Epigenetics articles of the month: December 2015

Keep up with the most exciting Epigenetics research published in December.

DNA methylation changes in plasticity genes accompany the formation and maintenance of memory

The role of chromatin modifications in learning and memory processes

Chromatin modifications are necessary for the acquisition and maintenance of memory. However, the extent of DNA methylation and histone post-translational modification changes, and their functional importance, remain unclear.​​​

To reveal the epigenetic network underlying short- and long-term memory, a team led by Stefan Bonn from the German Center for Neurodegenerative Diseases studied chromatin changes in mice before and after contextual learning. Using high-resolution brain region and cell-type specific chromatin modification data, they found the following:

  • Histone post-translational modifications change during memory formation, in both neuronal and non-neuronal cells.
  • Activity-related modifications H3K4me3 and H3K9ac increase, whereas the inactivity-related modification H3K27me3 decreased during cellular consolidation.
  • DNA methylation patterns change substantially during memory consolidation and maintenance, particularly within neuron-specific genes.
  • DNA methylation correlates with the spacio-temporal location of associated memory, and DNA methylation changes are associated with expression of functional and synaptic plasticity genes.​

These results provide insights into the role of chromatin modifications in learning and memory processes. The authors suggest that inhibiting these changes should lead to a concomitant loss of memory.

Read the full paper in Nature Neuroscience, December 2015

Dicer and microRNA regulation in post-traumatic stress disorder with comorbid depression

DICER1 implicated in post-traumatic stress with comorbid depression

Post-traumatic stress disorder with comorbid depression (PTSD&Dep) is a prevalent occurrence following traumatic events. Although the condition causes significant suffering, still very little is known about the molecular mechanisms behind it.

To further understand this condition, a team led by Kerry Ressler from Emory University, Georgia studied genome-wide expression changes in blood samples from patients with PTSD&Dep. They found the following: 

  • Expression of DICER1 – a protein involved in miRNA synthesis – is reduced in blood from PTSD&Dep patients versus controls.
  • A DICER1 single nucleotide polymorphism (SNP) influences blood DICER1 levels and is associated with PTSD&Dep.
  • miRNAS are significantly downregulated in blood samples from PTSD&Dep patients versus controls.
  • Reduced blood DICER1 expression is associated with increased amygdala activation to fearful stimuli, a neural correlate for PTSD.​

These data suggest that DICER1 and miRNA regulation are involved in the molecular mechanisms behind PTSD&Dep. This study paves the way for future research into the prevention and treatment of stress-related psychiatric disorders.

Read the full paper in Nature Communications, December 2015.

Hypomethylation of smoking-related genes is associated with future lung cancer in four prospective cohorts

DNA methylation in two genes is inversely correlated with lung cancer risk

Smoking is a major risk factor for diseases including cancer; continuing smokers experience a 25% lifetime risk of developing a smoking-related cancer. Although it is known that tobacco exposure is associated with hypomethylation of certain genes, it is unknown whether this translates into increased lung cancer risk.

A team led by Paolo Vineis from Imperial College, London performed an epigenome-wide study on DNA from pre-diagnostic blood samples. By using samples from the Norweigan Women and Cancer (NOWAC) study, Melbourne Collaborative Cohort Study (MCCS), Northern Sweden Health and Disease Study (NSHDS) and the EPIC Heidlberg studies, they found the following:

  • The methylation levels of two CpG sites – cg05575921 in the AHRR gene and cg03636183 in the F2RL3 gene – are inversely associated with lung cancer risk.
  • Methylation of these sites on the two genes mediates 37% of the total effect of smoking on lung cancer odds.

This is the first study to use genome-wide methylation analysis to evaluate the importance of peripheral blood epigenetic alterations in lung cancer. The results suggest that methylation of smoking-related AHRR and F2RL3 CpG sites may explain approximately one-third of the risk induced by tobacco exposure.

Read the full article in Nature Communications, December 2015.

Epigenetic switch drives the conversion of fibroblasts into proinvasive cancer-associated fibroblasts

Epigenetic changes initiate and maintain the proinvasive phenotype of cancer-associated fibroblasts

Carcinoma-associated fibroblasts (CAFs) are important for establishing a proinvasive tumor microenvironment, and CAF presence is associated with poor clinical outcome. Although it is known that the proinvasive stromal fibroblast phenotype observed in cancers is initiated by leukemia inhibitory factor (LIF), it is unknown how the activated state is sustained.

In this paper, a team led by Cedric Gaggioli from the University of Nice Sophia Antipolis in France establish a mechanism for the acquisition and maintenance of CAF proinvasive ability. Here is what they found:

  • Long-term activation of proinvasive fibroblasts involves DNA methyltransferase (DNMT) and p300 activity.
  • LIF induces p300 acetylation of STAT3, which results in DNMT3 activation.
  • DNMT3b methylates and inactivates the SHP-1 phosphatase, resulting in constitutive phosphorylation of JAK1 and sustained JAK/STAT activity.
  • STAT3 acetylation and phosphorylation are inversely correlated with SHP-1 expression in human carcinomas.

This study demonstrates that an epigenetic switch initiates and maintains the proinvasive phenotype of CAF. These results highlight an attractive potential approach for inhibiting the onset of the proinvasive tumor microenvironment in cancer.

