Top Epigenetics articles: February 2015

Want a hand keeping up with the most exciting new research in the field of epigenetics? We have hand-picked our favorite epigenetics articles from February.

SWI/SNF chromatin remodeling regulates alcohol response behaviors in Caenorhabditis elegans and is associated with alcohol dependence in humans

Chromatin remodeling clues to alcohol dependence

Alcohol dependence is a serious and widespread public health concern, having a prevalence of almost 13% in the United States. Both genetic and environmental components contribute to alcohol dependence, but specific underlying factors have been difficult to identify.

Alcohol dependence is associated with modification of gene expression, and epigenetic changes have been implicated in alcohol-dependent gene expression and tolerance to ethanol.

To understand how changes in chromatin structure affect ethanol response, Laura Mathies, Jill Bettinger and colleagues from Virginia Commonweath University examined the role of SWI/SNF chromatin remodeling complexes in ethanol response behaviors.

Using the neurobiological model organism C. elegans and genome-wide human data, the authors found that:

  • SWI/SNF components are required for normal acute response to ethanol in C. elegans.
  • Different SWI/SNF complexes regulate distinct aspects of acute ethanol response.
  • Two SWI/SNF subunits, SWSN-9 and SWSN-7, are required in neurons and muscle for the development of acute functional tolerance to ethanol.
  • Allelic variation in SWI/SNF genes in human populations influences alcohol response phenotypes.

These findings indicate that chromatin remodeling plays a role in the behavioral response to alcohol. This study also provides a step forward in our understanding of human alcohol dependence by demonstrating that variation in regulation of SWI/SNF targets may influence susceptibility of individuals to develop abuse disorders.

Read the full report in PNAS, February 2015.

Chromatin architecture reorganization during stem cell differentiation

Chromatin interaction maps show extensive chromatin reorganization during lineage specification

Higher-order chromatin structure is an important regulator of gene expression. However, our understanding of chromatin architecture and its effect on the cellular identity of human cell types during development and lineage specification is incomplete.

A team led by Bing Ren at the Ludwig Institute for Cancer Research in California mapped genome-wide chromatin interactions in human embryonic stem (ES) cells and four human ES-cell-derived lineages that had been extensively characterized by the Epigenome Roadmap project.

By comparing genome-wide variability in higher-order chromatin structure with underlying gene expression, the team found that:

  • Higher-order chromatin structure is dynamically reorganized during ES cell differentiation, with 36% of the genome switching between active and inactive chromosome compartments.
  • Local alterations in chromatin interaction frequency occur within topologically associated domains.
  • A Random Forest classification model based on chromatin features identified H3K4me1 density as the most important feature for predicting changes in long-range chromatin interactions.

As well as providing a global view of chromatin dynamics, the chromatin interaction maps generated by this study will be a valuable resource for researchers investigating long-range control of gene expression.

Read the full report in Nature, February 2015.

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m6A RNA methylation is regulated by microRNAs and promotes reprogramming to pluripotency

MicroRNAs regulate m6A by mediating METTL3-mRNA binding

N6-methyladenosine (m6A) has been recently identified as a conserved epitranscriptomic mRNA modification. However, the regulatory mechanisms of m6A and its dynamics among different cell types remain unknown.

Tong Chen, Ya-Juan Hao and colleagues from the Chinese Academy of Sciences, Beijing sought to further understand m6A regulation and dynamics during cell reprogramming by investigating the modification profiles of mRNA transcriptomes of four cell types with differing degrees of pluripotency.

By examining transcriptome-wide distribution of m6A modification in mouse embryonic stem cells, induced pluripotent stem cells, neural stem cells and testicular sertoli cells, the authors found that:

  • Dicer knockdown lowers miRNA production and reduces m6A abundance. Conversely, Dicer overexpression increases m6A modification level.
  • Overexpression of miRNAs with sequences pairing to m6A peak regions significantly increases m6A at these sites.
  • miRNA overexpression significantly increases the amount of mRNA associated with METTL3, suggesting that miRNAs regulate m6A by modulating METTL3 binding to mRNA.
  • Overexpression of METTL3 in mouse embryonic fibroblasts expressing the four Yamanaka factors increases m6A abundance and improves efficiency of reprogramming to pluripotency.

