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August 2017

ChromEMT: Visualizing 3D chromatin structure and compaction in interphase and mitotic cells.
In the current issue of Science, Ou et al describe a DNA-labeling method, ChromEMT, that allows them to visualize chromatin organization in human cells. This methodology combines electron microscopy tomography (EMT) with a labeling method (ChromEM) that selectivity enhances the contrast of DNA. The authors were able to describe Chromatin as more flexible and disordered in contrast to the current model, forming a 5- to 24-nm-diameter granular chain that is packed together at different concentration densities in interphase nuclei and mitotic chromosomes.
Ou, H.D. et al: Science. 2017 July 28. DOI: 10.1126/science.aag0025
Abstract.

Tribbles 2 mediates cisplatin sensitivity and DNA damage response in epithelial ovarian cancer.
In this recent study, Kritsch et al use Active Motif’s Methyl Collector assay to screen for hyper-methylated genes that are resistant to cisplatin treatment in epithelial ovarian cancer. Genome-wide analyses of hypermethylated CpG-islands in resistant cell lines, in combination with qRT-PCR analyses, were performed in order to identify epigenetically silenced genes. Tribbles 2 (TRIB2), a pseudokinase of unknown function, was found to be hypermethylated and downregulated during cisplatin resistance development.
Kritsch, D. et al: Int J Cancer. 2017 Jul 3. doi: 10.1002/ijc.30860
Abstract.

Hypothalamic stem cells control ageing speed partly through exosomal miRNAs.
In the current issue of Nature, Zhang and collaborators investigate the role the hypothalamus plays in controling ageing. Through the development of several mouse models, the authors conclude that ageing speed is substantially controlled by hypothalamic stem cells, partially through the release of exosomal miRNAs.
Zhang, Y. et al: Nature. 2017 Jul 26. doi: 10.1038/nature23282
Abstract.
 

July 2017

Identification of physical interactions between genomic regions by enChIP-Seq.
Physical interactions between genomic regions play critical roles in the regulation of genome functions, including gene expression. However, the methods for confidently detecting physical interactions between genomic regions remain limited. This recent study demonstrates the feasibility of using engineered DNA-binding molecule-mediated chromatin immunoprecipitation (enChIP) in combination with next-generation sequencing to detect physical interactions between genomic regions.
Fujita, T. et al: Genes to Cells. 2017 May 5. doi: 10.1111/gtc.12492. [Epub ahead of print]
Abstract.

DUX-family transcription factors regulate zygotic genome activation in placental mammals.
In animal embryos, transcription is mostly silent for several cell divisions, until the release of the first major wave of embryonic transcripts through so-called zygotic genome activation (ZGA). Maternally provided ZGA-triggering factors have been identified in Drosophila melanogaster and Danio rerio, but their mammalian homologs remain undefined. This recent Nature Genetics publication provides evidence that the DUX family of transcription factors is essential to the ZGA process in mice and potentially in humans.
De Iaco, A. et al: Nature Genetics. 2017 Jun;49(6):941-945. doi: 10.1038/ng.3858. Epub 2017 May 1.
Abstract.

Simultaneous overactivation of Wnt/b-catenin and TGFb signalling by miR-128-3p confers chemoresistance-associated metastasis in NSCLC.
Cancer chemoresistance and metastasis are tightly associated features. However, whether they share common molecular mechanisms and thus can be targeted with one common strategy remain unclear in non-small cell lung cancer (NSCLC). This recent Nature Communications article shows that high levels of microRNA-128-3p (miR-128-3p) are key to concomitant development of chemoresistance and metastasis in residual NSCLC cells having survived repeated chemotherapy and that these high levels also correlate with chemoresistance, aggressiveness and poor prognosis in NSCLC patients.
Cai, J. et al: Nature Communications. 2017 Jun 19;8:15870. doi: 10.1038/ncomms15870
Abstract.
 

June 2017

Systematic Epigenomic Analysis Reveals Chromatin States Associated with Melanoma Progression.
The mammalian TET enzymes catalyze DNA demethylation. While they have been intensely studied as major epigenetic regulators, little is known about their physiological roles and the extent of functional redundancy following embryo implantation. In this study, scientists from KU University in Leuven investigate the physiological role of TET1 in embryo development and highlight the interplay between the catalytic and non-catalytic activities of TET1 that is essential for normal development.
Khoueiry, R. et al: Nature Genetics. 2017 May 15. doi: 10.1038/ng.3868
Abstract.