Read the full paper in Nature Communications, December 2015

Ezh2 regulates differentiation and function of natural killer cells through histone methyltransferase activity

Histone methyltransferase regulates natural kill cell formation

Natural killer (NK) cells are essential for the surveillance and destruction of infected and transformed cells. NK-based immunotherapy is a promising avenue of cancer research, but further understanding of NK cell biology is required to maximize the efficacy of such treatments.

To understand regulatory mechanisms of NK cell development, a team led by Xi Wang from Tianjin Medical University in China investigated the role of  the histone-lysine N-methyltransferase Ezh2 in NK cell lineage commitment. They found the following:

  • Loss of enhancer of zeste homolog 2 (Ezh2) activity increases NK-cell development in mouse and human.
  • Loss of Ezh2 upregulates expression of the C-type lectin receptor NKG2D, which is important for the transition of NK cells from an immature to mature form.
  • NK cells treated with Ezh2 inhibitors exhibit increased cytotoxicity against tumor cell lines.

These results suggest that histone methyltransferase activity regulates generation of NK cells. This raises the possibility that preconditioning patients' cells with Ezh2 inhibitors may improve the efficacy of NK cell-based therapies.

Read the full paper in PNAS, December 2015.

Dynamic reorganization of extremely long-range promoter-promoter interactions between two states of pluripotency

​H3K27me3 and PRC2 are involved in the serum-to-2i interconversion

Pluripotent mouse embryonic stem cells (mESCs) are frequently used as a developmental model. mESCs grown in serum + leukemia inhibitory factor (LIF, serum mESCs) and 2i + LIF media (2i mESCs) are both pluripotent; however, 2i mESCs represent a ground-state pluripotency whereas serum mESCs are reminiscent of post-implantation pluripotent stem cells.

The serum-to-2i transition can be used as a model to study early developmental processes. A team led by Hendrik Stunnenberg from Radboud University in the Netherlands sought to understand the dynamic reorganization of 3D chromatin architecture during this transition. Using a capture Hi-C approach, they found the following: 

  • Prominent intra- and inter-chromosomal interactions (extremely long-range interactions, ELRIs) exist in serum mESCs, but these interactions are strongly reduced in 2i mESCs.
  • Trimethylation of H3K27 is a prominent feature of ELRI loci.
  • Loss of Eed, a core PRC2 component necessary for H3K27 trimethylation results in a strong reduction in the number of ELRIs in serum mESCs.    
  • ELRIs are lost three days after serum-to-2i medium exchange, mirroring a decreased occupancy of the Ring1B component of PRC1.

These results implicate H3K27me3 and PRC2 as critical players in chromatin alteration during the serum-to-2i interconversion.

Read the full paper in Cell Stem Cell, December 2015.

Epigenetic regulation of puberty via zinc finger protein-mediated transcriptional repression

Zinc finger proteins repress puberty during juvenile development

The onset of puberty is accompanied by increased pulsatile gonadotropin-releasing hormone (GnRH) secretion from the hypothalamus. During juvenile development, GnRH release is prevented; however the molecular mechanisms behind this are not known.

Zinc finger proteins have been implicated in puberty onset. A team led by Sergio Ojeda from Oregon National Primate Research Center in the US tested the hypothesis that zinc finger proteins may play a role in arresting GnRH pulsing during juvenile development. By probing the transcriptome of agonadal male rhesus monkeys at the infantile-juvenile and juvenile-pubertal transitions, they found the following:

  • Expression of eight ZNF genes, including GATAD1 and ZNF573, decreased at the time of pubertal gonadotrophin rise.
  • Overexpression of GATAD1 and ZNF573 delayed puberty in mouse gain-of-function mutants.
  • GATAD1 overexpression resulted in an immature pattern of connectivity between genes involved in diverse cellular functions.
  • GATAD1 represses transcription of key puberty activating genes, KISS1 and TAC3, by increasing recruitment of the H3K4me2 demethylase KDM1A/LSD1 to their promoters.

This paper provides evidence that certain ZNF proteins play an important molecular role in dampening GnRH pulse generation and respressing primate puberty during juvenile development. 

Read the full paper in Nature Communications, December 2015.

The histone chaperone CAF-1 safeguards somatic cell identity

Although transcription factors can be used to reprogram cells, this process is slow and inefficient, suggesting the existence of mechanisms to safeguard cell identity.​

A team led by Konrad Hochedlinger from Harvard Stem Cell Institute in Boston tested the hypothesis that chromatin factors may provide such safeguarding ability. The team performed RNAi screens to identify chromatin barriers to remodeling of fibroblasts to induced pluripotent stem cells (iPS cells). They found that subunits of the chromatin assembly factor CAF-1 were the most prominent hits. 

  • Suppression of either CAF-1 subunit results in dramatic acceleration of iPS cell formation.
  • The reprogramming phenotype induced by CAF-1 suppression is dependent on the duration and levels of expression of pluripotency transcription factors, Oct4, Klf4, Sox2 and c-Myc (OKSM).
  • CAF-1 suppression enhances induction of pluripotency in a range of cell conversion systems.
  • CAF-1  contributes to reprogramming by increasing chromatin accessibility at pluripotency-specific enhancer elements, promoting SOX2 binding to ES-cell specific targets and activating associated genes.

These results suggest that CAF-1 plays a role in regulating somatic cell identity, and provides a potential strategy to modulate cell plasticity.

Read the full paper in Nature, December 2015.