Research

The Bose lab is interested in how the epigenetic-machinery that controls gene expression can be regulated by RNA to produce a broad spectrum of activities across the genome. We use diverse techniques to study how RNA interacts with these machines over a range of scales, from functional genomics at a cellular level, to biochemistry and cryo-electron microscopy to understand the molecular mechanisms and structural architectures of these complex machines.

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     Figure 1: Enhancers and chromatin modifications.     A)     Enhancers are fundamental regulators of gene expression that operate far away from gene promoters, looping to contact their target genes. Different patterns of enhancer usage allow fine control of tissue and stimulus-specific gene expression patterns.   B)     In higher eukaryotes, DNA is packaged into a structure called chromatin. Tightly packed chromatin presents a barrier to gene transcription. However, chromatin structure can be regulated by post-translational epigenetic modifications of the histones that form nucleosomes around which DNA is wrapped. These modifications are controlled by a plethora of epigenetic-enzyme complexes to regulate gene expression.

Figure 1: Enhancers and chromatin modifications.

A)    Enhancers are fundamental regulators of gene expression that operate far away from gene promoters, looping to contact their target genes. Different patterns of enhancer usage allow fine control of tissue and stimulus-specific gene expression patterns.

B)    In higher eukaryotes, DNA is packaged into a structure called chromatin. Tightly packed chromatin presents a barrier to gene transcription. However, chromatin structure can be regulated by post-translational epigenetic modifications of the histones that form nucleosomes around which DNA is wrapped. These modifications are controlled by a plethora of epigenetic-enzyme complexes to regulate gene expression.

The patterns of genes expressed in multicellular organisms are critical for determining a cell’s identity, and for controlling how that cell responds to its environment. Gene transcription is regulated at regions adjacent to genes called promoters, but also from regions called enhancers that are often located tens-of-thousands of base-pairs away from the promoter. Enhancers are fundamental regulatory DNA sequences; they are crucial for driving development, and for generating cell-lineage specific transcriptional responses to environmental stimuli. 

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     Figure 2: How eRNA stimulates CBP activity.   Our work demonstrated that eRNAs bind to a regulatory region within the catalytic acetyltransferase domain of the key transcription co-activator CBP. By displacing this region from the active site of the enzyme, eRNAs could stimulate the acetyltransferase activity and promote histone acetylation and transcription. 

Figure 2: How eRNA stimulates CBP activity.

Our work demonstrated that eRNAs bind to a regulatory region within the catalytic acetyltransferase domain of the key transcription co-activator CBP. By displacing this region from the active site of the enzyme, eRNAs could stimulate the acetyltransferase activity and promote histone acetylation and transcription. 

Across the genome, enhancers have unique activities and their mutation and aberrant usage is causative for many human diseases, including cancer. A defining feature of enhancers is their regulation at the level of chromatin, i.e how DNA is made more or less accessible by epigenetic modifications of the nucleosomes that package DNA. This process of regulation is carried out by a vast array of epigenetic-enzyme machinery that controls accessibility. However, although enhancers display a spectrum of activities across the genome, the core machinery that modifies chromatin to drive enhancer function is largely conserved.

 

We are interested in how different patterns of enhancer activity are generated from the core epigenetic-machinery, and how this regulation is disrupted in cancer and disease.

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     Figure 3: How do eRNAs affect enhancer activity?   As the sequence and structure of eRNAs differs between enhancers, they are prime candidates to drive alternative profiles of enhancer activity to control gene expression.

Figure 3: How do eRNAs affect enhancer activity?

As the sequence and structure of eRNAs differs between enhancers, they are prime candidates to drive alternative profiles of enhancer activity to control gene expression.

A key candidate for developing diverse enhancer-activity profiles are non-protein coding RNAs, called enhancer RNAs (eRNAs), that are transcribed from active enhancers. Our work has shown how eRNAs can interact with epigenetic-enzymes to stimulate enhancer activity by changing epigenetic modifications of the chromatin structure. As enhancers differ in sequence, this suggests that eRNAs are critical drivers of enhancer-specific activity profiles. Moreover, disease-related mutations at enhancers could fundamentally alter interactions between eRNAs and enzymes to disrupt enhancer activity.

 

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     Figure 4: How do eRNAs contribute to enzyme organization at enhancers?   The flexible structures of epigenetic enzymes such as CBP allows them to adopt different conformations. We are investigating whether eRNA binding contributes to these distinct arrangements to promote engagement of the enzymes with chromatin at different enhancer regions.

Figure 4: How do eRNAs contribute to enzyme organization at enhancers?

The flexible structures of epigenetic enzymes such as CBP allows them to adopt different conformations. We are investigating whether eRNA binding contributes to these distinct arrangements to promote engagement of the enzymes with chromatin at different enhancer regions.

Our research is focused in three main areas:

 

1.     Using functional genomics (including high throughput sequencing) to investigate how eRNAs and disease-related mutations at enhancers alter enzyme-activity profiles and enhancer function across the genome.

2.     Understanding how eRNAs contribute to stimulus-specific decision-making by epigenetic enzymes using classical biochemistry.

3.     Investigating the role of eRNAs in organizing the structural architecture of epigenetic-enzyme complexes using high-resolution single-particle cryo-EM.