Joint profiling of chromatin accessibility, DNA methylation and transcription in single cells.
Parallel single-cell sequencing protocols represent powerful methods for investigating regulatory relationships, including epigenome-transcriptome interactions. This recent publication describes the first single-cell method for parallel chromatin accessibility, DNA methylation, and transcriptome profiling, which the authors have dubbed scNMT-seq (single-cell nucleosome, methylation and transcription sequencing).
Clark, S.J. et al: BioRxiv Beta. 2017 May 17. doi: https://doi.org/10.1101/138685
Abstract.

Light-inducible antimiR-92a as a therapeutic strategy to promote skin repair in healing-impaired diabetic mice.
MicroRNAs (miRs) are small non-coding RNAs that post-transcriptionally control gene expression. Inhibition of miRs by antisense RNAs (antimiRs) might be a therapeutic option for many diseases, but systemic inhibition can have adverse effects. This recent Nature Communications article shows that light-activatable antimiRs efficiently and locally restrict target miR activity in vivo.
Lucas, T. et al: Nature Communications. 2017 May 2;8:15162. doi: 10.1038/ncomms15162. [Epub ahead of print]
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May 2017

Systematic Epigenomic Analysis Reveals Chromatin States Associated with Melanoma Progression.
The extent and nature of epigenomic changes associated with melanoma progression is poorly understood. This study examines the Epigenomic Profile of a cell phenotypic model and reveals a specific chromatin state associated with melanoma progression. Computation of specific chromatin state transitions showed loss of histone acetylations and H3K4me2/3 on regulatory regions proximal to specific cancer-regulatory genes in important melanoma-driving cell signaling pathways. By checking 35 epigenetic modifications, scientists were able to precisely map the histone modification marks associated with disease. Interestingly, computation of specific chromatin state transitions showed loss of histone acetylations and H3K4me2/3 on regulatory regions proximal to specific cancer.
Fiziev, P. et al: Cell Reports. 2017 Apr 25;19(4):875-889. doi: 10.1016/j.celrep.2017.03.078.
Abstract.

Empirical comparison of reduced representation bisulfite sequencing and Infinium BeadChip reproducibility and coverage of DNA methylation in humans.
This study represents an examination of the strengths and weaknesses of two human genome-wide DNA methylation platforms: a derivative of rapid multiplexed reduced representation bisulfite sequencing that is optimized for high-throughput, which they have dubbed rmRRBS, and Illumina’s Infinium BeadChip technology. Compared to the Infinium array, NGS-based rmRRBS is capable of covering more CpG loci, which are thought to be important for exposure-related epigenetic modifications, as well as open sea regions, with less input DNA compared to Infinium.
Carmona, J.J. et al: Genomic Reports Article number: 13 (2017) doi:10.1038/s41525-017-0012-9
Abstract.

Nucleic acid detection with CRISPR-Cas13a/C2c2.
Scientists from Broad Institute of MIT and Harvard have recently developed a rapid, inexpensive, and sensitive method for nucleic acid detection. This Cas13a-based molecular detection platform, termed SHERLOCK (Specific High Sensitivity Enzymatic Reporter UnLOCKing), is used to detect specific strains of Zika and Dengue virus, distinguish pathogenic bacteria, genotype human DNA, and identify cell-free tumor DNA mutations. Furthermore, SHERLOCK reaction reagents can be lyophilized for cold-chain independence and long-term storage, and readily reconstituted on paper for field applications.
Gootenberg, J. et al: Science. 2017 Apr 13. pii: eaam9321. doi: 10.1126/science.aam9321. [Epub ahead of print]
Abstract.
 

April 2017

An atlas of human long non-coding RNAs with accurate 5′ ends.
Scientists from the RIKEN-led FANTOM5 consortium have developed an atlas of human long non-coding RNA using a transcriptomics protocol which they’ve dubbed CAGE (Cap Analysis of Gene Expression). By using CAGE in different cell types, the authors were able to generate a comprehensive atlas of 27,919 human lncRNA genes with high-confidence 5′ ends and expression profiles across 1,829 samples. Genomic and epigenomic classification of these lncRNAs reveals that most intergenic lncRNAs originate from enhancers rather than from promoters. Combining expression data with genetics and genomics datasets, the authors were also able to show that lncRNAs overlapping trait-associated single nucleotide polymorphisms are specifically expressed in cell types relevant to the traits, implicating these lncRNAs in multiple diseases.
Hon, C.C. et al: Nature. 2017 Mar 9;543(7644):199-204. doi: 10.1038/nature21374. Epub 2017 Mar 1.
Abstract.

