EpiGenie | Epigenetics, Stem Cell, and Synthetic Biology News http://epigenie.com Scientific News, Technology, and Product Information Thu, 14 Dec 2017 07:49:41 +0000 en-US hourly 1 https://wordpress.org/?v=4.9.1 TET Proteins: Defending Differentiation by denying de novo Methylation! http://epigenie.com/tet-proteins-defending-differentiation-denying-de-novo-methylation/ http://epigenie.com/tet-proteins-defending-differentiation-denying-de-novo-methylation/#respond Thu, 14 Dec 2017 07:49:41 +0000 http://epigenie.com/?p=26747 I don´t overeat! I’m not lazy! I’m not eating the agar plates when I´m working in the lab late, honest!

Psychologists consider denial as one of our most primitive defense mechanisms and recent studies of epigenetic defense mechanisms in embryonic stem cells (ESCs) by the labs of Olivier Elemento (Weill Cornell Medical College) and Danwei Huangfu (Sloan Kettering Institute, New York) have further strengthened this association.

This new study initially sought to discover any direct connections between the Ten-eleven translocation (TET) protein family-mediated DNA demethylation and transcriptional output at specific loci, as previous studies tended to be more global in their approach. Now, after some more targeted analysis, Verma and colleagues have established that TET proteins defend the lineage-specific differentiation of ESCs by denying DNA methylation at primed chromatin states known as bivalent domains, thus permitting ESCs to express differentiation-associated genes only when required. The TET enzymes themselves normally catalyze the first step of active DNA demethylation.

So what are the details of this new ESC-based study?

  • The team first created TET1, TET2, and TET3 triple-knockout (TKO) ESCs
    • TET knockout increased de novo DNA methylation at bivalent domains, but this did not alter gene expression
    • However, TET knockout increased DNA methylation elsewhere in the genome, prompting a general decrease in gene expression under self-renewing conditions
  • Focusing in on the PAX6 locus, a neural differentiation-associated factor, the authors observed increased DNA (cytosine-5)-methyltransferase 3B (DNMT3B) binding upon TET knockout
    • The study observed no alterations to PAX6 expression under self-renewing conditions
    • Following neural priming, DNMT3B-directed de novo DNA methylation of the PAX6 bivalent domain led to the repression of PAX6 gene expression and inhibited neural differentiation of TKO-ESCs
    • Epigenetic editing of the PAX6-associated bivalent domain by dCas9 fused to the catalytic domain of TET1 prompted DNA demethylation and improved neural differentiation

There’s no denying it; these findings firmly establish the requirement for DNA demethylation by the TET enzymes at bivalent domains to defend the expression of differentiation-associated genes in ESCs. The authors hope that future studies will delineate the various factors that influence methylation status at bivalent domains and apply this combined knowledge to predict cell-type-specific gene transcription patterns during differentiation.

Don´t deny yourself a quick glance at this new study, head to Nature Genetics, December 2017 now!

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Maternal Asthma Alters DNA Methylation at Autism Linked Genes in the Gardeners of the Developing Brain http://epigenie.com/maternal-asthma-alters-dna-methylation-autism-linked-genes-gardeners-developing-brain/ http://epigenie.com/maternal-asthma-alters-dna-methylation-autism-linked-genes-gardeners-developing-brain/#respond Mon, 11 Dec 2017 21:59:40 +0000 http://epigenie.com/?p=26742 Every good gardener appreciates that pruning represents an essential part of encouraging healthy development. This principle holds true not only on the macroscopic level but also at the microscopic level of our brain’s synaptic connections, which rely on pruning by its resident immune cells: the microglia. In order to sculpt neurodevelopment, microglia rely on environmental signals, which has spurred the labs of Paul Ashwood and Janine LaSalle at the University of California, Davis, to investigate how they fit into the interplay of environment and DNA methylation in autism spectrum disorders (ASD).

First author Annie Vogel Ciernia shares, “We wanted to identify some of the mechanisms underlying the epidemiology findings that maternal allergic asthma increases the risk of having a child with ASD. You have this maternal allergic asthma event during pregnancy, and then you have these very long-lasting effects on the offspring’s behavior. We wanted to figure out what mechanisms might underlie some of these long-term effects. We looked at immune cells in brain, which were prime suspects for contributing to the long-term changes in the offspring.”

