple mechanisms. By combining different genome-wide approaches, I have discovered two modes of SMAD2 binding. SMAD2 can bind pre-acetylated nucleosome-depleted sites, where it promotes a further increase in H3K9ac/H3K27ac. However, SMAD2 also binds to unacetylated, closed chromatin, independently of pioneer factors, where it induces nucleosome displacement and H3 acetylation. For a subset of genes, this requires cooperation with the remodeller SMARCA4 and the transcription factor FOXH1. I demonstrate that SMAD2 regulates RNA Polymerase II via de novo recruitment to target promoters, and that long term modulation of the transcriptional responses requires continued NODAL/Activin signalling. Moreover, SMAD2 binding does not necessarily equate with transcriptional kinetics, and my data suggest that SMAD2 recruits multiple co-factors during sustained signaling to shape the downstream transcriptional programme. I have used ATAC-seq to identify specific transcription factor footprints at SMAD2 binding sites, and future work will aim to unveil and characterise the network of transcription factors that collaborate with SMAD2 and enable cells to correctly interpret NODAL/Activin signaling over time.

Type: Thesis (Doctoral)
Qualification: Ph.D
Title: NODAL/Activin signalling to chromatin: mechanisms of SMAD2-regulated transcription
Event: UCL
Open access status: An open access version is available from UCL Discovery
Language: English
UCL classification: UCL
UCL > Provost and Vice Provost Offices
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Life Sciences
URI: https://discovery.ucl.ac.uk/id/eprint/10041515
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