Class IIa HDAC inhibition reduces breast tumours and metastases through anti-tumour macrophages.
In this recent Nature publication, Gurriero and collaborators investigate the role of an HDAC inhibitor in breast tumors and metastasis. Utilizing a macrophage-dependent autochthonous mouse model of breast cancer, they demonstrate that in vivo TMP195 (HDAC inhibitor) treatment alters the tumor microenvironment and reduces tumor burden and pulmonary metastases by modulating macrophage phenotypes.
Guerriero, J.L. et al: Nature 2017 Mar 16;543(7645):428-432. doi: 10.1038/nature21409. Epub 2017 Mar 8.
Abstract.

SNF2 Family Protein Fft3 Suppresses Nucleosome Turnover to Promote Epigenetic Inheritance and Proper Replication.
Heterochromatin can be epigenetically inherited in cis, leading to stable gene silencing, however, the mechanisms underlying heterochromatin inheritance remain unclear. In the current issue of Molecular Cell, scientists from Grewal lab have revealed a novel function for SFN2 family protein Fft3 in Heterochromatin inheritance rather than de novo assembly. In addition to uncovering a conserved factor critical for epigenetic inheritance of heterochromatin, this work also describes a mechanism in which suppression of nucleosome turnover prevents formation of structural barriers that impede replication at fragile regions in the genome..
Taneja, N. et al: Mol Cell. 2017 Mar 8. pii: S1097-2765(17)30098-9. doi: 10.1016/j.molcel.2017.02.006. [Epub ahead of print]
Abstract.
 

March 2017

UV Irradiation Induces a Non-coding RNA that Functionally Opposes the Protein Encoded by the Same Gene.
In this recent publication from the Svejstrup laboratory, the transcription-related DNA damage response was analyzed on a genome-wide scale - with great spatial and temporal resolution. Upon UV irradiation, a slowdown of transcript elongation and restriction of gene activity to the promoter-proximal ∼25 kb was observed, and found to be associated with a shift from expression of long mRNAs to shorter isoforms, incorporating alternative last exons (ALEs) that are more proximal to the transcription start site. Notably, the authors observed a shift from a protein-coding ASCC3 mRNA to a shorter isoform of which the non-coding RNA, rather than an encoded protein, is critical for the eventual recovery of transcription. Upon UV-irradiation ASCC3 protein and its counterpart, non coding RNA, work antagonistically to regulate global gene expression.
Williamson, L. et al: Cell. 2017 Feb 23;168(5):843-855.e13. doi: 10.1016/j.cell.2017.01.019. Epub 2017 Feb 16.
Abstract.

Systematic Investigation of Transcription Factor Activity in the Context of Chromatin Using Massively Parallel Binding and Expression Assays.
In this recent publication, scientists from the Segal lab present BE-MPRA, a massively parallel, binding and expression reporter assay that allows for accurate measurements of DNA occupancy in large-scale reporter libraries. The authors screened more than 1500 promoter variants and classified different transcription factor categories, based on effects of chromatin accessibility and levels of gene expression. Moreover, the authors uncovered synergistic effects of TF binding events and nucleosome occupancy in broad gene regulation.
Levo, M. et al: Mol. Cell 2017 Feb 16;65(4):604-617.e6. doi: 10.1016/j.molcel.2017.01.007.
Abstract.

CpG Island Hypermethylation Mediated by DNMT3A Is a Consequence of AML Progression.
Various studies have revealed the importance of DNMT3A in Acute Myeloid Leukemia cells (AMLs) however, little is known about how DNMT3A contributes to specific methylation patterns in these cells. In this current study, Spencer and collaborators elucidate the combined role of DNA methylation, driven by DNMT3A, in both cancer initiation and progression. Together their findings support a model in which the CpG island Hypermethylation is rather an effect of proliferation caused by DNMT3A and conversely, hypomethylation is an initiating phenotype in AMLs with the DNMT3AR882 mutation..
Spencer, D.H. et al: Cell. 2017 Feb 23;168(5):801-816.e13. doi: 10.1016/j.cell.2017.01.021. Epub 2017 Feb 16.
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February 2017

Distinctive patterns of transcription and RNA processing of human lincRNAs.
Scientists in the Proudfoot lab developed this technique called mNET-seq, which allowed them to investigate the biology of a novel and less-studied category of long non coding RNA called long intervening non coding RNA (lincRNA). By using antibodies against different modifications of Pol II, they were able to identify different patterns in canonical mRNA and lincRNAs. Results indicate that lincRNA does not follow the transcriptional CTD code defined for protein-coding genes and that it is mostly restricted to chromatin, since it is rapidly degraded by the RNA exosome. Substantial differences between the two classes of RNA were also found and the authors suggest that the biological significance of lincRNA is more likely related to their actual transcription rather than their sequence.
Schlackow, M. et al: Mol Cell. 2017 Jan 5;65(1):25-38. doi: 10.1016/j.molcel.2016.11.029. Epub 2016 De22
Abstract.