To accomplish this, the team utilized a mouse model of maternal allergic asthma and examined microglia in juvenile offspring. Here’s what transpired when they analyzed DNA methylation and gene expression via whole-genome bisulfite sequencing (WGBS) and RNA-seq:

  • A comparison of the DNA methylation and gene expression signatures with other cell-type specific data sets via principal component analysis (PCA) confirmed the purity of their microglia
  • The differentially methylated regions (DMRs) are primarily intronic and intergenic, enriched for in transcription factor binding sites related to early microglia development, and regulate genes involved in immune signaling pathways
  • The differentially expressed genes (DEGs) are related to neurodevelopment, specifically the shaping of neuronal connections, as well as the response of microglia to environmental signals
  • Notably, there is very little overlap between DMRs and DEGs, although the genes that do overlap are related to neurodevelopment and autism risk

Finally, as Vogel Ciernia summarizes, “The genes we identified that had differences in methylation and changes in expression showed an enrichment for genes that had been identified as genetic risk factors for autism, as well as genes that were differentially expressed in autism human brain samples.” Co-senior author Janine LaSalle adds, “This is an environmental model, but we’re coming back to the same genes that can be genetically mutated and cause autism in rare cases. That overlap with some of the genes was pretty striking.”

Overall, the findings leave Vogel Ciernia with the outlook that “The ultimate goal would be to identify the pathways that are impacted, which could be a therapeutic target to reverse changes and potentially improve behaviors. But we need to have a better handle on whether these changes are driving the condition or compensation to a disruption in brain development.”

Go see why these findings are nothing to sneeze at in Glia, November 2017.

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Hit-and-Run Epigenetic Editing Helps Breast Cells Evade Cycle Arrest http://epigenie.com/hit-run-epigenetic-editing-helps-breast-cells-evade-cycle-arrest/ http://epigenie.com/hit-run-epigenetic-editing-helps-breast-cells-evade-cycle-arrest/#respond Mon, 11 Dec 2017 17:28:53 +0000 http://epigenie.com/?p=26736 While a hit-and-run typically leads to an arrest, in the world of epigenetic editing it turns out to be the key to evading cell cycle arrest (senescence) and promoting the transformation of a law-abiding cell into a cancerous criminal! The hypermethylation of promoters at the wrong time and wrong place is a trademark of cancer, and the labs of Gabriella Ficz (Queen Mary University of London, UK) and Tomasz Jurkowski (University of Stuttgart, Germany) sought to interrogate this phenomenon. To aid their investigation, this crime-solving team employed the ultra-potent dCas9-Dnmt3a-Dnmt3L methyltransferase previously established the Jurkowski lab.

The group turned to primary human myoepithelial cells from the healthy breast tissue of multiple donors and analyzed DNA methylation via the EPIC array. They chose to target a panel of tumor suppressor genes CDKN2A, RASSF1, HIC1 and PTEN, given the link between promoter hypermethylation and breast cancer.

The team delivered their designer methyltransferase and 26 guide gRNAs targeting the abovementioned promoters by transient transfection, where the term hit-and-run represents the temporary presence of their designer system in the edited cells. Here’s what they found:

  • A greater than 20% increase in the methylation of the target genes
    • The only decrease in gene expression caused by their construct occurs in CDKN2A transcripts
  • The edited cells are hyper-proliferative and evade senescence
    • However, the edited cells are not immortal and eventually enter cell cycle arrest through a different telomere-dependent mechanism
  • RNA-seq revealed altered gene expression profiles related to senescence
    • This subset of genes more closely resembles unmodified early passage cells
  • By breaking up their panel of targets to investigate different regions of single genes, the team discovered that the repression of p16, a CDKN2A transcript, drove the observed alterations

First author Emily Saunderson shares, “This has been an amazing project to work on as there isn’t really a rule book yet when it comes to epigenetic editing using CRISPR so we’ve been learning as we go. I think a key factor to the success of the project has been the combination of expertise from different groups.”

