Epigenetics articles of the month: August 2015

Read our favorite articles published in August

An epigenetic regulator emerges as a microtubule minus-end binding and stabilizing factor in mitosis

A role for KANSL chromatin modifiers in mitosis

During mitosis, a unique, highly condensed chromatin structure is formed. The vast majority of chromatin modifiers are evicted from the mitotic chromatin, freeing them to perform functions in other cellular compartments, for example some nuclear proteins play a role in mitotic spindle assembly.

To investigate if other epigenetic complexes have functions in mitosis not related to chromatin states or gene expression, a team led by Asifa Akhtar from the Max Planck Institute of Immunology and Epigenetics in Freiburg looked at the role of KAT8-associated non-specific lethal (KANSL) chromatin modifiers during mitosis. They found that:

  • Knockdown of KANSL1 or KANSL3 results in marked mitotic defects including prolonged arrests in a prometaphase-like state.
  • KANSL1 and KANSL3 are enriched at spindle poles throughout mitosis.  
  • In complex with spindle assembly factors, KANSL1 and KANSL3 promote microtubule assembly in a RanGTP dependent manner in vitro.
  • KANSL1 and KANSL3 are required with MCRS1 for chromosomal microtubule assembly and K-fibre stabilization.
  • KANSL3 is a microtubule minus-end-binding protein and recruits MCRS1 to the minus end.

The results in this paper show KANSL proteins to have an important role in cellular homeostasis during different stages of the cell cycle. As well as regulating essential housekeeping genes during interphase, they are involved in spindle stabilization during mitosis.

Read the full paper in Nature Communications, August 2015.

Local generation of fumarate promotes DNA repair through inhibition of histone H3 demethylation

Fumarate production regulates histone methylation during DNA repair

DNA damage such as double strand breaks (DSBs) drive cancer development. DNA double strand break repair involves chromosome and nucleosome remodeling, involving histone methylation to recruit p53 binding protein 1 (53BP1) to DSBs. However, the mechanisms that underlie histone methylation regulation during DNA repair are unknown.

A team led by Zhimin Lu from The University of Texas MD Anderson Cancer Center investigated the role of localized fumarate production in regulating this process. They found that:

  • H2A.Z mediates binding of fumarase to chromatin at DSBs after exposure to ionizing radiation.
  • Chromatin-localized fumarase promotes the accumulation of Ku70; a protein required for the non-homologous end joining (NHEJ) pathway of DNA repair.
  • Phosphorylation of fumarase by DNA-dependent protein kinase (DNA-PK) is required for chromatin binding, and in turn fumarase binding to H2A.Z promotes DNA-PK accumulation at DSBs.
  • Local fumarate production by chromatin-bound fumarase promotes NHEJ DNA repair by inhibiting lysine-specific demethylase 2B (KDM2B) and preventing H3K6me2 demethylation.

These results uncover a molecular mechanism for the regulation of histone methylation during DNA repair. This is an intriguing example of how local metabolite production can regulate cellular activity not linked to metabolism.

Read the full paper in Nature Cell Biology, August 2015.

Early embryonic-like cells are induced by downregulating replication-dependent chromatin assembly

CAF-1 depletion induces early embryonic-like cells with enhanced reprogammability

Totipotent cells are able to generate cells of the whole organism, including extraembryonic tissue, and have greater plasticity than pluripotent cells. Whereas induced reprogramming to pluripotency is well established, it is unknown whether reprogramming to totipotency is possible, and totipotent cells remain poorly characterized.

A team led by Maria-Elena Torres-Padilla from the Institute of Genetics and Molecular and Cellular Biology in France sought to characterize totipotent stem cells by identifying molecular players associated with transitions between pluripotent and totipotent states. They found that:

  • Depletion of the CAF-1 chromatin assembly factor in embryonic stem cells dramatically induces the emergence of cells resembling 2-cell-stage embryos (2C-like cells).
  • Although 2-cell embryos commonly exhibit a lack of chromocenters, disrupting the chromocenters of ES cells does not induce 2C-like cell formation.
  • ES cell transcriptome after knockdown of either of the two CAF-1 subunits resembles that of the 2-cell stage.
  • Mobility of core histones is similar in CAF1 depletion-induced 2C-like cells and 2-cell-stage embryos.
  • Like 2-cell embryos, endogenous and induced 2C-like cells have higher reprogrammability for somatic-cell nuclear transfer than ES cells.

Understanding the molecular pathways leading to totipotency is essential to provide options for efficient reprogramming, and to explore new therapeutic avenues. This research suggests that chromatin reprogramming may be a key process in developing totipotency, and that ES cells acquire high reprogammability after depletion of CAF-1.

Read the full text in Nature Structural and Molecular Biology, August 2015.

In a recent podcast, Maria-Elena Torres-Padilla spoke to Abcam about recent publications that are offering new insights into the field of Epigenetics. Find out more.

Role of DNA methylation in modulating transcription factor occupancy

DNA methylation does not regulate CTCF transcription factor binding at the majority of sites

Methylation of cytosine bases within CpG dinucleotides is a common mechanism of transcriptional repression. However, the extent to which DNA methylation actively silences transcription factor binding sites rather than by causing secondary effects is unknown.

Matthew Maurano and colleagues from the University of Washington, Seattle investigated the relationship between genome-wide DNA methylation and transcription factor occupancy. By looking at the effect of reducing DNA methylation levels on the occupancy patterns of an abundant, methylation sensitive transcription factor, CTCF, the authors found that:

  • Upon depletion of DNA methyltransferases, there are major changes to gene expression and chromatin structure, but the majority of CTCF binding is unaltered.
  • A small number of CTCF occupation sites are significantly sensitive to methylation status, and disruption of DNA methylation increases CTCF binding at these sites.
  • DNA methylation sensitive sites are distinguished by solitary CTCF binding and CpG presence at key positions in the protein/DNA binding interface

These results suggest that DNA methylation does not significantly regulate transcription factor binding at the majority of sites. The revelation that there is only limited transcription factor-mediated coupling between DNA methylation and genome organization has important consequences for interpreting DNA methylation changes in diseases such as cancer.