This study reveals a role of miRNA in regulating the formation of m6A in mouse and human cells through mediation of METTL3 binding to mRNA. The finding that increased m6A abundance improves efficiency of reprogramming to pluripotency may serve as a strategy for regulated cell reprogramming for future functional studies of cell reprogramming.

Read the full report in Cell Stem Cell, February 2015.

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N6-methyladenosine-dependent RNA structural switches regulate RNA-protein interactions

Role of m6A in chromatin remodeling to mediate RNA-protein binding

RNA binding proteins (RBPs) are an essential component of cellular biology, but the RNA binding motifs that they bind to are often buried within local RNA structures. m6A is an essential and abundant mRNA modification with wide-ranging physiological roles; however, the functional mechanisms of m6A are poorly understood.

Nian Liu, Tao Pan and colleagues from the University of Chicago, Illinois sought to investigate the effect that m6A modification has on RNA structure and the binding of RBPs. By studying global m6A modifications in human cells, they found that:

  • m6A alters RNA structure to expose binding sites and enhance binding of heterogeneous nuclear ribonucleoprotein C (HNRNPC), an RNA binding protein responsible for pre-mRNA processing.
  • There is widespread presence of m6A residues in the vicinity of HNRNPC binding sites transcriptome wide.
  • METTL3 and METTL14 knockdown cells have decreased m6A abundance and show decreased HNRNPC binding.
  • m6A regulated HNRNPC binding affects the abundance of mRNAs and regulates splicing patterns of nearby exons.

This study provides evidence for the m6A dependent structural remodeling of RNA that affects RNA-protein interactions for biological regulation. This function of m6A might explain why it has such wide-ranging physiological roles.

Read the full paper in Nature, February 2015.

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Integrative analysis of 111 reference human epigenomes

Analysis of the largest collection of human epigenomes to date

There is considerable variation in the epigenetic landscapes of different cells. However, systematic understanding of the contribution of the epigenome to cellular function, differentiation and disease is still lacking.

To gain a better understanding of how epigenetics contributes to human biology and disease, the Roadmap Epigenetics Consortium used high-throughput molecular assays to generate the largest collection of human epigenomes so far.

All epigenomes generated in the study were profiled for histone modification patterns, DNA accessibility, DNA methylation and RNA expression. This integrative analysis generated a huge quantity of epigenetic data that gave insights into epigenome differences during cell differentiation, identity and role of regulatory regions, and epigenetic regulation in disease.

Highlighted findings include:

  • Histone modifications are highly informative of the methylation and accessibility levels of different genomic regions.
  • On average, two-thirds of each reference epigenome is quiescent and enriched in gene-poor stably-repressed regions.
  • Genetic variants associated with complex traits are highly enriched in epigenomic annotations of trait relevant tissues.

The Roadmap Consortium has created an extensive resource for the future study of epigenetics in the form of a comprehensive map of the human epigenomic landscape. This map will be of broad use to researchers studying disciplines including cellular differentiation, genetic variation and human disease.

Read the full paper in Nature, February 2015.

If you want to learn how to analyze genome-wide ChIP data, watch our on demand webinar: Exploring genome-wide organization of chromatin structure by ChIP.

Single-base resolution analysis of 5-formyl and 5-carboxyl cytosine reveals promoter DNA methylation dynamics

A new method for the mapping and quantification of 5-fC and 5-caC

Active DNA methylation by Ten eleven ten (TET) proteins results in the sequential oxidation of 5-methylcytosine (5-mC) to 5-hydroxymethylcytosine (5-hmC), 5-formylcytosine (5-fC) and 5-carboxycytosine (5-caC).

Although methods have been developed to map 5-fC and 5-hmC, these lack the ability to map to single cytosine resolution or to quantify 5-fC and 5-caC abundance.