Senior author Gabriella Ficz concludes, “It’s surprising that cells from several healthy individuals are so permissive to gaining this epigenetic change and that one ‘hit’ from an epigenetic editing tool is sufficient to set off this chain reaction of epigenetic inheritance and establish a cancer cell-like gene expression signature. Epigenetic fluctuations happen all the time in our cells. We know that, during ageing, our epigenome is progressively distorted – so called ‘epigenetic drift’. It will therefore be exciting to find out if this drift is responsible for initiating or accelerating ageing-associated diseases. Age is the biggest risk in cancer so our work highlights the importance of understanding the mechanism behind epigenetic drift.”

Drift on over to Nature Communications, November 2017

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eBook: Key Chromatin Players | H3K27 http://epigenie.com/ebook-key-chromatin-players-h3k27/ http://epigenie.com/ebook-key-chromatin-players-h3k27/#respond Wed, 06 Dec 2017 18:38:51 +0000 http://epigenie.com/?p=26724 Histone H3 lysine 27 (H3K27) is one of the most studied histone modifications with a complex biological role. Trimethyaltion of K27 is a hallmark of repressed transcription, while acetylation is associated with active transcription. Recent work has supported these roles as well as provided evidence for novel functions.

This ebook covers the basics of H3K27 modifications, their role in transcription, and their broader significance in disease and development. Assembled here are summaries of various notable studies that examine H3K27 modifications in five broad categories.

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One-Carbon, One Long Life: Methyl Donors Linked to Longevity http://epigenie.com/one-carbon-one-long-life-methyl-donors-linked-longevity/ http://epigenie.com/one-carbon-one-long-life-methyl-donors-linked-longevity/#respond Wed, 22 Nov 2017 18:31:23 +0000 http://epigenie.com/?p=26715 While manipulating DNA methylation has taken up most of our lifespans, the manipulation of methyl donors critical to this process may just be the key to making up for the lost time.

During one-carbon metabolism, the essential amino acid methionine is metabolized into S-adenosylmethionine (SAM), a methyl donor responsible for DNA and histone methylation. Donation of the methyl group by SAM produces S-adenosylhomocysteine (SAH), which also acts as a feedback inhibitor for DNA methylation.

SAMTOR Senses SAM Levels for the mTOR Pathway

If the quest for longevity has your senses tingling, you are not alone, since Gu et al. from the lab of David Sabatini at MIT have just demonstrated how a crucial longevity pathway senses SAM levels.

The mTOR complex 1 (mTORC1) is an environmentally responsive regulator of cellular metabolism and growth that responds to nutrients. The amino acids leucine and arginine activate this pathway; however, a role for other amino acids has yet to be fully appreciated.

By making use of human embryonic kidney (HEK-293T) cells, the talented team characterized a previously unstudied protein that putatively interacts with key players of the pathway, which they termed SAMTOR (S-adenosylmethionine sensor upstream of mTORC1). Here’s what the team discovered:

  • True to its name, SAMTOR binds SAM and interacts with members of the mTORC1 pathway
  • SAMTOR inhibits the mTORC1 pathway upon methionine starvation
  • Methionine activation of mTORC1 signaling requires the SAM binding ability of SAMTOR, thus demonstrating that SAMTOR lets a cell know when there’s enough methionine via the mTORC1 pathway

Co-first author Jose Orozco shares, “People have been trying to figure out how methionine was sensed in cells for a really long time. I think that this is the first time in mammalian cells a mechanism has been found to describe the way methionine can regulate a major signaling pathway like mTOR.” Senior author David Sabatini adds, “There are a lot of similarities between the phenotypes of methionine restriction and mTOR inhibition. The existence of this protein SAMTOR provides some tantalizing data suggesting that those phenotypes may be mechanistically connected.”

Co-first author Xin Gu concludes, “It is very interesting to consider mechanistically how methionine restriction might be associated in multiple organisms with beneficial effects, and identification of this protein provides us a potential molecular handle to further investigate this question. The nutrient-sensing pathway upstream of mTOR is a very elegant system in terms of responding to the availability of certain nutrients with specific mechanisms to regulate cell growth. The currently known sensors raise some interesting questions about why cells evolved sensing mechanisms to these specific nutrients and how cells treat these nutrients differently.”

