Epigenetics articles of the month: November 2015

The most exciting epigenetics research from the past month.

Histone H3 threonine phosphorylation regulates asymmetric histone inheritance in the Drosophila male germline

Histone phosphorylation enables differential H3 inheritance by daughter cells

To ensure that stem cell populations are maintained, adult stem cells undergo asymmetric cell division to generate a self-renewed stem cell and a differentiated daughter cell. Epigenetics is known to play an important role in ensuring proper maintenance and differentiation of stem cell populations, but the molecular pathways behind this are not fully understood.

Previous research showed that during asymmetric division of Drosophila male germline stem cells (GSCs), pre-existing histone H3 is selectively incorporated into the self-renewed GSC daughter cell. In this paper, a team led by Xin Chen from John Hopkins University in Baltimore propose and test the hypothesis that asymmetric histone inheritance allows GSCs to establish unique epigenetic identities in each of the two daughter cells. Here is what they found:

  • Phosphorylation of H3 at threonine 3 (H3T3P) is enriched in existing H3 compared with newly synthesized H3.
  • Converting T3 to unphosphorylatable alanine (H3T3A) or phosphomimetric aspartate (H3T3D) disrupts asymmetric histone inheritance and causes germline defects including improper GSC maintenance and germline tumors.
  • Knockdown of the H3T3 kinase Haspin in early stage germ cells enhances the H3T3A phenotype but suppresses the H3T3D phenotype.

The authors have demonstrated that H3T3P is differentially deposited on existing and newly-synthesized H3, and that this coordinates asymmetric H3 segregation into daughter cells.

Read the full paper in Cell, November 2015.

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Ikaros mediates gene silencing in T cells through Polycomb repressive complex

The Ikaros transcription factor regulates PRC2 function to repress gene expression in T cells

T lymphocytes develop from hematopoetic stem cells (HSCs) in a process that requires the loss of stem cell properties and the activation of T lymphocyte-specific programmes. Epigenetic factors are important mediators of this switch, but the effect of specific regulators in this process has not been established.

To find out more about epigenetics in T cell development, a team led by Philippe Kastner from the University of Strasbourg in France looked at the role of Ikaros; a transcription factor that is essential for T cell development.

  • Ikaros deficiency results in widespread loss of the repressive H3K27me3 histone mark during thymocyte development and ectopic expression of HSC genes.
  • Ikaros is required for Polycomb repressive complex 2 (PRC2) binding to a specific set of target genes in CD4-CD8- cells.
  • PRC2 forms a complex with Ikaros and is recruited to target genes.

These results indicate that by mediating PRC2 function, Ikaros is a key repressor of gene expression in developing T cells.

Read the full paper in Nature Communications, November 2015.

Find out more about Polycombs. Watch our on-demand webinar on Polycombs in cancer.

The metabolome regulates the epigenetic landscape during naive-to-primed human embryonic stem cell transition

Metabolic characterization of the naive-to-primed stem cell transition

Embryonic stem cells (ESCs) have two states of pluripotency; naive preimplantation stem cells have high developmental potential and post-implantation primed ESCs have more limited potential. During the transition between naive and primed states, ESCs undergo a distinct change in both metabolic and epigenetic profiles.

To explore this transition further, a team led by Hannele Ruohola-Baker from the University of Washington investigated regulation and metabolomics as cells progress from a naive to primed state.

  • In naive ESCs, nicotinamide N-methyltransferase (NNMT) and its product 1-methylnicotinamide are highly upregulated compared with primed ESCs.
  • NNMT consumes S-adenosyl methionine (SAM), rendering it unavailable for histone methylation.
  • NNMT overexpression reduces repressive H3K27me3 and H3K9me3 methylation marks in naive ESCs. These marks are elevated in primed cells.
  • Altering NNMT expression shows components of the Wnt pathway and regulators of HIF to be targets for NNMT-mediated methylation.

This study demonstrates that histone marks are regulated by SAM levels and NNMT in nave hESCs. The authors propose that SAM activates PRC2, increasing repressive H3K27me3 epigenetic marks on the promoters of genes that regulate the naive to primed transition.

Read the full paper in Nature Cell Biology, November 2015

SWI/SNF-mutant cancers depend on catalytic and non-catalytic activity of EZH2

EZH2 stabilization of PRC2 is crucial for SWI/SNF-mutant cancers

SWI/SNF complexes are important chromatin remodelers that, when mutated, can lead to cancer development. However, it is unknown if other factors contribute to the growth of SWI/SNF-mutant cancers.

