Chromatin profiling transcriptional programmes in response to dietary intake to maintain homeostasis

Supervisors: Nimesh Mody, Nicholas Morton, Alasdair MacKenzie

Project description:

Dietary intake of macronutrients (i.e. carbohydrates, fats and proteins) elicits major alterations in transcriptional programmes in hepatocytes to maintain homeostasis. These nutrients engage a network of specific transcription factors to change target gene expression via chromatin remodelling and major alterations in chromatin accessibility (1,2).  Aberrant regulation of these networks appears to be key in the development of many metabolic diseases in response to excess consumption of calories from processed carbohydrates, fats and proteins.

Vitamin A (or retinol) is the parent compound of all bioactive retinoids including the key signalling metabolite retinoic acid. Alterations in retinoid levels and genes have been observed in several models of type-2 diabetes. Moreover, targeted genetic alterations or pharmaceutical interventions in retinoid homeostasis genes or signalling have been shown to have major effects on lipid and glucose homeostasis. We have shown that a synthetic retinoid called Fenretinide can inhibit the development of obesity, insulin resistance and impaired glucose homeostasis in mice.

We have now used next-generation DNA sequencing to gain an insight into how retinoic acid receptor (RAR) transcription factor genome-wide signalling is altered in these impaired metabolic states. Firstly, using RNA-sequencing, we have identified hepatic FGF-21, a novel metabolic regulator with a growing list of biological functions, as a potential link to RAR signalling in liver (3). We have also found that in association with the beneficial effect of Fenretinide treatment on metabolic diseases, that Fenretinide can suppress a transcriptional programme mediated by gene targets of the transcription factor PPAR-alpha in liver.

Moreover, using DNA sequencing data obtained from our RAR genome-wide binding experiment and bioinformatics analysis with Dnase 1 hypersensitivity data available in public databases, we have also found that chromatin accessibility is linked to RAR binding sites. Specifically, RAR binding is highly associated with open chromatin sites in lean, insulin sensitive states, but RAR binding sites in the obese, insulin resistant state is inaccessible (i.e. protected from Dnase 1 digestion). Our findings suggest that broad changes in chromatin accessibility with high-fat diet feeding, obesity and impaired glucose homeostasis leads to extensive changes in RAR occupancy (or vice versa).

Our aim in this PhD project to elucidate the complex network of transcription factors, chromatin accessibility and RAR occupancy

induced by altered dietary intake of macronutrients and

that regulate transcriptional programmes involved in energy balance and glucose homeostasis.

This will be tested by a series of specific DNA sequencing studies in livers from mice treated with various combinations of carbohydrates, fats and proteins. We will examine

  • DNase hypersensitivity;
  • RNA Pol II binding (a direct readout of transcriptional activity); epigenomic marks indicative transcriptional or enhancer activity (e.g. histone H3 lysine methylation/acetylation).

Utilising computational bioinformatics analysis, we will also investigate the level of binding to shared genomic sites by other key regulators/coregulators (eg. PPAR-alpha).

We hypothesise that Fenretinide treatment of mice alters binding of inducible RAR isoforms. This will be tested by performing genome-wide binding for these RAR isoforms in liver from mice treated with Fenretinide (and derivatives with modified signalling effects).

  • References:

    1: Leung A, Parks BW, Du J, Trac C, Setten R, Chen Y, Brown K, Lusis AJ, Natarajan R, Schones DE. Open chromatin profiling in mice livers reveals unique chromatin variations induced by high fat diet. J Biol Chem. 2014 Aug 22;289(34):23557-67. doi: 10.1074/jbc.M114.581439. Epub 2014 Jul 8. PubMed PMID: 25006255; PubMed Central PMCID: PMC4156056.

    2: Goldstein I, Baek S, Presman DM, Paakinaho V, Swinstead EE, Hager GL. Transcription factor assisted loading and enhancer dynamics dictate the hepatic fasting response. Genome Res. 2017 Mar;27(3):427-439. doi: 10.1101/gr.212175.116. Epub 2016 Dec 28. PubMed PMID: 28031249; PubMed Central PMCID: PMC5340970.

    3: Morrice N, Mcilroy GD, Tammireddy SR, Reekie J, Shearer KD, Doherty MK, Delibegović M, Whitfield PD, Mody N. Elevated Fibroblast growth factor 21 (FGF21) in obese, insulin resistant states is normalised by the synthetic retinoid Fenretinide in mice. Sci Rep. 2017 Mar 3;7:43782. doi: 10.1038/srep43782. PubMed PMID: 28256636; PubMed Central PMCID: PMC5335663.