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Enhancer H3K4 Dimethylation Linked to Asthma
Worldwide asthma cases have been consistently rising, highlighting the need for an even deeper understanding of the molecular basis of the disease. Asthma sufferers have an overabundance of memory CD4(+) T cells that produce type 2 cytokines (TH2 cells). Researchers at the La Jolla Institute for Allergy & Immunology mapped genome-wide histone modification profiles for T cells in order to determine their role in asthma.
The group, led by corresponding author Pandurangan Vijayanand, surveyed T cell populations isolated from healthy and asthmatic peripheral blood, and used that information to identify enhancers that may have a role in human TH1 and TH2 cell differentiation. Analysis of the results revealed:
The study confirms the role for TH2 cells in asthma, and establishes the utility of enhancer profiling for the investigation of disease pathogenesis.
See the complete analysis at Nature Immunology, August 2014.
Chromatin, Long Noncoding RNA Interactions Revealed by dChIRP
Using traditional approaches makes it a challenge to investigate the functional domains of long noncoding RNAs (lncRNAs). In this article, the authors from Howard Hughes Medical Institute and Stanford University introduce a new method, named domain-specific chromatin isolation by RNA purification (dChIRP), aimed at better deciphering lncRNA function and architecture.
A team led by Howard Chang used dChIRP to inspect lncRNAs domain by domain, and help them identify functional elements. To demonstrate the technique, the researchers analyzed dChIRP of the Drosophila melanogaster lncRNA, roX1. Here is what they learned:
The scientists were able to obtain RNA genomic localization signals over 20 fold more robust than previous methods. Based on those results, the authors claim that dChIRP is highly useful for decoding RNA-RNA, RNA-protein and RNA-chromatin interactions at the level of individual RNA domains in living cells with very high precision and sensitivity.
Find more details on the dChIPR method at Nature Biotechnology, July 2014.
Uses our Rabbit polyclonal to actin (ab1801).
DNA-barcoded Nucleosomes Advance Chromatin Exploration
Delving into the molecular underpinnings of histone post-translational modifications (PTMs) remains a difficult task for epigenetics researchers. Current technologies are adept at either generating large amounts of correlative, genome-scale data; or consist of traditional biochemical approaches that focus on direct and quantitative detection of relationships. A scientific team from Princeton University has developed a new platform that combines the advantages of previous approaches and enhances the biochemical study of chromatin recognition and signaling.
Tom Muir and his colleagues based the new approach on the streamlined semisynthesis of DNA-barcoded nucleosome libraries (DNLs) with specific combinations of PTMs. The DNLs are chromatin immunoprecipitated after treatment with purified chromatin effectors or the nuclear proteome, and then analyzed by multiplexed DNA-barcode sequencing. The new workflow has several advantages including:
The authors suggest that their new high throughput and highly sensitive technology will catalyze the understanding of molecular factors operating at the chromatin level.
See the complete DNL platform at Nature Methods, August 2014.
Development of Retroviral enChIP Using CRISPR
The ability to isolate and analyze the molecular interactions of specific genomic regions is critical to epigenomic investigations. A recent advancement in this area, the engineered DNA-binding molecule-mediated chromatin immunoprecipitation (enChIP) technology was developed for improved purification of targeted genomic sites.
In this publication, Hodaka Fuji and a team from Osaka University added a new retroviral expression system for enChIP using CRISPR technology. The researchers proved that target genomic loci may be purified with very high efficiency, and that any potential off-target sites can be kept to a minimum if the guide RNA (gRNA) design for the target site has an appropriately long unique seed sequence.
The authors combined enChIP with stable isotope labeling using amino acids in cell culture (SILAC) analysis to demonstrate a potential application of the technique. The resulting data showed that:
The scientists suggest that the new retroviral enChIP system with CRISPR creates a very useful tool for biochemical genomic studies in live cells, especially for functions like transcription and epigenetic regulation.
Read more about enChIP at PLoS One, July 2014.