A team led by Charles Roberts from the Dana-Farber Cancer Institute in Boston, Massachusetts investigated whether SWI/SNF mutant cancers are dependent on EZH2; a Polycomb repressive complex 2 (PRC2) component with antagonistic effects to SWI/SNF. Here is what they found:

  • SWI/SNF-mutant cancer cells are dependent on the presence of EZH2.
  • SWI/SNF subunit mutation confers sensitivity to treatment with EZH2 inhibitors in six of ten cell lines examined.
  • In EZH2 knockdown SWI/SNF mutants, expression of EZH2 in which the catalytic domain has been deleted rescues cell growth.
  • SWI/SNF-mutant cancer are dependent on PRC2 integrity.

Collectively, these results show that the dependence on EZH2 in some SWI/SNF-mutant cancer is largely dictated by a non-enzymatic contribution of EZH2, potentially by stabilizating the PRC2 complex. It also highlights that inhibitors of EZH2 enzymatic may not fully suppress its oncogenic activity.

Read the full paper in Nature Medicine, November 2015.

H3K4/H3K9me3 bivalent chromatin domains targeted by lineage-specific DNA methylation pauses adipocyte differentiation

Bivalent domains maintain developmental genes in a poised state

Lineage committed multipotent progenitor cells are essential for self-renewal and repair in adult tissues. These cells are maintained in an undifferentiated state, but poised for differentation into cells of a specific lineage; however, the mechanisms that maintain cells in this state is currently unclear.

To understand this further, a team led by Juro Sakai from the University of Tokyo looked at bivalent chromatin domains that contain both activating and inactivating epigenetic marks in mesenchymal stem cells and preadipocytes. They uncovered the following:

  • Depletion of the H3K9 methyltransferase SETDB1 induces adipogenesis.
  • SETDB1 establishes bivalent H3K4/H3K9me3 chromatin domains that regulate gene expression during adipogenesis.
  • Reduction of H3K9me3 upon differentiation or SETDB1 knockdown releases paused RNA polymerase II and allows transcription elongation.
  • A SETDB-MBD1-MCAF1 complex is recruited to chromatin by lineage-specific gene-body DNA methylation.

This paper highlights the role of H3K4/H3K9me3 bivalent domains in maintaining developmental genes in a poised state and restricting the differentiation potential of preadipocytes. 

Read the full paper in Molecular Cell, November 2015.

Chemical basis for the recognition of trimethyllysine by epigenetic reader proteins

Displacement of water molecules is essential for trimethyllysine-reader recognition

Histone lysine methylation has a huge impact on global gene activation and repression. Interaction between histone methylation and effectors – proteins that recognize modified lysine and effect downstream processes – occurs through an interaction between the positively charged side chain of trimethyllysine (Kme3) and the elecron-rich aromatic cage present in effector proteins.

A team led by Jasmin Mecinović from Radboud University in the Netherlands used a computational approach to further characterize this interaction. They found the following:

  • There is an energetic preference for reader protein binding to trimethyllysine over an uncharged analogue.
  • Cation-π interactions are not solely responsible for the strong binding affinity of H3K4me3 to effector proteins.
  • Displacement of water molecules from the aromatic cage by Kme3 and Cme3 enhances association with effectors.

These data indicate that as well as cation-π interactions, favorable release of water molecules from the aromatic cages of reader proteins is required for specific interation between trimethyllysine histones and their effector proteins. This is the first study to highlight the importance of water molecules in this interaction.

Read the full paper in Nature Communications, November 2015.

miRNA-target chimeras reveal miRNA 3'-end pairing as a major determinant of Argonaute target specificity

A new technique to map in vivo miRNA targets

MicroRNAs (miRNAs) post-transcriptionally silence genes by directing Argonaute to messenger RNA. miRNAs recognize target mRNA sequences through complementary base pairing; however, most in vivo miRNA targets are unknown.

Identification of miRNA targets is challenging, but a team led by Robert Darnell from the Rockefeller University in New York has developed a new technique that ligates miRNAs to their endogenous mRNAs. By using this technique – called covalent ligation of endogenous Argonaute-bound RNAs with crosslink immunoprecipitatiom (CLEAR-CLIP)  the team mapped 130,000 miRNA-target interactions in the mouse brain and 35,000 in human hepatoma cells.

  • CLEAR-CLIP unambiguously identifies functional in vivo mRNA-target interactions.
  • miRNA binding is dependent on both seed-based pairing and miRNA-specific patterns of auxiliary pairing.
  • Auxiliary miRNA 3' pairing with targets is extensive, stabilizes interactions and regulates miRNA target specificity.

This technique enables identification of in vivo miRNA sites. The authors have used it to demonstrate that most interactions combine seed-based pairing with distinct miRNA-specific patterns of auxiliary pairing.

Read the full in Nature Communications, November 2015.