Selective Activation of Alternative MYC Core Promoters by Wnt-Responsive Enhancers.

Jorge Bardales,Hideya Kawaji,Xavier Darzacq,Yasuhiro Murakawa,Evin Wieser

doi:10.3390/genes9060270

Jorge Bardales, Hideya Kawaji + Show 3 more

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https://doi.org/10.3390/genes9060270

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Abstract

In Metazoans, transcription of most genes is driven by the use of multiple alternative promoters. Although the precise regulation of alternative promoters is important for proper gene expression, the mechanisms that mediates their differential utilization remains unclear. Here, we investigate how the two alternative promoters (P1, P2) that drive MYC expression are regulated. We find that P1 and P2 can be differentially regulated across cell-types and that their selective usage is largely mediated by distal regulatory sequences. Moreover, we show that in colon carcinoma cells, Wnt-responsive enhancers preferentially upregulate transcription from the P1 promoter using reporter assays and in the context of the endogenous Wnt induction. In addition, multiple enhancer deletions using CRISPR/Cas9 corroborate the regulatory specificity of P1. Finally, we show that preferential activation between Wnt-responsive enhancers and the P1 promoter is influenced by the distinct core promoter elements that are present in the MYC promoters. Taken together, our results provide new insight into how enhancers can specifically target alternative promoters and suggest that formation of these selective interactions could allow more precise combinatorial regulation of transcription initiation.

Highlights

RNA Polymerase II-dependent transcription initiation is a complex process that must be precisely regulated for the proper generation of spatio-temporal patterns of gene expression
Core promoters are diverse in their composition of cis-control DNA and can contain multiple elements like transcription factor IIB (TFIIB) recognition sites (BREu and BREd ), TATA box binding sites, initiator sequences (INR), motif ten elements (MTE)
The usage of alternative promoters as drivers of transcription initiation is a prevalent phenomenon that occurs throughout metazoans [12,48]

Summary

Introduction

RNA Polymerase II-dependent transcription initiation is a complex process that must be precisely regulated for the proper generation of spatio-temporal patterns of gene expression. Core promoters are diverse in their composition of cis-control DNA and can contain multiple elements like transcription factor IIB (TFIIB) recognition sites (BREu and BREd ), TATA box binding sites, initiator sequences (INR), motif ten elements (MTE). Alternative promoters have been found to be differentially utilized across different tissues [11,16], during development and upon the presence of specific stimuli [11,17,18], suggesting that fine tuning of alternative promoters may be important for proper gene expression. Some evidence suggests that promoter usage is largely dependent on the epigenetic landscape of chromatin [22,23,24,25] and the presence of proximal transcription factor binding sites [26,27,28], the specific mechanisms that could regulate alternative promoter usage remains poorly understood

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