A team led by Salvatore Oliviero from the University of Turin developed methylation-assisted bisulfite sequencing (MAB-seq), a new technology that enables genome-wide mapping of 5-fC and 5-caC to single base resolution.

Using this technique on mouse embryonic stem cells, the authors found that:

  • There is enrichment of 5-fC and 5-caC residues on the hypomethylated promoters of highly expressed genes.
  • 5-fC and 5-caC are present in H3K4me3-positive regions, revealing an active demethylation process on active promoters.
  • There is extensive colocalization of thymine DNA glycosylase (TDG) and TET1 with 5-fC and 5-caC on active promoters.

By developing MAB-seq, the authors have been able to demonstrate the occurrence of active DNA methylation and demethylation processes on the promoters of highly expressed genes. Furthermore, MAB-seq will aid the future high-resolution study of DNA methylation and demethylation processes.

Read the full report in Cell Reports, February 2015.

For more information about DNA methylation, take a look at our DNA methylation resources page.

Transcription factor binding dynamics during human ES cell differentiation

Analysis of transcription factor binding data during cell differentiation

Understanding the molecular mechanisms underpinning embryonic cell differentiation is key to deriving mature functional cell types. Epigenetic modifications, including DNA methylation, are essential for normal development and transcription factors have been shown to mediate epigenome remodeling.

How epigenome remodeling by transcription factors and signaling cues controls lineage specification is poorly understood. In this paper, Alexander Tsankov et al. analyzed genome-wide transcription factor binding data during differentiation of human embryonic stem cells into three germ layers.

They found that:

  • Targets of many lineage-specific transcription factors undergo DNA demethylation in those germ layers, while targets of transcription factors expressed in multiple lineages undergo DNA demethylation in multiple cell types.
  • There is a specific gain of DNA methylation at many transcription factor targets at later time points, or in parallel time points along different lineages, possibly to block factor binding sites.
  • Transcription factor enrichment at H3K27ac super-enhancer revealed that OTX2 and OSN regulate transition to endoderm, GATA4 regulated mesoderm formation and OTX2 regulates transition to ectoderm.​

This study demonstrates context-dependent rewiring of transcription factor binding, downstream signaling effectors and the epigenome during human embryonic stem cell differentiation.

Read the full paper in Nature, February 2015.

Collaborative rewiring of the pluripotency network by chromatin and signalling modulating pathways

Rewiring of the pluripotency network in the late stages of reprogramming

Somatic cells are converted to induced pluripotent stem cells (iPSCs) by transcription factor mediated reprogramming, during which the epigenome and transcriptome of somatic cells are reset to a pluripotent state.

Reprogramming efficiency can be improved by including specific components in the media. A team led by Rupa Sridharan from the University of Wisconsin found that by adding an epigenetic modifier (ascorbic acid) and a signaling modifier (2i media), the efficiency of fibroblast reprogramming to pluripotency was significantly increased.

The team used this high-efficiency conversion system to understand more about the mechanisms involved in the final stages of cell reprogramming to pluripotency. By performing genome-wide transcriptional analysis, they found the following:

  • Exposure to ascorbic acid must precede 2i exposure for efficient reprogramming to pluripotency.
  • Histone and DNA demethylating pathways contribute to ascorbic acid-mediated effects in the presence to 2i. However, histone demethylating effects are essential early, whereas TET-mediated effects must be sustained into the 2i-dependent phase.
  • Ascorbic acid and 2i treatments induce distinct transcriptional changes. Transcriptional change in some plutipotency genes, including Esrrb, was unique to the ascorbic acid + 2i treatment.
  • siRNA mediated knockdown of certain genes downregulated by the ascorbic acid + 2i treatment, was able to replace 2i function.
  • The genes Kdm3b, Egfr and Esrrb  have linked expression and play important roles in the conversion of pre-iPSCs to iPSCs.

By developing a high-efficiency system to generate iPSCs, the authors have provided insights into how the pluripotency network is rewired.

Read the full report in Nature Communications, February 2015.