Interestingly, since low methionine diets increase lifespan in rodents, the authors speculate that SAMTOR might play a role in these benefits and believe that it may be possible to control SAMTOR function by pharmacologically targeting its SAM binding pocket.

Metformin Manipulates Mitochondrial One-Carbon Metabolism to Increase DNA Methylation

On the subject of pharmacological targeting, metformin is a drug commonly employed to treat type 2 diabetes, which also comes with an unexpected side effect: it promotes longevity in healthy individuals too. This unexpected beneficial effect appears to be due, in part, to the targeting of a number of important metabolic pathways, including mTOR. However, a new epigenetic mechanism has emerged thanks to Cuyàs et al. from the lab Javier Menéndez at the Catalan Institute of Oncology (Catalonia, Spain).

Here’s what the team uncovered when examining non-cancerous, cancer-prone, and metastatic cancer cells:

  • Metformin promotes global DNA hypermethylation, which includes LINE-1 retrotransposons, by decreasing SAH levels and increasing SAM levels
    • This hypermethylation may help counter the hypomethylation typically observed in cancerous cells
  • Making use of a mitochondria/complex I (mCI)-targeted analog of metformin (norMitoMet), the team established a critical connection between one-carbon metabolism in the mitochondria and the increase in nuclear DNA methylation
    • CRISPR/Cas9 knockout of a crucial component of mitochondrial complex I (part of the respiratory chain) blunted this effect, thus demonstrating a functional role for mitochondrial metabolism

The team concludes, “The induction of an energy crisis in the cell by inhibiting the respiratory chain of the mitochondria produces a decrease in the levels of SAH, the natural inhibitor of epigenetic writers. Simultaneously, metformin and its derivatives are also able to break the flow of methyl groups through mitochondria, which leads to the accumulation of SAM, the ink used by epigenetic writers.”

Longer Living Through Pharmacology

 Overall, these two studies offer up new mechanistic insight into how one-carbon metabolism shapes our lifespans. Furthermore, this new research also suggests that pharmacological targeting of key players in pathways that connect epigenetics and metabolism may one day lead us to the fountain of youth.

Go learn how to extend your lifespan over at Science, November 2017 and Oncogene, October 2017

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Visualizing CRISPR-Cas9 Genome Editing: Seeing is Believing! http://epigenie.com/visualizing-crispr-cas9-genome-editing-seeing-believing/ http://epigenie.com/visualizing-crispr-cas9-genome-editing-seeing-believing/#respond Wed, 22 Nov 2017 18:06:58 +0000 http://epigenie.com/?p=26708 Many studies have put their faith in CRISPR-Cas9 as a means to edit genes in human embryos, to fight HIV, and to explore epigenetic regulation. However, if you are someone who really needs to see CRISPR-Cas9 in action to believe it, an epic new study has you covered! So, cast away those doubts and qualms, and read on for news of the first direct visualization of CRISPR-Cas9 genome editing!

This breathtaking new study originates from the labs of Mikihiro Shibata (Kanazawa University, Japan),  Hiroshi Nishimasu, and Osamu Nureki (University of Tokyo, Japan) where researchers have employed high-speed atomic force microscopy (HS-AFM) to capture live action movies of CRISPR-Cas9 to delineate the exact mechanism of action for genome editing. Other related single-molecule imaging methods typically employ the detection of fluorescent-probe labels, rather than the direct visualization of the structures and dynamics of intact molecules at the nanometer scale afforded by HS-AFM.

Lights! Camera! Action! What did these astounding new movies divulge about the process of CRISPR-Cas9 genome editing?

