Characterising how the HUSH complex can induce the epigenetic repression of retroviruses and retroelements

Supervisors: Richard SloanJose Garcia-Perez

Project Description:

The aim of this project is to use comparative analysis to understand how the recently identified antiviral HUSH complex can repress the expression of range of retroviruses and retroelements of medical, zoonotic and veterinary importance at the epigenetic level when they have integrated into host chromatin. Retroviruses must replicate within cells and so are highly susceptible to cellular antiviral genes and restriction factors which have evolved to directly inhibit viral replication and which are a major feature of interferon induced innate immune responses. Variation in restriction factor function is increasingly viewed as central to both pathogenesis and pandemic spread of viruses, while understanding their molecular basis can aid the development of novel antiviral therapies. As genome embedded endogenous retroelements are evolutionary and functionally related to extant retroviruses, they are also similarly susceptible antiviral restriction factors, which when deregulated can lead to inflammatory autoimmune diseases.

Using a range of genomic and proteomic screening strategies, we and others have identified the HUSH complex as able to repress the expression of both infectious retroviruses and endogenous retroelements at the epigenetic level via histone modification of proviral DNA. However, the underlying molecular mechanism is still not well characterised and nor is the importance to non-human retroviral pathogens known. Working with a range of data sources the aim of this project will be to define how the HUSH complex represses expression of cellular, retroviral and retroelement mRNA. Proteomic data has already identified putative nucleic acid binding sites in HUSH complex components which will be mutated and studies to identify functionally important regions using RNA-seq, ChIP-Seq and/or CLIP-Seq approaches in order to determine how HUSH complex components and nucleic acid binding motifs drive epigenetic repression of retroviruses and retroelements. Affinity proteomic analysis of HUSH complex proteins will also be performed to identify functionally important protein-protein interactions and these data will be integrated with pre-existing genomic screening data for retrovirus and retroelement restriction factors before pathway analysis to build new molecular models of HUSH restriction to be correlated with sequencing data.

Retroviruses and retroelements of medical (HIV-1, HIV-2, LINE-1), zoonotic (SIV) and veterinary importance (JSRV, EIAV, BLV) will then be assayed for replication capacity with wild type, nucleic acid binding site mutant, and knockout HUSH components according to prior analyses. Comparative analysis of patterns of susceptibility will allow the viral determinants of restriction to be identified. Collectively this project will identify the functionally important nucleic acid and protein interactions of HUSH restriction of retroviruses and retroelements. It will also reveal how medically and veterinary important viruses are susceptible to HUSH-mediated epigenetic silencing. Understanding retrovirus and retroelement control in this manner will allow new therapeutic strategies for retrovirus and retroelement control in humans and animals to be investigated. 

Epigenetic silencing by the HUSH complex mediates position-effect variegation in human cells. Tchasovnikarova IA, Timms RT, Matheson NJ, Wals K, Antrobus R, Göttgens B, Dougan G, Dawson MA, Lehner PJ. Science. 2015. 348(6242):1481-1485. 

Selective silencing of euchromatic L1s revealed by genome-wide screens for L1 regulators. Liu N, Lee CH, Swigut T, Grow E, Gu B, Bassik MC, Wysocka J.
Nature. 2018. 553(7687):228-232. 

HIV-2/SIV viral protein X counteracts HUSH repressor complex.
Chougui G, Munir-Matloob S, Matkovic R, Martin MM, Morel M, Lahouassa H, Leduc M, Ramirez BC, Etienne L, Margottin-Goguet F. Nat Microbiol. 2018. 3(8):891-897. 

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