Read the full text in Cell Reports, August 2015.

Generation of a synthetic GlcNAcylated nucleosome reveals regulation of stability by H1A-Thr101 GlcNAcylation

GlcNAcylation activates transcription through nucleosome destabilization

O-linked β-N-acetylglucosamine (GlcNAc) is a recently discovered histone modification that has been implicated in transcriptional activation. However, up to now, the molecular basis behind transcriptional regulation by O-GlcNAcylation has not been elucidated.

To find out more about the molecular roles of O-GlcNAcylation, Lukas Lercher and colleagues from the University of Oxford synthesized a nucleosome that contains histone H2A bearing a single O-GlcNAc mimic at threonine 101. The authors found that:

  • H2A-101 GlcNAcylation does not substantially influence H2A/B dimer structure and stability, but destabilizes the histone octamer.
  • GlcNAcylated nucleosomes contain multiple subspecies including an intact nucleosome, a species lacking one H3 subunit and a nucleosome lacking a H2A/B dimer.
  • GlcNAcylation increases accessibility of DNA to proteins, including E box binding proteins, and proteins involved in mismatch repair.

The results presented in this paper suggest that GlcNAcylation directly destabilizes nucleosomes, creating an open chromatin state. This leads to a lower barrier for RNA polymerase passage, resulting in an increase in gene transcription.

Read the full paper in Nature Communications, August 2015.

Integrator mediates the biogenesis of enhancer RNAs

Integrator has a role in eRNA 3' processing

Integrator is a multi-subunit complex with RNA endonuclease activity, which is essential for processing of certain small nuclear RNA genes including enhancer RNAs (eRNAs). Integrator is recruited to enhancers in response to various stimuli.

Fan Lai and colleagues from the University of Miami Miller School of Medicine, in Florida investigated the role of Integrator in the eRNA biogenesis. By studying signal-dependent recruitment of the Integrator complex to enhancer sites, they found that:

  • Epidermal growth factor (EGF) stimulation of HeLa cells results in enrichment of Integrator complex at enhancers.
  • Depletion of Integrator subunits diminishes eRNA induction after EGF stimulation.
  • Integrator is required for chromatin looping between NR4A1 and DUSP1 enhancers and their respective promoters.
  • Integrator is required for 3’-end cleavage of primary eRNA transcripts and depletion of Integrator leads to eRNA processing defects at all active enhancers.

These results suggest that Integrator has a role in enhancer regulation globally, by regulating eRNA maturation and enhancer-promoter communication.

Read the full paper in Nature, August 2015.

Deregulation of the Ras-Erk signalling Axis modulates the enhancer landscape

Enhancer epigenetic reprogramming is key to oncogenic effects of RTK signaling

Receptor tyrosine kinase (RTK) signaling pathways are necessary for normal cellular function, and are often dysregulated in diseases such as cancer. RTK pathway dysregulation can be brought about by expression of oncogenes including RAS or BRAF, or through loss of Sprouty (Spry), a gene encoding RTK feedback inhibitors.

To understand how aberrant RTK signaling coordinates gene expression changes that promote oncogenesis, a team led by Jonathan Licht from the Northwestern University Feinburg School of Medicine in Chicago looked at enhancer chromatin signatures after Spry knockdown or oncogene expression. They found that:

  • Spry knockout in mouse embryonic fibroblasts (MEFs) leads to ERK-dependent changes in gene expression and H3K27 acetylation at oncogene enhancers.
  • Expression of the oncogenes KRasG12V, HRasG12V and BRafV600E results in H3K27 acetylation at Spry targets and aberrant activation of these genes.
  • HRas expression activates transcription factor networks that are distinct from those activated by the loss of Spry.
  • Gata4 is required for aberrant enhancer H3K27 acetylation upon HRas expression.

These results demonstrate that epigenetic reprogramming of enhancers is a key effect of oncogenic RTK signaling. Aberrant RTK signaling, brought about either through HRasG12V expression of loss of Spry, results in histone acetylation at enhancer and subsequent gene activation.

Read the full paper in Cell Reports, August 2015.

Tet2 is required to resolve inflammation by recruiting Hdac2 to specifically repress IL-6

Novel role for Tet2 in regulating inflammation

Ten eleven translocase (TET) enzymes are involved in DNA demethylation. However, it is becoming apparent that Tet proteins have a role in regulating chromatin architecture independent of DNA methylation. A role of TET proteins in processes associated with inflammation has not previously been established.

Qian Zhang and colleagues from the Chinese Academy of Medical Sciences in Beijing and the Second Military Medical University in Shanghai investigated the role of Tet proteins in regulating inflammation and immunity, independent of their role in DNA methylation regulation. They found that:

  • Tet2 deficiency or knockdown results in higher expression of IL-6 in cell lines and in vivo.
  • The IκBζ transcription factor mediates selective targeting of Tet2 to the IL6 promoter.
  • Tet2 interacts with the histone deacetylase Hdac2 to repress IL-6 through histone deacetylation.

The results presented in this paper show that Tet2 has a novel role in regulating inflammation. The authors suggest that this may provide clues to how Tet2 contributes to development of myeloid cancer independent of its intrinsic role in leukemia cells themselves.

Read the full paper in Nature, August 2015.