<< Back to MOTIFvations Blog Home Page

HDAC Inhibition Reveals the Role of 3D Chromatin Conformation in the Cellular Memory of Gene Expression

By Stuart P. Atkinson, Ph.D.

May 4, 2026

Tweet

Exploring the Epigenetic Interplay Involved in the HDAC-induced Cellular Memory of Gene Expression

A transient cell stimulus can induce long-lasting alterations to gene expression through the activity of numerous distinct epigenetic pathways; however, the involvement of changes to 3D chromatin conformation – recently reported as a critical regulator of gene expression (Willemin et al.) – in this so-called “cellular memory of gene expression” (D’Urso & Brickner and Atlasi & Stunnenberg) remains somewhat unexplored. A team of researchers from the laboratory of Giacomo Cavalli (University of Montpellier) recently sought to explore this concept in depth by evaluating epigenome dynamics in mouse embryonic stem cells (mESCs) following the acute disruption of their chromatin state. Specifically, they employed the pulsed inhibition of histone deacetylase (HDAC) activity (Yoshida et al.), which prompts rapid, global, but reversible effects on histone acetylation. In their recent Nature Genetics article, Paldi et al. now describe the application of RNA-seq, ChIP–seq, ATAC–seq, and ultradeep Micro-C to explore the interplay between gene expression, histone modification levels, chromatin accessibility, and 3D chromatin conformation, respectively, in this model system; excitingly, their “memorable” results now reveal an important link between 3D genome organization and cellular memory of gene expression.

 Back to Table of Contents

3D Chromatin Conformation: The Epigenetic Concept Behind HDAC-induced Cellular Memory of Gene Expression

The authors pulsed mESCs with the HDAC inhibitor trichostatin A for 4 h to increase genome-wide levels of H3K27 hyperacetylation and, as a result, induce a brief period of chromatin state disruption that would prompt alterations in the gene expression profile. This acute stimulus induced a more epigenetically “active” state in mESCs, as reflected in the deposition of additional histone modifications (including methylated and ubiquitinated residues). These HDAC-induced alterations led to the formation of an open and active state at many gene promoters, while the widespread deposition of H3K4me1 following HDAC inhibition also suggested the formation/activation of gene enhancer elements. These epigenetic alterations triggered a gene expression program characterized by the increased expression of developmentally associated genes and the decreased expression of pluripotency-associated genes, suggesting the exit of mESCs from the pluripotent state and the induction of differentiation. Subsequent ultradeep Micro-C mapping of HDAC inhibition-induced 3D chromatin conformation alterations revealed a dramatic increase in trans-interactions and a marked decrease in cis-interactions, as well as a loss of interactions between active chromatin compartments and an increase in cis-interactions between repressive chromatin compartments. Overall, HDAC inhibition induced greater alterations in permissive histone modifications and gene expression in active chromatin compartments compared to repressive chromatin compartments. Interestingly, biophysical modeling simulations revealed that increased stiffness, particularly in active chromatin compartments, may underlie these alterations. Subsequent characterization of chromatin looping revealed that HDAC inhibition weakened CTCF-dependent loops at developmental gene loci but increased the strength of non-CTCF loops carrying either active (H3K27ac and H3K4me1) or repressive (H3K9me3 and H3K27me3) histone modifications. Analysis of the transcriptomic alterations induced by HDAC inhibition revealed a link between increased gene expression, the accumulation of permissive histone modifications, and enhancer overactivation (via increased histone acetylation) without an increase in the number of enhancer-prompter contacts. Meanwhile, downregulated gene expression occurred without the accumulation of repressive histone modifications and instead correlated with repressive chromatin looping, highlighting the importance of this perhaps overlooked regulatory mode.

The authors next removed the perturbing effect of HDAC inhibition from mESCs to explore the formation of the cellular memory of gene expression, focusing on potentially enduring chromatin alterations after the initial causative event. Overall, mESCs mostly recovered the initial transcriptional and histone modification profiles lost in response to this acute epigenetic stimulus; however, the data strongly indicated that they retained a partial memory of HDAC inhibition at the gene expression level. The study turned to 3D chromatin conformation analysis in search of an answer; overall, they discovered that a pulse of HDAC inhibition prompted a persistent loss of cis-interactions, a gain of repressive cis-interactions, and strengthening of chromatin looping.

Finally, the authors next re-exposed the mESCs to trichostatin A to determine whether an additional pulse of HDAC inhibition would lead to more severe consequences and to confirm that the persisting conformational and transcriptional alterations truly reflected a cellular memory of gene expression. The impact of the second exposure to this acute stimulus prompted alterations comparable to those of the first; however, analyses revealed a less complete level of recovery after stimulus withdrawal, with the robust deregulation of developmentally associated genes suggesting a greater impact of the second exposure on cellular identity. The study linked these lasting gene expression alterations to the presence of strong conformational features surrounding deregulated gene regulatory elements; the sustained upregulation of gene expression correlated with the prominent presence of preformed enhancer-promoter contacts, while they hypothesized that the increased involvement of repressive Polycomb-mediated chromatin loops contributed to the sustained downregulation of gene expression.

 Back to Table of Contents

HDACs, Epigenetic Memory, and More: Can Active Motif Help Your Research Aims?

Overall, the findings of this “unforgettable” study suggest that 3D chromatin conformation carries an epigenetic memory of past perturbations, which enable enhanced responses to subsequent similar perturbations. Importantly, the authors note the potential implications of their findings for human health; specifically, epigenetic drugs are commonly employed therapeutic agents, and acute cell responses and recovery may lead to long-term effects in patients that warrant further exploration.

Of note, the research behind these exciting findings employed a range of antibodies - H3K27ac, H3K4me1, H3K27me3, CTCF, and an ATAC–seq kit from Active Motif; in addition, Active Motif provides a range of HDAC antibodies, kits, recombinant proteins, and small molecules to support all of your epigenetic studies.

 Back to Table of Contents

About the author

Stuart P. Atkinson, Ph.D.

Stuart was born and grew up in the idyllic town of Lanark (Scotland). He later studied biochemistry at the University of Strathclyde in Glasgow (Scotland) before gaining his Ph.D. in medical oncology; his thesis described the epigenetic regulation of the telomerase gene promoters in cancer cells. Following Post-doctoral stays in Newcastle (England) and Valencia (Spain) where his varied research aims included the exploration of epigenetics in embryonic and induced pluripotent stem cells, Stuart moved into project management and scientific writing/editing where his current interests include polymer chemistry, cancer research, regenerative medicine, and epigenetics. While not glued to his laptop, Stuart enjoys exploring the Spanish mountains and coastlines (and everywhere in between) and the food and drink that it provides!

Contact Stuart on X with any questions

Related Articles

<< Back to MOTIFvations Blog Home Page