SARS-CoV-2 restructures host chromatin architecture

Wang, Ruo–Yu; Lee, Joo-Hyung; Kim, Jieun; Xiong, Feng; Hasani, Lana Al; Shi, Yuqiang; Simpson, Erin N.; Zhu, Xiaoyu; Chen, Yi-Ting; Shivshankar, Pooja; Krakowiak, Joanna; Wang, Yanyu; Gilbert, David M.; Yuan, Xiaoyi; Eltzschig, Holger K.; Li, Wenbo

doi:10.1038/s41564-023-01344-8

Cited by 32 publications

(63 citation statements)

References 53 publications

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“…Research on human cells infected with SARS‐CoV‐2 shows that about 30% of the genome undergoes compartment switching, which is accompanied by a decrease in chromatin interaction levels within the A compartment. This may be linked to the high incidence of acute sequelae resulting from SARS‐CoV‐2 infection 257 …”

Section: D Genome Structural Variations and Diseasementioning

confidence: 99%

Three‐dimensional genome structure and function

Líu

Tsai

Yang

et al. 2023

MedComm

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Linear DNA undergoes a series of compression and folding events, forming various three‐dimensional (3D) structural units in mammalian cells, including chromosomal territory, compartment, topologically associating domain, and chromatin loop. These structures play crucial roles in regulating gene expression, cell differentiation, and disease progression. Deciphering the principles underlying 3D genome folding and the molecular mechanisms governing cell fate determination remains a challenge. With advancements in high‐throughput sequencing and imaging techniques, the hierarchical organization and functional roles of higher‐order chromatin structures have been gradually illuminated. This review systematically discussed the structural hierarchy of the 3D genome, the effects and mechanisms of cis‐regulatory elements interaction in the 3D genome for regulating spatiotemporally specific gene expression, the roles and mechanisms of dynamic changes in 3D chromatin conformation during embryonic development, and the pathological mechanisms of diseases such as congenital developmental abnormalities and cancer, which are attributed to alterations in 3D genome organization and aberrations in key structural proteins. Finally, prospects were made for the research about 3D genome structure, function, and genetic intervention, and the roles in disease development, prevention, and treatment, which may offer some clues for precise diagnosis and treatment of related diseases.

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Section: D Genome Structural Variations and Diseasementioning

confidence: 99%

Three‐dimensional genome structure and function

Líu

Tsai

Yang

et al. 2023

MedComm

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“…More generally, the role of viral infection in shaping the human immune system and subsequent immune responses has been studied extensively. It is well appreciated that viral infection can rewire the chromatin of immune cells and shape subsequent responses of a person towards additional inflammatory insults 49,50 . For example, a viral response that results in an interferon-based immune response could be protective in the context of diseases driven by T cell helper-2 type inflammation 51 .…”

Section: Discussionmentioning

confidence: 99%

After the Infection: A Survey of Pathogens and Non-communicable Human Disease

Lape,

Schnell,

Parameswaran

et al. 2023

Preprint

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There are many well-established relationships between pathogens and human disease, but far fewer when focusing on non-communicable diseases (NCDs). We leverage data from The UK Biobank and TriNetX to perform a systematic survey across 20 pathogens and 426 diseases, focused primarily on NCDs. To this end, we assess the association between disease status and infection history proxies. We identify 206 pathogen-disease pairs that replicate in both cohorts. We replicate many established relationships, includingHelicobacter pyloriwith several gastroenterological diseases, and connections between Epstein-Barr virus with multiple sclerosis and lupus. Overall, our approach identified evidence of association for 15 of the pathogens and 96 distinct diseases, including a currently controversial link between human cytomegalovirus (CMV) and ulcerative colitis (UC). We validate this connection through two orthogonal analyses, revealing increased CMV gene expression in UC patients and enrichment for UC genetic risk signal near human genes that have altered expression upon CMV infection. Collectively, these results form a foundation for future investigations into mechanistic roles played by pathogens in disease.

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“…Both mechanisms propose epigenetic changes that modulate resource availability and it could be complicated to assess the correctness of either of those. However, epigenetic changes occur post SARS-Cov2 infection [56], and manipulation of epigenetic machinery such as HDAC2 has already been reported [57]. Therefore epigenetic modifications are a result of SASR-Cov2 infection but its meaning remains to be addressed.…”

Section: Post Acute Sequelaementioning

confidence: 99%

SARS-Cov2 seasonality and adaptation are driven by solar activity.

Gonzalez-Lugo¹

2023

Preprint

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Since its isolation in Wuhan SARS-Cov2 showed a high mutation rate hindering the ability to properly characterize. Also as a consequence of its size, traditional sequence analysis methods were computationally constrained. However, applying variational autoencoders (VAEs) to custom sequence representations results in a series of clusters sorted by the sunshine duration (SD) rate of change (SDRC) and other solar-derived features. The transition between clusters is characterized by changes in viral genome size, apparent deletions can be found throughout the SARS-Cov2 genome. This series of deletions might behave as an internal clock inside the genome. SDRC-derived features synchronize COVID-19 cases into a single period. Both SDRC-derived features and solar features correlate with COVID-19 cases pointing towards a solar-dependent seasonality. Atmospheric changes that affect solar radiation also showed a correlation with COVID-19 cases. Analyzing viral genome composition as time series displays an attractor-like behavior under different solar-derived time scales. While clustering them by environmental conditions shows a similar pattern as the one found by the VAE models. Further development of analysis techniques will help us to better understand the seasonality and adaptation of pathogenic organisms.

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SARS-CoV-2 restructures host chromatin architecture

Cited by 32 publications

References 53 publications

Three‐dimensional genome structure and function

Three‐dimensional genome structure and function

After the Infection: A Survey of Pathogens and Non-communicable Human Disease

SARS-Cov2 seasonality and adaptation are driven by solar activity.

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