Top Epigenetics articles: September 2014

Looking for an easy way to keep on top of the latest epigenetics literature? Sit back and read our top picks from September.

​Epigenetic reprogramming that prevents transgenerational inheritance of the vernalized state.

Mechanisms of embryonic epigenetic reprogramming.

The erasure of epigenetic states in germ line cells is vital for normal embryo development and incomplete erasure can result in transgenerational epigenetic inheritance. In plants, germ cells arise from somatic flower cells, making erasure particularity vital.

The floral repressor locus FLC is epigenetically silenced in plant soma by prolonged cold in a process called vernalization. This process must be reversed and the locus reactivated in seed development, however, little is known about this mechanism.

Caroline Dean and colleagues from the John Innes Centre in Norwich, UK sought to investigate the mechanism of FLC reactivation during seed development. Using mutant Arabidopsis thaliana lines defective in FLC reactivation, the researchers found that:

  • A SNP in ELF6 (a putative H3K27me3 demethylase) co-segregated with the mutant resetting phenotype in an F2 population generated from the mutant and the isogenic progenitor line.
  • Complementation with wild-type ELF6 restored wild-type FLC expression levels.
  • ELF6 showed H3K27 demethylase activity, specifically reducing H3K27me2 and H3K27me3 levels in tobacco.

These results support the previously hypothetical H3H27me2/3 demethylase activity of ELF6, and implicate it in the resetting of FLC expression in A. thaliana. More broadly, this research points to an ancient conservation of H3K27 demethylation in the reprogramming of epigenetic states in early embryos.

Read the full report in Nature Letters, September 2014.

Abcam products used: anti-histone H3 (trimethyl K36) (ab9050) and anti-histone H3 (ab1791) antibodies.​

Resetting transcription factor control circuitry toward ground-state pluripotency in human.

Transcription factor settings key to returning cells to pluripotency.

Investigators from the Babraham Institute, Cambridge Stem Cell Institute and the European Bioinformatics Institute, supervised by Professor Wolf Reik, have published data indicating that human stem cells can be returned to pluripotency, shedding the characteristics of their previous specific cell lineage and regaining the potential to develop into any cell lineage.

Current human pluripotent stem cells lack the transcription factor network that controls the ground state of mouse embryonic stem cells (mESC). However, the researchers found that the short-term expression of two critical components, NANOG and  KLF2, is enough to trigger the entire network, therefore restoring the human pluripotent state. 

Here is what the research team learned:

  • Transcription factor circuits become “rewired” in human pluripotent stem cells.
  • The transcriptome and metabolism in human stem cells are similar to mouse ground-state ES cells.
  • Genome-wide hypomethylation occurs in reset cells, indicating a global erasure of epigenetic marks.
  • Reset human cells are able to incorporate into mouse preimplantation epiblasts.

The authors suggest that their findings have substantial medical potential for generating reset stem cells and delivering them back into a patient as a therapeutic treatment for a variety of diseases.

Learn more about the restoration of pluripotency in Cell, September 2014.

Professor Wolf Reik will be co-chairing our Epigenetics, Obesity and Metabolism conference on October 11, 2015.

Predicting the human epigenome from DNA motifs.

Epigram analysis program predicts histone modifications and DNA methylation.

Deciphering the epigenome and the cis elements that regulate its modification is important for understanding the mechanisms that modulate gene expression profiles. However, techniques to detail the cis-regulatory system of the epigenome are still lacking. With that aim in mind, scientists John Whitaker, Zhao Chen and Wei Wang from UC San Diego developed Epigram, an analysis program that uses DNA motifs to predict the locations and patterns of DNA methylation and histone modifications. 

The Epigram platform successfully identified cis elements that interact with site-specific DNA-binding factors to form and regulate epigenomic modifications. The researchers applied Epigram to investigate various histone modifications and DNA methylation valleys (DMVs) in a set of five cell types:

  • Human embryonic stem cells (H1)
  • Neural progenitor cells (NPC)
  • Trophoblast-like cells (TBL)
  • Mesendoderm cells (ME)
  • Mesenchymal stem cells (MSC)

The team cataloged the cis elements and detected several motifs with distinct location preferences, including the center of H3K27ac or along the edges of  H3K4me3 and  H3K9me3.

This new data reveals mechanistic insights about how the epigenome is configured, and may prove useful in the development of new epigenome editing tools. The Epigram pipeline and predictive motifs are available here.

Find more on the Epigram analysis pipeline in Nature Methods, September 2014.

Molecular beacon-enabled purification of living cells by targeting cell type-specific mRNAs.

Molecular beacons allow purification of specific cell types.

The sorting of specific cell types from a mixed population is crucial for their proper characterization and study. Existing cell sorting approaches rely on cell surface markers or metabolic traits, however, scientists from Emory University, led by Dr. Gang Bao, have recently adapted molecular beacons (MBs) for highly efficient cell sorting.

MBs are dual-labeled oligonucleotides that fluoresce only when matched with a complementary mRNA. This feature allows researchers to design MBs to mRNAs that are cell type specific, and then remove and collect those positive cells for further study. The MB-based technique is applicable to the purification of a wide assortment of cells, including those generated from pluripotent stem cells (PSCs), which is a critical need in both basic research and therapeutic development.

The Nature Protocol article provides:

  • A general protocol for MB design and validation.
  • Hints on nucleofection into cells.
  • Describes the isolation of specific cell populations from differentiating PSCs.

The Emory group demonstrated their technique by successfully purifying cardiomyocytes differentiated from mouse or human PSCs, and achieving nearly 97% purity (confirmed through electrophysiology and immunocytochemistry).

The authors say that the MB design, ordering and validation takes approximately two weeks, and the actual cell sorting process can be completed in 3 hours.