Reversible methylation of m6Am in the 5′ cap controls mRNA stability.
An emerging concept in gene regulation is related to the idea that internal bases in mRNA can be subjected to modifications that influence the fate of mRNA in cells. If the first nucleotide following the m7G cap is 2´-O-methyladenosine (Am), it can be further methylated at the N6 position to form N6,2´-O- dimethyladenosine (m6Am) forming a specific epitranscriptomic code. In the current study, Jan Mauer and collaborators generate a transcriptome genome-wide map of m6Am, and determine that this modification is enriched at 5´ ends of mRNAs that are remarkably stable. The mRNA stability is due to the fact that m6Am-initiated transcripts are resistant to the activity of the decapping enzyme DCP2.
Mauer, J. et al: Nature 2017 Jan 19;541(7637):371-375. doi: 10.1038/nature21022. Epub 2016 Dec 21.
Abstract.

Broad histone H3K4me3 domains in mouse oocytes modulate maternal-to-zygotic transition
Maternal-to-zygotic transition (MZT) is essential for the formation of a new individual, but it remains poorly understood despite recent progress in the analysis of gene expression and DNA methylation in early embryogenesis. Dynamic changes in related histone modifications could play an important role in this transition but so far, due to technical limitations in ChIP-seq, it has been difficult to elucidate their proper connection to this event. In the current study, researchers have introduced a micro scale chromatin immunoprecipitation (μChIP–seq) method, which they used to profile genome-wide histone H3 lysine methylation (H3K4me3) and acetylation (H3K27ac) in mouse immature and metaphase II oocytes as well as 2-cell and 8-cell embryos. By introducing IgG and octamers into the input chromatin samples they were able to eliminate a lot of the background often observed in low-cell ChIP-seq experiments. As a result they were able to elucidate the developmental role of broad domains of H3K3Me3 in MZT.
Dahl, J.A. et al: Nature. 2016 Sep 22;537(7621):548-552. doi: 10.1038/nature19360. Epub 2016 Sep 14.
Abstract.
 

January 2017

Targeted epigenetic editing of SPDEF reduces mucus production in lung epithelial cells.
In this recent American Journal of Physiology publication, Juan Song and colleagues investigated the SPDEF mucus production pathway - since excess mucus production is a major cause of morbidity in chronic inflammatory lung disease. Using CRISPR/dCas9 and zinc finger nucleases, they were able to target repressive epigenetic enzymes, such as DNA and histone methyltransferases, to the promoter of the SPDEF gene. By artificially silencing expression, researchers were also able to inhibit downstream mucus-related genes. This type of epigenetic editing may one day be used as a therapy to provide long-term mucus reduction in patients, thereby significantly improving their quality of life.
Song, J. et al: Am J Physiol Lung Cell Mol Physiol. 2016 Dec 23:ajplung.00059.2016. doi: 10.1152/ajplung.00059.2016. [Epub ahead of print]
Abstract.

Tumor-suppressor genes that escape from X-inactivation contribute to cancer sex bias
Men have a higher risk of developing cancer than women, even when other factors such as age and environment are taken into account. Although women carry two X chromosomes, one is in fact "shut down" or inactivated in order to equalize with the single X chromosome carried by men. Enigmatically, this shutting down process is not 100% efficient, allowing some genes on the "inactive" X chromosome to remain transcribed. These genes are termed "escapers". In this recent Nature Genetics publication, Dunford et al found that some of these “escapers” can in fact act as tumor suppressors. When mutated, these tumor suppressor escaper genes manifest malignantly in males. However, in females, the presence of a second copy of the gene protects from the detrimental effects of the mutation.
Dunford, A. et al: Nature Genetics 2017 Jan; 49(1):10-16. doi: 10.1038/ng.3726. Epub 2016 Nov 21
Abstract.