  • Unexpectedly, Cas9 adopts a flexible modular architecture in the absence of a guide RNA (apo-Cas9)
    • However, the presence of guide RNA (Cas9-RNA) leads to the formation of a stable bi-lobed effector complex
    • This permits the interrogation of DNA target sites by three-dimensional diffusion rather than one-dimensional sliding
    • Recognition of the target site leads to the unwinding of double-stranded DNA to form a structure known as an R-loop, which consists of a RNA–DNA hybrid and the displaced non-target DNA strand
  • Real-time visualization of the Cas9-mediated DNA cleavage process demonstrates that the Cas9 HNH nuclease domain fluctuates between intermediate (I) and active docked (D) states upon DNA binding
    • Drastic structural transitions mediated by the docking of the HNH active site to the cleavage site in the target DNA (near the scissile phosphate of the target strand) lead to the formation of the catalytically-active docked conformation and cleavage of the target strand
    • Meanwhile, the RuvC nuclease domain cleaves the non-target strand

These astounding nanoscale movies of complex assembly, target search, and target cleavage are surely enough to make even the most ardent skeptic a CRISPR-Cas9 believer! As the researchers (or should we say directors?) note “this study provides unprecedented details about the functional dynamics of CRISPR-Cas9, and highlights the potential of HS-AFM to elucidate the action mechanisms of RNA-guided effector nucleases from distinct CRISPR-Cas systems.”

CRISPR-Cas9 in Action! (CC BY 4.0)

For CRISPR-Cas9 genome editing, seeing is believing; for all the details see Nature Communications, November 2017.

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dCas9 Shoots Down Microsatellite Repeat Expansion http://epigenie.com/dcas9-shoots-microsatellite-repeat-expansion/ http://epigenie.com/dcas9-shoots-microsatellite-repeat-expansion/#respond Wed, 22 Nov 2017 14:51:06 +0000 http://epigenie.com/?p=26692 Dealing with microsatellite disorders has been as difficult as shooting down actual satellites, but thanks to dCas9 its gotten a lot easier. The CRISPR/Cas9 system has proven to be much more than just a pair of scissors. For instance, CRISPR interference (CRISPRi) uses deactivated Cas9 (dCas9) to create site-specific steric hinderance to perturb gene expression. A new study from Eric Wang’s lab at the University of Florida examines several dCas9 approaches to treat repeat expansion disorders.

The talented has previously examined various approaches to treat conditions such as myotonic dystrophy, a muscle wasting disorder. Type 1 (DM1) is caused by a (CTG)n triple repeat expansion in DMPK 3’UTR, while type 2 (DM2) is caused by a (CCTG)n repeat expansion in CNBP intron 1. These expanded transcripts sequester specific proteins from their RNA targets leading to abnormal RNA splicing stability. Researchers believe that the efficiency of transcription through the expanded repeats is decreased relative to non-repetitive sequences. If this is true, further impairing the transcription of the expanded allele could effectively silence it. The authors attempted this by targeting the expanded alleles from various disorders in a repeat-length dependent manner using dCas9. This would result in premature RNA polymerase termination and nascent transcript turnover of the expanded allele, while leaving the normal allele unaffected.

To do this, the authors used dCas9 and various guide RNAs to target microsatellite repeat sequences for DM1, DM2, and other repeat disorders. They hypothesized that the dCas9 proteins bound to the repeat would be sufficient to block transcription. The team optimized this system by testing various guide RNA/PAM sequence pairs for efficacy in silencing repeats of increasing length expressed from plasmids.

Here’s what they found:

  • Using plasmids in HeLa cells, only 1 of the 4 guide RNA/PAM pairs tested reduced expression of the expanded allele, and did so in a repeat-length dependent manner. This was repeated when these repeats were incorporated into the Hela cell genome
  • Targeting of (CCTG)n repeat expansion also blocked expression of the expanded gene from a plasmid in
  • In DM1 patient-derived cell lines, dCas9 treatment rescued repeat expansion phenotypes including reducing toxic RNA foci, and rescued splicing deficits
  • Using an ex vivo muscle culture from a DM1 mouse model, dCas9 application led to a ~50% restoration of muscle function

The team found that the longer the repeat, the better the dCas9-based silencing worked. This allows the non-expanded allele to be expressed normally, a major challenge for other approaches. Going forward, systems such as this may be useful as gene therapy for repeat disorders where pathogenesis is dependent on very long repeat lengths.

Get the full message over at Molecular Cell, November 2017

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An endosiRNA Trap Shoots Down the Transposable Element Rebellion of Embryonic Development http://epigenie.com/endosirna-trap-shoots-transposable-element-rebellion-embryonic-development/ http://epigenie.com/endosirna-trap-shoots-transposable-element-rebellion-embryonic-development/#respond Sun, 12 Nov 2017 18:21:36 +0000 http://epigenie.com/?p=26674 During early embryonic development, our genome lets down its DNA methylation defenses and becomes vulnerable to rebellious transposable elements (TEs). However, those rebel scum are quickly met with a barrage of endogenous short interfering RNAs (endosiRNAs), all before they realize even realize that “It’s A Trap!

