The epigenetically-encoded memory of the innate immune system

Sun, Sarah; Barreiro, Luis B.

doi:10.1016/j.coi.2020.02.002

Cited by 35 publications

(25 citation statements)

References 58 publications

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“…The major chromatin changes in immune cells occur by DNA methylation and histone modifications, but also ATP‐dependent chromatin remodelling. The DNA methylation pattern primarily changes during haematopoiesis to alter gene expression patterns, 34 while acetylation and methylation of histones contribute to changes in gene expression also during differentiation and activation of immune cells 35‐37 . The epigenetic modification of chromatin is precisely regulated via histone‐modifying enzymes and chromatin remodelling enzymes acting on specific loci, resulting in specific changes in gene expression, chromatin organization and other DNA regulatory processes.…”

Section: Epigenetic Mechanisms In Immunitymentioning

confidence: 99%

What will studies of Fulani individuals naturally exposed to malaria teach us about protective immunity to malaria?

et al. 2020

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Section: Epigenetic Mechanisms In Immunitymentioning

confidence: 99%

What will studies of Fulani individuals naturally exposed to malaria teach us about protective immunity to malaria?

et al. 2020

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“…The development of the ATACseq technique over the past decade has spurred a broad investigation of chromatin accessibility across cell types [4,18]. In particular, chromatin accessibility has been intensively studied using ATACseq across many hematopoietic cells types [8,20,32,21,5,43,39,42]. Hematopoiesis, which involves the differentiation of a single hematopoietic stem cell into the different blood cell types, is well characterized and the lineages through which the differentiation occurs can be described by a differentiation tree [33].…”

Section: Introductionmentioning

confidence: 99%

“…Chromatin accessibility has been shown to vary across different hematopoietic cell types, and these differences have been shown to be essential to cell differentiation and cell function, e.g. [13,38,36,16,21,39].…”

Section: Introductionmentioning

confidence: 99%

Tree Based Co-Clustering Identifies Variation in Chromatin Accessibility Across Hematopoietic Cell Types

Tb¹,

Nk²,

Leviyang³

2021

Preprint

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Chromatin accessibility, as measured by ATACseq, varies between hematopoietic cell types in different branches of the hematopoietic differentiation tree, e.g. T cells vs B cells, but methods that relate variation in chromatin accessibility to the placement of a cell type on the differentiation tree are lacking. Using an ATACseq dataset recently published by the ImmGen consortium, we construct associations between chromatin accessibility and hematopoietic cell types using a novel co-clustering approach that accounts for the structure of the hematopoietic, differentiation tree. Under a model in which all loci and cell types within a co-cluster have a shared accessibility state, we show that roughly 80\% of cell type associated accessibility variation can be captured through 12 cell type clusters and 20 genomic locus clusters. Using publicly available ChIPseq datasets, we show that our clustering reflects transcription factor binding patterns with implications for regulation across cell types. Our results provide a framework for analysis of chromatin state variation across cell types related by a tree or network.

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“…Epigenetic mechanisms are important for cellular reprogramming and for the cell-type specificity [ 36 ]. All our cells share the same DNA but mammalians comprise of a diverse repertoire of cell types with epigenetic mechanisms that regulate cell-specific functions and gene expression [ 37 ]. However, epigenetic mechanisms can contribute to the development and maintenance of cancer and autoimmune or inflammatory diseases, including periodontitis [ 38 , 39 ].…”

Section: Introductionmentioning

confidence: 99%

The Role of Epigenetic Functionalization of Implants and Biomaterials in Osseointegration and Bone Regeneration—A Review

et al. 2020

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The contribution of epigenetic mechanisms as a potential treatment model has been observed in cancer and autoimmune/inflammatory diseases. This review aims to put forward the epigenetic mechanisms as a promising strategy in implant surface functionalization and modification of biomaterials, to promote better osseointegration and bone regeneration, and could be applicable for alveolar bone regeneration and osseointegration in the future. Materials and Methods: Electronic and manual searches of the literature in PubMed, MEDLINE, and EMBASE were conducted, using a specific search strategy limited to publications in the last 5 years to identify preclinical studies in order to address the following focused questions: (i) Which, if any, are the epigenetic mechanisms used to functionalize implant surfaces to achieve better osseointegration? (ii) Which, if any, are the epigenetic mechanisms used to functionalize biomaterials to achieve better bone regeneration? Results: Findings from several studies have emphasized the role of miRNAs in functionalizing implants surfaces and biomaterials to promote osseointegration and bone regeneration, respectively. However, there are scarce data on the role of DNA methylation and histone modifications for these specific applications, despite being commonly applied in cancer research. Conclusions: Studies over the past few years have demonstrated that biomaterials are immunomodulatory rather than inert materials. In this context, epigenetics can act as next generation of advanced treatment tools for future regenerative techniques. Yet, there is a need to evaluate the efficacy/cost effectiveness of these techniques in comparison to current standards of care.

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The epigenetically-encoded memory of the innate immune system

Cited by 35 publications

References 58 publications

What will studies of Fulani individuals naturally exposed to malaria teach us about protective immunity to malaria?

What will studies of Fulani individuals naturally exposed to malaria teach us about protective immunity to malaria?

Tree Based Co-Clustering Identifies Variation in Chromatin Accessibility Across Hematopoietic Cell Types

The Role of Epigenetic Functionalization of Implants and Biomaterials in Osseointegration and Bone Regeneration—A Review

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