Targeting the histone methyltransferase G9a activates imprinted genes and improves survival of a mouse model of Prader–Willi syndrome
The regulation of gene expression is coordinated by an imprinting center (PWS-IC). Prader–Willi syndrome (PWS) is an imprinting disorder in which the maternally expressed genes are epigenetically silenced. In this current study, researchers used specific enzyme inhibitors to restore maternally inherited gene expression. By screening a library of more than 9,000 small molecules, scientists identified two specific inhibitors of N-methyltransferase-2 (also known as G9a). Both compounds, UNC0642 and UNC0638, caused a selective reduction of the dimethylation of histone H3 lysine 9 (H3K9me2) at PWS-IC, without changing DNA methylation status. This study provides the first proof of principle for an epigenetics-based therapy for PWS.
Kim, Y. et al: Nature Medicine. 2016 Dec 26. doi: 10.1038/nm.4257. [Epub ahead of print]
Abstract.
 

December 2016

An Alternative Approach to ChIP-Seq Normalization Enables Detection of Genome-Wide Changes in Histone H3 Lysine 27 Trimethylation upon EZH2 Inhibition.
Active Motif is proud to announce that our scientists, in collaboration with Constellation Pharmaceuticals, have developed a novel data normalization technique for ChIP-Seq by introducing a Drosophila chromatin spike-in and performing immunoprecipitation with a Drosophila-specific histone antibody. Applying this modified ChIP-Seq protocol to human cells treated with EZH2 inhibitors, they were able to identify global changes of H3K27me3 across the entire genome. This novel method could help scientists normalize ChIP-Seq data across samples with different treatments (i.e. inhibitors, knockdowns).
Egan, B. et al: PLoS One. 2016 Nov 22;11(11):e0166438. doi: 10.1371/journal.pone.0166438. eCollection 2016
Full Paper.

Efficient targeted DNA methylation with chimeric dCas9–Dnmt3a–Dnmt3L methyltransferase
Targeted editing of the epigenome can be exploited to elucidate the mechanisms of action of epigenetic enzymes at the chromatin level. This study specifically targeted DNMT3A-DNMT3L fusion protein to EpCAM, CXCR4 and TFRC gene promoters. The authors were able to show that targeting these loci with single gRNAs leads to efficient and widespread methylation of the promoters. Epigenomic silencing by targeted DNA methylation could be an important tool in human diseases related to gene misexpression.
Stepper, P. et al: Nucleic Acids Research 2016 doi: 10.1093/nar/gkw1112
Full Paper.

Nucleosome Density ChIP-Seq Identifies Distinct Chromatin Modification Signatures Associated with MNase Accessibility
In this study, researchers have developed a novel protocol combining native ChIP-Seq with an analytical framework that allows MNase accessibility to be integrated with histone modification profiles in order to obtain single nucleosome resolution. Applying this novel methodology to the primitive subset of normal human cord blood cells, using validated antibodies against H3K4me3 and H3K27me3, allowed the authors to identify that these marks are heterogeneously distributed in bivalent promoters.
Lorzadeh, A. et al: Cell Reports. 2016 Nov 15;17(8):2112-2124. doi: 10.1016/j.celrep.2016.10.055
Abstract.
 

November 2016

Expanding the Circuitry of Pluripotency by Selective Isolation of Chromatin-Associated Proteins
Maintenance of pluripotency is regulated by a network of transcription factors coordinated by Oct4, Sox2, and Nanog (OSN), yet little is known about their interaction with chromatin-related proteins and cofactors. In this paper, the authors introduce a novel protocol combining ChIP with selective isolation of chromatin-associated proteins (SICAP) followed by mass spectrometry to identify chromatin-bound partners of a protein of interest. Using mouse embryonic stem cells (ESC) as a model, they identified over 400 proteins associated with OSN.
Rafiee, M.R. et al: Mol. Cell. 2016 Oct 19. pii: S1097-2765(16)30568-8. doi: 10.1016/j.molcel.2016.09.019
Abstract.

Chromatin Kinases Act on Transcription Factors and Histone Tails in Regulation of Inducible Transcription
In the current study, researchers from C. David Allis’s lab investigate the crosstalk between mitogen- and stress-activated protein kinases (MSKs) and the transcription activation of genes involved in the inflammatory response. Results indicate that up-regulation of induced genes in mouse macrophages stimulated with bacterial lipopolysaccharide is followed by enrichment of H3K28ph through activation of MSKs, and that H3K28ph promotes p300/CBP-dependent transcription in cell-free transcription assays. This work uncovers the mechanistic action of MSK-induced transcription through crosstalk with chromatin factors.
Josefowicz, S.J. et al: Mol. Cell 2016 Oct 20;64(2):347-361. doi: 10.1016/j.molcel.2016.09.026
Abstract.

