EpiGenie | Epigenetics, Stem Cell, and Synthetic Biology News http://epigenie.com Scientific News, Technology, and Product Information Tue, 20 Feb 2018 17:01:20 +0000 en-US hourly 1 https://wordpress.org/?v=4.9.4 DNA Methylation Links Prenatal Famine Exposure to Adulthood Metabolic Conditions 6 Decades Later! http://epigenie.com/dna-methylation-links-prenatal-famine-exposure-adulthood-metabolic-conditions-6-decades-later/ http://epigenie.com/dna-methylation-links-prenatal-famine-exposure-adulthood-metabolic-conditions-6-decades-later/#respond Sun, 18 Feb 2018 19:51:34 +0000 http://epigenie.com/?p=26816 Researchers from Leiden University Medical Center in the Netherlands are back at it again: studying the long-term epigenetic effects of prenatal famine utilizing the Dutch Hunger Winter Cohort. The Dutch Hunger Winter was a famine that devastated the Netherlands in the winter of 1944-1945 amidst WWII, which produced a cohort that were in utero during this time frame, allowing for a population study of prenatal famine. Those individuals exposed to prenatal famine were found to be at a higher risk for malignant metabolic phenotypes as adults.

History lesson aside, previous work from the lab identified differentially methylated regions in adult individuals exposed to prenatal famine. Now, they have taken it one step further to more definitively identify DNA methylation as the link to adulthood metabolic conditions. Here, the talented team utilized Illumina’s 450K BeadChip array to screen over 450,000 methylation sites from whole-blood samples of 422 famine cohort members and 463 sibling controls to identify specific CpG sites associated with both prenatal famine and adult metabolic phenotypes. Mediation analysis was then used to determine the extent to which DNA methylation mediated the link between prenatal famine and adult outcome.

In their quest to find CpG sites linking prenatal famine to both BMI and serum triglyceride levels in adults, the talented team discovered that:

  • A single CpG site mediates 13.4% of the relationship between prenatal famine and adulthood BMI
    • Methylation at this CpG site is associated with PIM3 expression, which is involved in energy metabolism and glucose stimulated insulin secretion
  • Six CpG sites mediate the relationship between prenatal famine and serum triglycerides
    • Aggregately, these six sites mediate 80% of the relationship
    • Methylation at the various identified CpG sites is associated with expression of the nearby genes including TXNIP, which is associated with β cell function and insulin production
  • Focused analysis of those exposed to famine during early gestation (1-10 weeks) revealed two additional CpG sites linked to serum triglycerides, at PFKFB3 and METTL8 introns
    • These two sites account for 36.3% of the relationship between early exposure to prenatal famine and serum triglyceride levels
    • PFKFB3 and METTL8 are involved in glycolysis and adipogenesis, respectively

This work establishes DNA methylation as the link between prenatal famine and adulthood metabolic conditions. Co-senior author Bastiaan Heijmans concludes that “the nine genes we found are compelling candidates to explain the link between the prenatal environment and adult health. Now we need functional studies to unravel how an altered epigenetic regulation of these genes could impinge on metabolism in the long run.”

Although it may seem grim to consider that such adulthood phenotypes are being influenced from the earliest weeks of development, Heijmans added an optimistic note: “I hope that epigenetic studies like ours will at some point allow doctors to detect and treat health risks well before the development of disease.”

To learn more about the epigenetics involved in prenatal famine, click over to the full article in Science Advances, January 2018.

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Oh Sugar! Gestational Fructose Exposure Linked to Long-Term Brain DNA Methylation Changes http://epigenie.com/oh-sugar-gestational-fructose-exposure-linked-long-term-brain-dna-methylation-changes/ http://epigenie.com/oh-sugar-gestational-fructose-exposure-linked-long-term-brain-dna-methylation-changes/#respond Fri, 16 Feb 2018 19:02:47 +0000 http://epigenie.com/?p=26810 Here at EpiGenie, we don’t like to sugar-coat our headlines. The sickly-sweet truth is that fructose can be pretty bad for your health. Fructose has become a common additive in many foods in the form of high-fructose corn syrup. Sugary drinks are one of the most common forms. Heavy soft drink consumption is linked to heart disease, stroke, diabetes, and cognitive decline. However, the gestational effect of high fructose consumption remains unclear.