Learn more about molecular beacons in Nature Protocols, September 2014.

Abcam products used: Anti-cardiac troponin I antibody (ab10231).

Dynamic GATA4 enhancers shape the chromatin landscape central to heart development and disease.

Chromatin enhancers play major role in heart health.

The mechanisms of chromatin enhancers and how they manipulate the stage-specific gene expression patterns that regulate everything from development to disease states, is still poorly understood. Scientists from Boston Children’s Hospital, Peking University and the Harvard Stem Cell Institute, led by Dr. William Pu investigated the role of an enhancer, cardiac transcription factor GATA4, on heart disease and development.

The research team found that GATA4 binds and helps to create active chromatin regions. Here are some other important results from the study:

  • GATA4 encourages the deposit of H3K27ac marks, which drives gene expression.
  • There is a substantial shift in GATA4 chromatin occupancy between the fetal and adult heart, with only limited overlap of binding sites.
  • At some fetal sites, GATA4 occupancy was restored after cardiac stress.
  • Most of those stress-related GATA4 binding sites were not shown to be occupied by GATA4 through normal heart development.

The authors’ work outlines a regulatory mechanism in which the chromatin occupancy of transcription factors has a dynamic, context and stage-specific role in development, homeostasis and disease.

Read the full report in Nature Communications, September 2014.

Abcam products used: Anti-histone H3 (mono methyl K4) antibody (ab8895).

Histone H2A.Z subunit exchange controls consolidation of recent and remote memory.

Role for histone exchange in memory.

Memory consolidation is the process by which memories are transferred from the hippocampus to the neocortex for maintenance. Alteration of epigenetic regulation of gene expression is increasingly implicated in such memory processes. Histone variant exchange is an important epigenetic processes involved in many cellular processes, however its role in memory remains completely unexplored.

J. David Sweatt and colleagues from University of Alabama investigated the role of histone H2A.Z in memory consolidation. The presence of H2A.Z at the transcriptional start site (TSS) is associated with transcriptional repression. Using mice, the authors investigated H2A.Z dynamics in the hippocampus in cortex during fear conditioning.

Using this approach they found:

  • H2A.Z was reduced immediately after the TSS and transcription was increased at memory-promoting genes, while the reverse was found at memory-suppressing genes in the CA1 region.
  • H2A.Z depletion in the CA1 region was associated with improved fear memory and increased Bdnf and Arc expression.
  • H2A.Z is not involved in baseline memory-gene expression, but rather their response to learning.
  • H2A.Z depletion in the prefrontal cortex affected long term, but not short term, fear memory and increased Fos expression 30 minutes after training.

This research proposes a role for H2A.Z exchange as a negative regulator of hippocampal consolidation. Furthermore, it’s alteration at later stages of consolidation support a role in stable modifications that may underlie long-term memory encoding.

See the full article in Nature Letters, September 2014.

Abcam products used: Anti-histone H2A.Z (acetyl K4 + K7 + K11) antibody (ab18262) and anti-actin (ab3280) antibodies.

​Regulation of RNA polymerase II activation by histone acetylation in single living cells.

Epigenetic marks in transcription at high resolution.

While histone modifications are known to be involved in transcriptional regulation, it is not well understood how and when a specific modification interacts with RNA polymerase (RNAP) to accomplish that regulation. Determining if a modification guides RNAP to a target or is a by-product of its passage has been limited by the resolution of fixed cell population experiments.

Timothy J. Stasevich, Hiroshi Kimura, and colleagues from Osaka University sought to assess RNAP and histone modification dynamics in living cells to dramatically improve temporal resolution. Using a mouse cell line expressing a green fluorescent protein (GFP)-tagged version of the glucocorticoid receptor, they were able to hormonally induce RNAP activity and visualize changes with immunofluorescence.

Using this design they found:

  • Histone H3 lysine 27 acetylation at a locus can affect transcription kinetics by up to 50%. This arises by accelerating RNAP2 promoter escape rather than by altering elongation.
  • Experimentally reducing H3K27ac lead to less elongating RNAP2.
  • In the endogenous genome, GR-response genes are also hyperacetylated at H3K27 before activation.

The authors propose a model wherein H3K27ac acts as a transcription gate-keeper, guiding incoming factors and allowing the exit of outgoing factors. In this way, H3K27ac may facilitate the fine-tuning of transcriptional dynamics.

Read the full report in Nature Letters, September 2014.

Abcam products used: Anti-KAT3B / p300 antibody (ab3164)

Genome-wide identification and characterization of functional neuronal activity-dependent enhancers.

Epigenetic marks at enhancers guide neural circuitry.

Sensory experiences remodel synapses and circuits in the brain, a process achieved in part by activity-dependent gene expression. The early-response genes that react to calcium influx from membrane depolarization are relatively well understood. However, very little is known about how early-response genes trigger transcription of late-response genes.

Michael E. Greenberg and colleges at Harvard Medical School examined enhancers for their role in activity-dependent transcription. They looked for changes in histone H3 lysine 27 acetylation (H3K27ac) in 12,000 previously characterized activity-dependent enhancers.

The researchers found that:

  • A subset of previously characterized activity-dependent enhancers are rapidly acetylated at H3K27; these are actually responsible for activity-dependent gene expression.
  • A common feature of this subset is the binding  of early-response activity-induced transcription factor, FOS.
  • Expression of these target genes was induced by FOS binding at enhancers.

The identification of FOS at enhancers is quite novel; previously it was only known to act at promoter of activity-dependent genes. Understanding the importance of enhancers in brain development and function will allow better insight into potential neurological disease mutations and mechanisms.

Read the full report in Nature Neuroscience, September 2014.