MOF Acetyl Transferase Regulates Transcription and Respiration in Mitochondria
In this recent Cell publication, researchers from the Akhtar lab reveal that MOF is a dual-transcriptional regulator of nuclear and mitochondrial genomes connecting epigenetics and metabolism. Specifically, they found that Mof depletion in mice leads to severe myopathies and dysfunction of mitochondria. By investigating the mechanistic events underlying the dysfunction, the authors identified that Mof binds to mtDNA and regulates a series of respiratory genes. Moreover, members of the non specific lethal complex are located in mitochondria, influencing Mof localization and function.
Chatterjee, A. et al: Cell. 2016 Oct 20;167(3):722-738.e23.doi:10.1016/j.cell.2016.09.052
Abstract.
 

October 2016

L1-associated genomic regions are deleted in somatic cells of the healthy human brain.
Long interspersed element-1 (LINE-1 or L1) retrotransposition is known to create mosaicism by inserting L1 sequences into new locations of somatic cell genomes. In the current study, Erwin and collaborators examine the contribution of L1 in the somatic variation of healthy human brains. Using a novel protocol for single cell sequencing (SLAV-seq), they discovered that somatic L1-associated variants (SLAVs) are composed of two classes: L1 retrotransposition insertions and retrotransposition-independent L1-associated variants and are present in region of important neuronal genes such as DLG2.
Erwin, JA. et al: Nat Neurosci.. 2016 Sep 12. doi: 10.1038/nn.4388. [Epub ahead of print]
Abstract.

Helicase Lymphoid-Specific Enzyme Contributes to the Maintenance of Methylation of SST1 Pericentromeric Repeats That Are Frequently Demethylated in Colon Cancer and Associate with Genomic Damage
In this current study Samuelsson and collaborators from the Manuel Perucho lab investigate the epigenetic landscape of a pericentromeric repeat called SST1. SST1 somatic demethylation is often associated with genome damage, especially in tumors with wild-type TP53. Using the Active Motif FFPE ChIP kit, the authors validated the change from high levels of DNA methylation and H3K9me3 at SST1 in normal tissues to a reduction of H3K9me3 and enrichment of H3K27me3 in tumors exhibiting SST1 demethylation. Moreover, they revealed with in vivo experiments the contribution of the helicase lymphoid-specific (HELLS) enzyme in SST1 methylation status and in genomic stability.
Samuelsson, J.K. et al: Epigenomes 2016, 1(1), 2; doi:10.3390/epigenomes1010002
Abstract.

Inheritable Silencing of Endogenous Genes by Hit-and-Run Targeted Epigenetic Editing
Using gene editing technology based on CRISPR-Cas9, scientists from the Lombardo lab have obtained inheritable silencing in different cell types, including primary T lymphocytes. By utilizing embryonic stem cells along with combinations of engineered transcriptional repressors that bind to and synergize at the target locus to instruct repressive histone marks and de novo DNA methylation, the authors were able to achieve long term memory of the repressive marks, opening new methods for targeted epigenome editing in medical applications.
Amabile, A. et al: Cell. 2016 Sep 22;167(1):219-232.e14 DOI: http://dx.doi.org/10.1016/j.cell.2016.09.006
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Sep 2016

Functional screening implicates miR-371-3p and peroxiredoxin 6 in reversible tolerance to cancer drugs.
Drug resistance in cancer treatment continues to be major issue in oncology and recent studies have underlined the importance of chromatin related factors in reversible drug tolerance persistence. In this recent Nature Communications publication, the authors investigate a potential role for microRNAs in transient drug tolerance. By using Active Motif’s genome wide collection of 3´UTRs, the authors were able to uncover the role of miR371-3p as a potent suppressor of drug tolerance by regulating the expression of PRDX6 (peroxiredoxin 6).
Sahu, N. et al: Nature Commun.. 2016 Aug 3;7:12351. doi: 10.1038/ncomms12351
Abstract.

DNA hydroxymethylation controls cardiomyocyte gene expression in development and hypertrophy
Using Active Motif’s Epigenetic services for hMeDIP and high throughput sequencing, the authors of this recent Nature Communications publication were able to identify differential 5-hmC DNA modifications between embryonic, neonatal, adult and hypertrophic mouse cardiomyocytes and interestingly, that highly expressed genes related to heart development & failure are marked by DNA hydoxymethylation along the gene bodies and distal regulatory regions.
Greco, C.M. et al: 2016 Aug 4;7:12418. doi: 10.1038/ncomms12418
Abstract.

