The interplay of epigenetic marks during stem cell differentiation and development

Abstract

Chromatin, the template for epigenetic regulation, is a highly dynamic entity that is constantly reshaped during early development and differentiation. Epigenetic modification of chromatin provides the necessary plasticity for cells to respond to environmental and positional cues, and enables the maintenance of acquired information without changing the DNA sequence. The mechanisms involve, among others, chemical modifications of chromatin, changes in chromatin constituents and reconfiguration of chromatin interactions and 3D structure. New advances in genome-wide technologies have paved the way towards an integrative view of epigenome dynamics during cell state transitions, and recent findings in embryonic stem cells highlight how the interplay between different epigenetic layers reshapes the transcriptional landscape.

Fine mapping of 2q35 high‐risk neuroblastoma locus reveals independent functional risk variants and suggests full‐length BARD1 as tumor‐suppressor

“…Across the two defined regions, we identified 130 CRVs. H3K27 acetylation (H3K27ac) is linked to the activation of enhancers and promoters 26 . Therefore, in order to highlight potentially functional variants, we annotated each CRVs with histone marker H3K27ac by using ChIPseq data derived form 26 human derived-neuroblastoma and 6 patient-derived xenograft (PDX cell) lines deposited in GEO database (GSE90683) (Supplementary Table S4 and S5, Supplementary Fig.…”

DNA G‐Quadruplexes (G4s) Modulate Epigenetic (Re)Programming and Chromatin Remodeling

“…Epigenetic marks, including DNA methylation, histone modification, and nucleosome positioning, modulate chromatin organization and gene expression. During early development and cell differentiation, the epigenetic profile is dynamic, which enables chromatin reshaping in response to environmental or developmental stimuli and accounts for cell fate plasticity . Subsequently, DNA methylation and histone marks are maintained through cell division (and re‐established on newly assembled chromatin during replication) and thus constitute epigenetic memory .…”

“…During early development and cell differentiation, the epigenetic profile is dynamic, which enables chromatin reshaping in response to environmental or developmental stimuli and accounts for cell fate plasticity. [1] Subsequently, DNA methylation and histone marks are maintained through cell division (and re-established on newly assembled chromatin during replication) and thus constitute epigenetic memory. [2] Tight regulation of the epigenetic alteration and maintenance processes is ensured by the cross talk between related protein factors (DNA methyltransferases [DNMTs], histone chaperones, and chromatin remodelers) [3,4] and modulated by noncoding RNAs.…”

Transcriptional memory in skeletal muscle. Don't forget (to) exercise

“…While the predictive relationship between specific chromatin modifications and different states of transcriptional activity has been widely described in large‐scale profiling studies, whether and in which ways distinct marks are instructive or permissive, cause or consequence of transcriptional activity is still a matter of ongoing debate. Some chromatin marks are lineage‐specific or reflect cell‐type‐specific states that are inherited within the cell lineage, allowing the cells of our body to always remember what cell they are and from which cell they derive (Atlasi & Stunnenberg, 2017). Other chromatin modifications are dynamically associated with acute transcriptional activity and do not persist after the initial stimulus that drives the modification has ceased (Katan‐Khaykovich & Struhl, 2002).…”