RESEARCH

Gene-by-environment interactions through modifications to chromatin in metabolic disease

We previously reported that one manner by which external environmental factors can influence molecular pathways is through modification to chromatin, with a “western” high fat / high sucrose (HF/HS) diet leading to chromatin remodeling in the livers of mice. Intriguingly, regulatory regions of the genome, including binding sites for liver transcription factors displayed dramatic chromatin remodeling under HF/HS diet. By profiling chromatin modifications under HF/HS diet in several strains of mice, we found that the genomic loci with the greatest degree of diet-induced chromatin remodeling were largely strain-specific, indicating a role for genetics in this response. This work was published in JBC in 2014 [1]. We have now further demonstrated that diet-induced chromatin remodeling can persist upon reversal of HF/HS diet to a control diet and that regions of persistent chromatin modification are associated with persistent gene expression changes. These results indicate that diet-induced chromatin remodeling can contribute to long-term health risk even upon lifestyle changes such as alterations to diet. This work was published in JBC in 2016 [2] and was selected as a “Paper of the Week” at JBC.

Causes and consequences of obesity driven epigenetic dysregulation of transposons.

Through examining chromatin accessibility variation in liver tissue from seven strains of adult mice that have phenotypic diversity in response to a high-fat/high-sucrose diet, we found that nearly 40% of the loci with the greatest degree of chromatin variability across strains are at transposable elements (TEs). We found that evolutionary younger and older TEs have differential chromatin accessibility profiles and are enriched for binding sites of unique transcription factors, indicating a role for TEs in the evolution of regulatory networks in the liver. We also demonstrated that TE polymorphisms and epigenetic modifications at TEs contribute to regulatory variation across different strains of mice through providing binding sites for liver transcription factors. Our preliminary work on this was published in Epigenetics and Chromatin in 2016 [3] and was recently selected as a Research Highlight in Nature Reviews Genetics [4].

While our data indicates that obesity promotes the dysregulation of TEs in the liver, the mechanisms responsible for this dysregulation and how TE dysregulation can contribute to long-term disease risk remain unclear. We are working to: 1) determine the obesogenic conditions (dietary components, inflammatory state, etc.) involved in transposable element dysregulation, 2) examine the role of DNA methylation in TE dysregulation and 3) determine the consequences of TE dysregulation on gene expression changes. Notably, our work represents the first attempt to assess the consequences of TE dysregulation in obesity and how this contributes to long-term disease risk. We expect our proposed research will open a novel research avenue. Furthermore, investigating obesity induced epigenetic modifications, leading to the dysregulation of TEs, in the initiation and progression of disease is also novel. In addition to further elucidating the molecular mechanisms driving metabolic disease, we expect our results related to TE dysfunction will have far reaching implications.

3. Chromatin biology in development and disease.

It was recently shown that in adult human hematopoietic stem and progenitor cells (HSPCs), H3K9me2 chromatin territories are absent in primitive cells and are formed de novo during lineage commitment. In committed HSPCs, G9a/GLP activity nucleates H3K9me2 marks at CpG islands (CGIs) and other genomic sites within genic regions, which then spread across most genic regions during differentiation. HSPCs treated with UNC0638, a G9a/GLP small molecular inhibitor, better retain stem cell-like phenotypes and function during in vitro expansion and increased expression of lineage-affiliated genes and certain gene clusters, suggestive of changes in regulation of chromatin structure. We examined the chromatin accessibility, DNA methylation and H3K9me2 profiles of donor derived CD34+ HSPCs treated with UNC0638 (or DMSO control). Our results indicated that H3K9me2 nucleates at CpG-island-like regions of the genome, at both promoter and “orphan” sites. Furthermore, removal of H3K9me2 by treatment with UNC0638 leads to increases in chromatin accessibility at the majority of H3K9me2 nucleation sites. Interestingly, the presence of DNA methylation mitigates the effect of increased chromatin accessibility upon removal of H3K9me2. To our knowledge, this is the first observation of coordination between H3K9me2 patterning, promoter and orphan CGIs, DNA methylation and chromatin structure. This work was published in Epigenetics and Chromatin in 2014 [5].

Nickel compounds are environmental pollutants that cause a multitude of health risks including lung and nasal cancers in humans. Similar to most carcinogenic metals, the mutagenic potential of nickel compounds is very low and does not correlate with their potent carcinogenicity. Recent evidence suggests that nickel could alter transcriptional regulation through epigenetic alterations. We have been investigating this by profiling H3K9me2 in immortalized non-cancerous human lung epithelial BEAS-2B cells treated with nickel as well as control BEAS-2B cells. Our results indicate that nickel alters H3K9me2 domain structure globally, resulting in the spreading of H3K9me2 in active regions of the genome. We demonstrated that nickel-induced H3K9me2 disruption occurred preferentially at the H3K9me2 domain boundaries possessing weak CTCF binding sites, suggesting inhibition of DNA binding ability of CTCF as one of the causes of H3K9me2 domain disruption. We furthermore demonstrated that euchromatin islands, local regions of active chromatin, can protect genes from H3K9me2 induced gene silencing. These results provide insight into the regulation of chromatin dynamics and the consequences of chromatin domain disruption. Moreover, since nickel is a well-known carcinogen that has been conclusively shown to induce lung and nasal cancers in humans, our finding of chromatin domain disruption by nickel would have profound implications in understanding the process of carcinogenesis. This work was published in PNAS in 2014 [6].

Our previous results have demonstrated that the heterochromatin mark, H3K9me2, is nucleated at specific CpG-island-like regions of the genome during hematopoiesis. One outstanding question is whether the nucleation of H3K9me2 is lineage specific or if there are general rules that govern the nucleation of these sites across different tissues regardless of type. We are now investigating if H3K9me2 is nucleated at a similar set of sites in pancreatic development. This work has the potential to reveal fundamental mechanisms regarding the establishment of chromatin domains in normal development as well as the molecular pathways involved in pancreatic development.

In collaboration with Mei Kong’s lab at City of Hope, we have furthermore been examining how glutamine deficiency in solid tumor core regions influences histone methylation levels and how this impacts tumor heterogeneity and therapeutic response. This work was published in Nature Cell Bio in 2016 [7].

References

1. Leung, A., et al., Open chromatin profiling in mice livers reveals unique chromatin variations induced by high fat diet. J Biol Chem, 2014. 289(34): p. 23557-67.
2. Leung, A., et al., Persistent Chromatin Modifications Induced by High Fat Diet. J Biol Chem, 2016. 291(20): p. 10446-55.
3. Du, J., et al., Chromatin variation associated with liver metabolism is mediated by transposable elements. Epigenetics Chromatin, 2016. 9: p. 28.
4. Waldron, D., Chromatin: Chromatin variation underLINEd. Nat Rev Genet, 2016. 17(9): p. 504-5.
5. Schones, D.E., et al., G9a/GLP-dependent H3K9me2 patterning alters chromatin structure at CpG islands in hematopoietic progenitors. Epigenetics Chromatin, 2014. 7: p. 23.
6. Jose, C.C., et al., Epigenetic dysregulation by nickel through repressive chromatin domain disruption. Proceedings of the National Academy of Sciences of the United States of America, 2014. 111(40): p. 14631-14636.
7. Pan, M., et al., Regional glutamine deficiency in tumours promotes dedifferentiation through inhibition of histone demethylation. Nat Cell Biol, 2016. 18(10): p. 1090-101.