Dissecting the precise role of H3K9 methylation in crosstalk with DNA maintenance methylation in mammals
In this current issue of Nature Communications, researchers investigate the cross talk between H3K9me2/3 and DNA methylation. In order to study the effects of DNA methylation across the genome, an Uhrf1 knock-in (KI) mouse model has been generated that specifically abolishes the H3K9me2/3-binding activity of Uhrf1. Global effects on DNA methylation have been observed and are not restricted to highly H3k9me2/3 marked regions. Moreover, in vitro UHRF1 binds nucleosome with hemi-mCpGs better than with H3K9me3, thus providing a molecular explanation that UHRF1-mediated DNA maintenance methylation is largely independent of its H3K9me2/3-binding activity.
Zhao, Q. et al: Nature Commun.. 2016 Aug 24;7:12464. doi: 10.1038/ncomms12464
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Aug 2016

CTCF contributes in a critical way to spermatogenesis and male fertility
This recent Scientific Reports publication examines the role of the architectural protein CTCF (CCCTC-binding factor) during spermatogenesis. Among other things, the authors show that CTCF inactivation results in impaired spermiogenesis & infertility and that CTCF regulates chromatin compaction and is necessary for packaging of the paternal genome into mature sperm.
Hernández-Hernández A. et al: Sci Rep. 2016 Jun 27;6:28355. doi: 10.1038/srep28355
Abstract.

Comprehensive Identification of RNA-Binding Domains in Human Cells
The Interaction between RNA binding proteins (RBPs) and RNA plays an essential role in RNA metabolism and has implications for many hereditary diseases. In this current issue of Mol. Cell, scientists from M. Hentze’s lab outline RBDmap, which they have developed as a method for the in vivo identification of RBDs on a proteome-wide scale. Using this map, they were able to map 1,174 binding sites within 529 HeLa cell RBPs, discovering numerous RNA-binding domains (RBDs).
Alfredo Castello et al: DOI: http://dx.doi.org/10.1016/j.molcel.2016.06.029.
Abstract.

Nfib Promotes Metastasis through a Widespread Increase in Chromatin Accessibility
In this current study, Denny and collaborators analyse small cell lung cancer (SCLC) cells from primary tumors and metastases to identify global changes in chromatin accessibility during metastasic progression. Their results indicate that high expression of a single transcription factor, Nfib, alters chromatin state globally and enacts a program of gene expression that promotes multiple steps of the metastatic cascade.
Denny SK et al: Cell. 2016 Jul 14;166(2):328-42. doi: 10.1016/j.cell.2016.05.052. Epub 2016 Jun 30
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July 2016

Functional interdependence of BRD4 and DOT1L in MLL leukemia
In this recent publication, the histone methyltransferase DOT1L and the acetylation "reader" BRD4 are found to work synergistically to mediate transcription of cancer genes in leukemia. Using a series of in vivo and in vitro experiments, the authors also discover a functional link between DOT1L and BRD4 binding at H4 acetylated histones. This interaction takes place close to super-enhancer regions in highly transcribed genes and provides new insights into the regulation of transcription.
Gilan, O. et al. Nat Struct Mol Biol. 2016 Jun 13. doi: 10.1038/nsmb.3249
Abstract.

Mapping RNA–RNA interactome and RNA structure in vivo by MARIO
Scientists from University of California, San Diego present the novel Mapping RNA interactome in vivo (MARIO) technology, which is capable of revealing RNA–RNA interactions from unperturbed cells on a massive scale. Using a crosslinking approach, the authors were able to capture interactions of different molecules of RNA in close proximity, mediated by protein binding in vivo. In addition, MARIO data reveal thousands of intra-molecule interactions, providing in vivo data on high-order RNA structures
Nguyen, T.C. et al. Nat Commun. 2016 Jun 24;7:12023. doi: 10.1038/ncomms12023.
Abstract.

MLL1 Inhibition Reprograms Epiblast Stem Cells to Naive Pluripotency
Epiblast Stem Cells (EpiSC) reprograming is associated with a drastic alteration of the epigenetic landscape but mechanistic studies showing the precise changes that occur at the molecular level during reprogramming remain sparse. In the current issue of Cell Stem Cell scientists from the lab of Yali Dou were able to demonstrate the role of the MLL1 histone methyltransferase in EpiSC conversion to “naïve” pluripotent stem cells. Using a specific inhibitor against the MLL1 enzyme they were able to re-activate the silenced X-chromosome. Moreover, they observed a global redistribution of the H3K4me1 active mark, which is directly linked to gene expression programs responsible for stem cell reprogramming.
Zhang, H. et al. Cell Stem Cell. 2016 Apr 7;18(4):481-94. doi: 10.1016/j.stem.2016.02.004. Epub 2016 Mar 17
Abstract.
 

