Doctoral thesis

Deciphering the complexity of human noncoding promoter-proximal transcriptome : different scales of transcriptional control : from a single gene to the whole epigenome


224 p

Thèse de doctorat: Università della Svizzera italiana, 2019

English Long noncoding RNAs (lncRNAs) have gained increasing interest in molecular studies, their active participation in important biological functions has emerged and their direct involvement in genomic reprogramming during development and diseases, including cancer, has been demonstrated. Several studies have shown their active contribution in transcriptional control and they are emerging as relevant players in the epigenetic machinery, with key roles in nuclear functional organization. High- throughput sequencing approaches have revealed frequent noncoding transcription in promoter-proximal regions, defining the need of disclosing the complexity of mechanisms underlying regulatory elements. In our work, we uncover a complex network based on a promoter-associated noncoding RNA (paRNA), which coordinates a microRNA and epigenetic effectors able to modulate the transcription of the tumour suppressor E-cadherin in epithelial cancers. E-cadherin (CDH1) silencing relies on the formation of a complex between the paRNA and microRNA-guided Argonaute 1 that, together, recruit SUV39H1 and induce repressive chromatin modifications in the gene promoter. A single nucleotide polymorphism (rs16260) linked to increased cancer risk alters the secondary structure of the paRNA, with the risk allele facilitating the assembly of the microRNA-guided Argonaute 1 complex and gene silencing. After demonstrating the role of paRNA-based epigenetic networks and how its deregulation may contribute to cancer and other diseases, we extended this model to a genome-wide perspective, generating a comprehensive catalogue of promoter-associated RNA and a synoptic analysis of their features, functions and interactome. Integrating data from multiple cell types and experimental platforms we identified thousands of paRNA in the human genome, transcribed in both sense and antisense orientation, mostly non-polyadenylated and retained in nuclei. Their case and context specific relation with adjacent genes confirmed that paRNA execute their functions interacting with a variety of network components, regulating epigenetics at multiple levels. Positive transcriptional regulators, epigenetic effectors and chromatin marks are enriched in paRNA-positive promoters. Furthermore, paRNA-positive promoters exhibit chromatin signatures of active promoters and enhancers, denoting a dual function. paRNA-positive promoters also reside preferentially at chromatin loop boundaries, suggesting that an involvement in anchor site recognition and establishment of chromatin loops. Importantly, these features were independent of the transcriptional state of neighbouring genes. Thus, paRNA may act as cis-regulatory modules with an impact on local recruitment of transcription factors, epigenetic state and chromatin loop organization. Providing a comprehensive analysis of the promoter-proximal transcriptome and its interactome, this study offers novel insights into the roles of paRNA in epigenetic processes and human diseases, making them promising targets for drug discovery.
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Computer science and technology
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