Koji Ohashi’s group at Tottori University (Japan) wanted to investigate whether gestational fructose had long-term epigenetic consequences in the brain. This group previously showed that in rats, excess maternal fructose consumption alters hippocampal gene expression in offspring. Others have shown that excess maternal fructose consumption impairs hippocampal-dependent learning and memory. However, no previous study has examined the role of epigenetics in mediating these effects. Ohashi’s group focused on the hippocampus, since it is known to be highly sensitive to prenatal/early life stress. Environmental stress and malnutrition can cause inflammation, apoptosis, and reduced levels of neurotrophic factors resulting in decreased hippocampal neurogenesis. The authors hypothesised that a maternal high fructose diet would result in altered brain-derived neurotrophic factor (Bdnf) expression & methylation, reduced neurogenesis, and impaired hippocampal-dependent learning in offspring. They provided rats with access 20% fructose or 20% glucose compared to a water control during gestation and lactation.

Here’s what they found when examining juvenile (day 21) and adult (day 60) offspring:

  • High fructose offspring spend significantly less time exploring a novel object than either other group as adults, suggesting impaired learning
  • Similarly, in a fear conditioning task, the high fructose offspring exhibit less freezing behavior in the contextual task than either other group, but there are no differences in the auditory-cued fear memory task, implying impaired hippocampal- but not amygdala-dependent learning
  • High fructose offspring (but not glucose) have 20% fewer BrdU/NeuN hippocampal neurons, while there is no significant difference in apoptosis, suggesting reduced neurogenesis
  • qPCR revealed that the BDNF gene expression was reduced in high fructose (but not glucose) juvenile offspring but only in high fructose males at adulthood
  • Pyrosequencing uncovered that the CREB binding site in the Bdnf promoter is hypermethylated in juvenile and adult male fructose-exposed offspring. A luciferase assay showed that deletion of the affected CG sites affects BDNF gene expression, suggesting a functional relationship

Taken together, the findings demonstrate that gestational fructose leads to long-term changes in the epigenetic regulation of Bdnf, which lead to decreased cognitive performance and reduced adult hippocampal neurogenesis. If high gestational fructose acts as an epigenetic disruptor of neurogenesis, it would add yet another entry to the long list of reasons to be sure as sugar to avoid it.

Catch the rest of this sugar rush over at FASEB, January 2018


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Epigenetic Aging Analysis Suggests That TERT Isn´t the Anti-aging Target You Are Looking For! http://epigenie.com/epigenetic-aging-analysis-suggests-tert-isnt-anti-aging-target-looking/ http://epigenie.com/epigenetic-aging-analysis-suggests-tert-isnt-anti-aging-target-looking/#respond Tue, 13 Feb 2018 18:11:21 +0000 http://epigenie.com/?p=26808 This isn’t some sort of Jedi mind trick, we promise, but TERT may not be the anti-aging target you are looking for! TERT, or telomerase reverse transcriptase, plays an essential role in the elongation and maintenance of telomeres and as telomeres shorten with age, many surmise that activation of TERT represents an exciting approach to stave off the signs of aging.

However, a recent study from a multidisciplinary team of padawans and apprentices led by the Jedi Masters Ken K. Ong, Kenneth Raj, Kathryn L. Lunetta, and Steve Horvath has now established that longer telomeres do not correlate to younger biological age as measured by the DNA methylation level of select CpGs on the 450K array, a measure known as the epigenetic clock. Of note, individuals exhibiting an epigenetic age older than their chronological age display a higher risk of all-cause mortality, while the children of parents who reach over 100 years of age generally exhibit a younger epigenetic age.