The mechanism of this cunning tactic employed by our imperial epigenomes was deciphered by the lab of Wolf Reik at the Babraham Institute (UK). Here’s what happened when the talented team probed mouse embryonic stem cells with a combination whole-genome bisulfite sequencing, total RNA-seq, small RNA-seq, and histone modification ChIP-seq:

  • To recapitulate a global wave of DNA demethylation, the team employed a conditional Dnmt1 knockout, observing a surge in sense and anti-sense transcription from the now hypomethylated TEs
    • Since there is an abundance of sense and antisense transcription, these transcripts can form double stranded RNA and induce an RNA interference (RNAi) response, where DICER will chop them up and generate endosiRNAs
  • Immunoprecipitation of ARGONAUTE2 (AGO2), a key part of the RNA-induced silencing complex followed by small RNA-seq revealed that AGO2 binds the endosiRNAs
  • Knockdown of either Dicer or Ago2 leads to an increase in TE expression over time, demonstrating that endosiRNAs bound by AGO2 are on a search and destroy mission for their host TE
  • There’s also a second line of defense, as ChIP-seq of H3K9me2, H3K9me3, and H3K27me3, which are associated with repression, revealed that chronic repression of TEs depends on these modifications

Overall, these findings describe how a surge in TE expression driven by global demethylation is given away by its antisense transcription, which then sets up a trap to slice and dice TE transcripts before they can wreak havoc. This quick-acting endosiRNA trap is also complemented in the long-term by repressive histone modifications.

First author Rebecca Berrens shares, “Epigenetic reprogramming plays a vital role in wiping the genome clean at the start of development, but it leaves our genes vulnerable. Understanding the arms race between our genes and transposon activity has been a long-running question in molecular biology. This is the first evidence that endosiRNAs moderate transposon activity during DNA demethylation. EndosiRNAs provide a first line of defence against transposons during epigenetic reprogramming.”

Senior Author Wolf Reik concludes, “Transposons make up a large part of our genome and keeping them under control is vital for survival. If left unchecked their ability to move around the genome could cause extensive genetic damage. Understanding transposons helps us to make sense of what happens when they become active and whether there is anything we can do to prevent it.”

Go fall into this trap over at Cell Stem Cell, November 2017

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Base Resolution Profiling Details the Intricacies of the m1A RNA Modification http://epigenie.com/base-resolution-profiling-details-intricacies-m1a-rna-modification/ http://epigenie.com/base-resolution-profiling-details-intricacies-m1a-rna-modification/#respond Sat, 04 Nov 2017 08:34:48 +0000 http://epigenie.com/?p=26669 Insurance contracts, loan agreements, and scientific studies; while it’s easy to pretend that we know what´s going on after a quick skim, we often require a detailed interpretation of the complex combinations of letters, numbers, symbols, and accents to gain a fuller comprehension of the matter at hand.

In the realm of our epitranscriptomic language, years of research has uncovered a range of RNA modifications, including N1-methyladenosine (m1A), that gladly complicate our comprehension. To decipher the complex meaning of the epitranscriptome, studies have employed a plethora of advanced techniques to profile the location and abundance of epitranscriptomic modifications and delineate regulatory pathways. A study using quantitative mass spectrometry (LC-MS/MS) and methylated RNA immunoprecipitation sequencing (MeRIP-seq) obtained a “ball-park” idea of m1A abundance and location, and when combined with other findings, led to the understanding that the m1A modification maintains the structure and function of non-coding RNA (ncRNA) and messenger RNA (mRNA) and promotes translation.

To assess the precise location and further decipher the regulation of m1A, researchers from the laboratory of Chengqi Yi (Peking University, Beijing, China) now describe an intricate new approach: single-base resolution misincorporation-assisted profiling of m1A, or m1A-MAP.

