SARS-CoV-2 reprograms host chromatic network to induce immune dysfunction

A recent study conducted at the University of Texas Science Center, Houston, in the USA, has revealed that upon infection, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) alters the host chromatin architecture to suppress antiviral interferon-responsive genes and augment inflammatory genes. The study is currently available on the bioRxiv* preprint server.

Study: SARS-CoV-2 Restructures the Host Chromatin Architecture. Image Credit: Design_Cells / Shutterstock
Study: SARS-CoV-2 Restructures the Host Chromatin Architecture. Image Credit: Design_Cells / Shutterstock


SARS-CoV-2, the causative pathogen of coronavirus disease 2019 (COVID-19), is an enveloped, positive-sense, single-stranded RNA virus that primarily attacks epithelial cells in the human respiratory tract. From the perspective of viral evolution, it is well known that mutations appearing in SARS-CoV-2 spike protein under positive selection pressure are primarily responsible for increasing viral fitness into host cells. However, it is equally important to understand how SARS-CoV-2 modulates the host chromatin network to facilitate immune evasion and induce persistent clinical consequences.

The entire mammalian chromatin network contains several layers of architectures, including A/B compartments, Topological Associating Domains (TADs), and chromatin loops, which collectively regulate vital nuclear functions, including gene transcription, replication, recombination, and DNA damage repair.

In the current study, the scientists have investigated how SARS-CoV-2 affects the three-dimensional chromatin architecture of the host to improve immune fitness. They have assessed the host chromatin modification in angiotensin-converting enzyme 2 (ACE2)-expressing human alveolar epithelial cells that were infected with SARS-CoV-2.

Important observations

By conducting in situ Hi-C, the scientists detected and quantified the pairwise interactions between chromosome regions across the entire genome in virus-infected and mock-infected (control) cells. The findings revealed a significantly widespread alteration of the chromatic architecture in SARS-CoV-2-infected cells, with the highest deregulation in long-distance chromatic interactions. With further analysis, the scientists observed that chromatin domains are frequently weakened, and chromatin loops are frequently deregulated. Moreover, at the intra-chromosomal level, they observed a global reduction in short-distance chromatin interactions and an increase in mid-to-long distance and extremely long-distance interactions. Similarly, at the inter-chromosomal level, they observed an increased trans-chromosomal interaction. Collectively, these observations indicate SARS-CoV-2-induced alteration of chromatic compartmentalization.

Regarding chromatin compartmentalization defects, they noted a global reduction of A compartment and A-to-B switching, with 30% of genomic regions showing compartmental reduction or switching. By evaluating epigenomic characteristics of the regions susceptible to compartmental alterations, they observed that both A and B compartments are losing identity and switching to each other.

Epigenomic reprogramming

To understand the mechanism of compartmental alterations, the scientists conducted ChIP-Seq of active and repressive histone modifications as these modifications are enriched in A and B compartments, respectively. Interestingly, they observed that although overall modifications remained unchanged after infection, there was a significant reduction of H3K27ac, which is an active histone mark associated with higher transcriptional activation.

Simultaneously, they observed a moderate increase of recessive histone marks, including H3K9me3, following infection. Importantly, they observed a significant correlation between the weakening of the A compartment and the reduction of the active histone mark. Collectively, the findings indicate that SARS-CoV-2 induces compartmentalization defects by reprogramming chromatin modification.

Intra-TAD interactions

Regarding other chromatic structures, the scientists observed a global reduction in cis-interactions within TADs (intra-TAD interactions) after infection, which was accompanied by unchanged or increased cis-interactions outside of TADs. However, these changes were not associated with a loss of TAD identity. To understand the basis of reduced intra-TAD interactions, they assessed chromatin binding of two main TAD organizers, namely CTCF and cohesion. The findings revealed that a drastic depletion of cohesion from intra-TAD regions is primarily responsible for the weakening of interactions. Regarding epigenetic changes in virus-sensitive TADs, they identified that following infection, an induction of H3K9me3 is associated with cohesion depletion and subsequent reduction of intra-TAD interactions.            

Immuno-pathological impacts of chromatin reprogramming

Two major immuno-pathological changes observed in severe COVID-19 patients include delayed or suppressed type 1 interferon response and excessive inflammation. In this study, the scientists developed three-dimensional genome and epigenome maps. They observed that SARS-CoV-2 infection caused transcriptional suppression of type 1 interferon-responsive antiviral genes and virus sensors by remarkably changing enhancer activity and enhancer–promotor interactions. Moreover, they noticed that SARS-CoV-2 caused transcriptional induction of inflammatory genes by uniquely and significantly increasing the H3K9me3 mark at their promoters.

Study significance

The study highlights a potential mechanism of SARS-CoV-2-mediated reprogramming of host chromatin network and its impact on immuno-pathological features of COVID-19. The study findings provide a novel path to further characterize persistent epigenomic impacts of SARS-CoV-2 infection.

*Important notice

bioRxiv publishes preliminary scientific reports that are not peer-reviewed and, therefore, should not be regarded as conclusive, guide clinical practice/health-related behavior, or treated as established information.

Journal reference:
Dr. Sanchari Sinha Dutta

Written by

Dr. Sanchari Sinha Dutta

Dr. Sanchari Sinha Dutta is a science communicator who believes in spreading the power of science in every corner of the world. She has a Bachelor of Science (B.Sc.) degree and a Master's of Science (M.Sc.) in biology and human physiology. Following her Master's degree, Sanchari went on to study a Ph.D. in human physiology. She has authored more than 10 original research articles, all of which have been published in world renowned international journals.


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