Embyronic CpG Dynamics and Parental Origins
CpG dinucleotides have been observed to show changes in relation to disease but it is relatively static in adults aside from a few environmentally responsive loci. In embryos, however, it is a different case, with an enormous amount of reprogramming occurring. While extensively studied in mice, much less is known about how this process occurs in humans.
The labs of Drs. Alexander Meissner and Kevin Eggan from the Broad Institute of MIT and Harvard (Cambridge) used reduced representation bisuflite sequencing (RRBS) to examine the dynamics of over 1 million CpGs in developing human embryos. Using this technique they developed genome-scale DNA methylation maps of embryonic development. Here’s what they discovered:
The authors conclude that parental contributions do take on differences in embryonic development, with paternal demethylation appearing to be a general feature of early mammalian embryonic development and the maternal contributions appearing to take on more species-specific roles.
See the full report in Nature, July 2014.
The Developing Epigenetic Landscape of Human Embryos
DNA methylation is an important player in embryonic development that interacts with the rest of the epigenetic landscape, like histone modifications, to ensure the proper developmental programming. Human preimplantation embryos are in rare supply and as a result, have not yet had their epigenetic landscape examined systematically despite extensive evidence from mice that early embryos undergo dramatic reprogramming.
In order to fill this void, Drs. Jie Qian and Fuchou Tang from Peking University (Beijing) used reduced representation bisulphite sequencing (RRBS) and whole-genome bisulphite sequencing (WGBS) to map the development of early embryos from the zygotic stage through to post- implantation. Here’s what they discovered:
Overall, this work sheds light on the methylation dynamics of human early embryos, their relationship to a histone modification and how this relates to regulation of gene expression and transposons.
Find the complete article in Nature, July 2014.
Hippo signaling acts to block activating chromatin marks
Limitation of organ growth by the Hippo signaling pathway is accomplished by downregulation of the transcriptional coactivator Yorkie (Yki) in many species. The Hippo and Warts kinases phosphorylate Yki and promote its cytoplasmic localization. The two WW domains of Yki are required for transcriptional activation via histone H3 lysine 4 methylation. However, the precise method of Yki transcriptional co-activation remains unclear.
Dr. Kenneth Irvine and colleagues at Rutgers University hypothesized that Yki interacts with histone H3 lysine 4 methyltransferase complexes to fulfil its regulatory role. Since H3K4me3 promotes gene expression, this may represent the mechanism of action of Yki, and thus the mechanism blocked by Hippo signaling.
Using ChIP and in silco analyses in cultured Drosophila S2 cells and in vivo embryos the authors found that:
The authors propose a model wherein Yorkie binds to target genes, recruiting the Trr complex by binding to NcoA6. Trr then methylates H3K4 leading to increased transcription. The implication of NcoA6 in Hippo signaling may mean that H3K4me3-induced gene expression occurs in pathways that crosstalk via Yki.
Read the full report in Cell Reports, July 2014.
CpG dense regions are a conserved open chromatin signal
Highly Occupied Target (HOT) regions are bound by many transcription factors, too many to be explained by sequence motif binding alone. They are also characterized by open chromatin and are present near active elements, but their precise role remains unclear. These regions are found in many species including C. elegans and humans.
Julie Ahringer and colleagues at Cambridge University examined the role of CpG dinucleotide density in HOT region activity. Unmethylated CpG dense regions are common in active mammalian DNA elements. Methylation of CpGs in other genomic regions is thought to play a role in their silencing. Unmethylated CpGs are bound by the CXXC1 protein. Curiously a homolog of this protein, CFP-1, is found in C. elegans which lack DNA methylation. CFP-1 is required for the H3K4me3, the mark of active genes.
Using the ENCODE database, ChIP-seq, and transgenic C. elegans lines the authors found that:
These data support the view that unmethylated CpG dense regions serve as a conserved promoter signal that predates DNA methylation. These regions promote an open chromatin state and CXXC1 homolog targeting and are associated with H3K4me3.
See the full report in Genome Research, July 2014.