Employing this new technique, Li et al. analyzed the location of m1A throughout the transcriptome of human embryonic kidney cells (HEK293T) and discovered that:

  • Of 740 m1A modifications detected, 473 sites locate to mRNAs and lncRNAs
    • The majority of m1A occurs in the 5′ untranslated region (UTR) and correlates to increased translation efficiency
  • m1A also labels a small subset (53) of transfer RNA (tRNA)-like sites, which are evenly distributed in the transcriptome and require transfer RNA methyltransferase activity (TRMT6/61A)
  • Additionally, mitochondrial-encoded transcripts also display enrichment for m1A
    • For these mitochondrial mRNAs, m1A in the coding sequence inhibits translation
    • Manipulation of m1A levels via a mitochondrial m1A methyltransferase (TRMT61B) confirmed that m1A interferes with translation of mitochondrial mRNA

The authors hope that this intricate and highly detailed study will provide a highly useful resource towards deciphering the specificities behind the m1A modification of mRNA.

To further your understanding of the meaning of m1A in our epitranscriptomic language, read the full story over at Molecular Cell, October 2017.

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High-Resolution Hi-C Delivers High-End Chromatin Conformation Maps of Neural Development http://epigenie.com/hi-resolution-hi-c-delivers-high-end-chromatin-conformation-maps-neural-development/ http://epigenie.com/hi-resolution-hi-c-delivers-high-end-chromatin-conformation-maps-neural-development/#respond Thu, 02 Nov 2017 19:28:05 +0000 http://epigenie.com/?p=26663 Hi-C-based three-dimensional chromatin conformation analysis is currently living the high-life, with multiple high-impact studies recently employing this high-flying molecular technique to gain new insight into the cell cycle, fertilization, and reprogramming.

Now, researchers under the high command of Boyan Bonev and Giacomo Cavalli (Université de Montpellier, France) have applied this high-class technique to understand how the spatial proximity of functional chromatin elements relates to gene expression and cell fate via the creation of high-resolution Hi-C maps of neural cell differentiation.

And when we say high-resolution, we mean high-resolution! The authors sequenced over 40 billion paired-end reads, resulting in around 17 billion uniquely mapped contacts derived from sorted mouse embryonic stem cells (ESCs) and ESC-derived neural progenitor cells (NPCs) and cortical neurons to act as a model of sequential neuronal differentiation in vitro (See Figure).

This high-fidelity dataset facilitated the creation of high-end 3D chromatin conformation maps at a maximum resolution of 750 bp, the highest of any reported study. The authors then correlated these findings with chromatin modification analysis (ChIP-Seq and reappraisals of ENCODE datasets) and RNA sequencing (RNA-Seq) to explore the relationship between gene expression, the epigenome, and 3D genome conformation.

So what did this high-resolution Hi-C analysis tell these highly motivated researchers?

  • In vitro modelled neural development led to the dynamic global reorganization of chromatin interactions
    • Topologically associating domains (TADs) reduced in number but increased in size
    • The number of long-range active domain (A) interactions decreased, while the number of inactive domain (B) interactions increased
    • Strong polycomb-mediated interactions present in ESCs destabilized
  • Gene transcription highly correlated to chromatin domain insulation and long-range interactions
    • All cell types exhibited long-range contacts between different active gene promoters and also between the bodies of different exon-rich active genes
    • TAD boundary formation at or close to active gene promoters also increased during differentiation suggesting that novel borders can form at the promoters of developmentally regulated genes
  • In vivo analysis of neural development via the purification of NPCs and cortical neurons from the mouse neocortex (∼3 billion uniquely aligned contacts per cell type) also demonstrated global chromatin reorganization
    • Neural transcription factors mediate dynamic and cell-type specific enhancer-promoter interactions that are constrained by TADs
    • These interactions are established concomitantly with gene expression and become disrupted following gene repression

Overall, this remarkably high-resolution high-impact study represents a treasure trove of data concerning how three-dimension chromatin conformation changes during neural differentiation and how this correlates to gene expression and in vivo function.

To gain a high-resolution view of this new Hi-C study, get off your high horse (!) and head over to Molecular Cell, October 2017.

Schematic representation of the in vitro neural differentiation system (CC BY 4.0)

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