June 2016

Bivalent Regions of Cytosine Methylation and H3K27 Acetylation Suggest an Active Role for DNA Methylation at Enhancers
In the current issue of Molecular Cell, researchers from the P. Jones lab investigate the role of DNA methylation in enhancer regions. By comparing the epigenomes of the HCT116 and DKO1 cell lines, they were able to identify that a portion of regular and super- or stretch enhancers show active H3K27ac marks co-existing with extensive DNA methylation. Additionally, DNA methylation appears to play an unexpected dual role at enhancer regions, being anti-correlated focally at transcription factor-binding sites but positively correlated globally with the active H3K27ac mark to ensure structural enhancer integrity.
Charlet, J. et al. Mol. Cell. 2016 May 5;62(3):422-31 doi: 10.1016/j.molcel.2016.03.033.
Abstract.

Methylome-wide Analysis of Chronic HIV Infection Reveals Five-Year Increase in Biological Age and Epigenetic Targeting of HLA
In this recent publication, researchers investigate and quantify the impact of chronic HIV infection on aging. Using 137 HIV+ individuals under sustained therapy along with 44 matched HIV- individuals, a global analysis of the whole-blood DNA methylomes was conducted. Using epigenetic models that were created and validated, it was found that chronic and recent HIV infection lead to an average aging advancement of 4.9 years and increased expected mortality risk by 19%. Additionally, decreased HLA methylation was found to be predictive of lower CD4 / CD8 T cell ratio, linking molecular aging, epigenetic regulation, and disease progression.
Gross, A.M. et al. Mol Cell. 2016 Apr 21;62(2):157-68 doi: 10.1016/j.molcel.2016.03.019
Abstract.

Pooled ChIP-Seq Links Variation in Transcription Factor Binding to Complex Disease Risk
In this recent Cell publication, researchers in the Hunter Fraser lab introduce a pooling-based approach to mapping quantitative trait loci (QTLs) for molecular-level traits. Applying this method to five transcription factors (TFs) and a histone modification, they were able to map thousands of cis-acting QTLs, with over 25-fold lower cost compared to standard QTL mapping.
Tehranchi, A.K. et al. Cell. 2016 Apr 21;165(3):730-41 doi:10.1016/j.cell.2016.03.041. Epub 2016 Apr 14
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May 2016

DNA methylation on N6-adenine in mammalian embryonic stem cells.
In this recent publication, researchers from Yale University identified a new DNA methylation mark in mammalian embryonic stem cells. To investigate this new mark, researchers applied a targeted ChIP-Seq method focusing on genomic regions enriched in the H2A.X marker. Results indicate that this new mark, N6-methyladenine, is localized at the 5’UTRs and ORFs of LINE-1 retroelements and that enrichment of N6-methyladenine is correlated with the epigenetic silencing and downregulation of neighbouring genes. This study elucidates the importance of a novel DNA modification mark in regulating epigenetic mechanisms related to retrotransposon and gene silencing in early embryonic development.
Wu, T.P. et al. Nature. 21 Apr 2016. DOI: 10.1038/nature17640. Epub 2016 Mar 30.
Abstract.

Dynamic Competing Histone H4 K5K8 Acetylation and Butyrylation Are Hallmarks of Highly Active Gene Promoters.
Histone lysine butyrylation is a conserved post-translational modification that is correlated with high gene expression. In the current issue of Molecular Cell, researchers investigate the role of butyrylation during mammalian spermatogenesis through a series of in vitro and genome wide analyses. Results indicate that, despite acting as a direct stimulator of transcription, histone butyrylation competes with acetylation, especially at H4 K5, to prevent Brdt binding and that alternating H4 acetylation and butyrylation could impact the final male epigenome features.
Goudarzi, A. et al. Mol Cell. 2016 Apr 21;62(2):169-80. doi: 10.1016/j.molcel.2016.03.014.
Abstract.

TRIBE: Hijacking an RNA Editing Enzyme to Identify Cell-Specific Targets of RNA-Binding Protein.
A novel technology for studying which RNA molecules interact with specific RNA binding proteins (RBPs) is presented in this issue of Cell. Taking advantage of the catalytic domain of the RNA editing protein, ADAR, scientists have developed a method called TRIBE (targets of RNA-binding proteins identified by editing). This method is based on the construction of a fusion protein containing an RNA binding protein and the catalytic domain of ADAR. After transfection into cells, RBP targets are marked with novel RNA editing events and identified by RNA-sequencing.
McMahon, A.C. et al. Cell. 2016 Apr 21;165(3):742-53. doi: 10.1016/j.cell.2016.03.007. Epub 2016 Mar 31
Full Article.