Here are the details of this fascinating new study:

  • The authors undertook a genome wide association study (GWAS) of white blood cells from around 10,000 individuals to discover genetic variants associated with accelerated epigenetic aging
    • 5 loci correlated to intrinsic epigenetic age acceleration (IEAA), a measure based on 353 CpGs that is independent of age-related changes in blood cell composition
    • 3 loci correlated to extrinsic epigenetic age acceleration (EEAA), a measure based on 71 CpGs that takes the contribution of blood cell composition into consideration
  • Interestingly, one loci associated with IEAA mapped to the TERT gene
    • This finding associates accelerated epigenetic aging with telomere elongation/longer telomeres, an unexpected outcome
    • In vitro analysis confirmed that TERT expression in human primary fibroblast cells leads to increased epigenetic aging, which studies have linked to multiple detrimental signs of aging
  • Mendelian randomization analyses also revealed that age of onset of first menstruation (menarche) and menopause have causal effects on IEAA

Co-author Douglas P. Kiel provides some more thoughts, “TERT is a subunit of the enzyme telomerase, which is a widely known enzyme because it has been touted as an anti-aging enzyme. It has been called a modern fountain of youth. However, some scientists have pointed out that it is unlikely to become a source of anti-aging therapies. Our study highlights the error in the notion that activation of telomerase (as advocated by some) will cure aging. Instead, our study shows that an anti-aging therapy based on telomerase expression would be accompanied by continued aging.”

For a more in-depth look for the data you are most definitely looking for, take your speeder over to Nature Communications, January 2018.

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Epigenetic Editing Misses the Mark: dCas9-DNMT3A Causes Off-Target Genome-Wide DNA Hypermethylation http://epigenie.com/epigenetic-editing-misses-mark-dcas9-dnmt3a-causes-off-target-genome-wide-dna-hypermethylation/ http://epigenie.com/epigenetic-editing-misses-mark-dcas9-dnmt3a-causes-off-target-genome-wide-dna-hypermethylation/#respond Mon, 12 Feb 2018 20:17:04 +0000 http://epigenie.com/?p=26805 While we’ve been captivated by the powerful applications of precision epigenetic editing via deactivated Cas9 (dCas9), we’ve also been mesmerized by the fact that epigenetic editing doesn’t always work as expected. Building on our need to take a step back and look at the bigger picture, new findings from the lab of Alexander Meissner at the Max Planck Institute for Molecular Genetics (Germany) demonstrate that epigenetic editing leaves a mark not only on target loci but also the whole-genome.

To understand the off-target effects specific to epigenetic editing systems, the talented team employed engineered mouse embryonic stem cells (mESCs) to track de novo methylation following epigenetic editing. This mESC model contains a double knockout for the de novo methyltransferases (DNMT3A & DNMT3B) as well as a transiently repressed maintenance methyltransferase (DNMT1). Therefore, their system is depleted of methylation but maintains de novo methylation caused by epigenetic editing, all without the interference of endogenous de novo methyltransferases or a highly methylated genome. Finally, the group utilized dCas9 fused to the catalytic domain of DNMT3A (dCas9-DNMT3A) to introduce de novo methylation.

Here’s what they discovered:

  • Whole-genome bisulfite sequencing uncovered that dCas9-DNMT3A leads to a rapid and global increase in DNA methylation levels (16% on Day 0, 28% on day 2, and 47% on day 7; 83% in wild-type)
    • This increase tends to occur at sites highly methylated in wild type mESCs and not in regions marked with H3K4me3 that are protected from methylation
  • Targeted bisulfite sequencing of the 20kb up- and down-stream of sgRNA target sites revealed that the addition of a single or multiple sgRNAs does not prevent the global increases in methylation
    • Interestingly, the target sites for some sgRNAs also exhibit increased methylation in the presence of dCas9-DNMT3A alone, demonstrating that the off-target effects can create a background signal that may appear as an on-target effect without this control
  • The introduction of the DNMT3A catalytic domain on its (not fused to dCas9) yields a similar global effect to dCas9-DNMT3A
  • Transient transfection of human somatic cell lines (human embryonic kidney [293T] and human breast adenocarcinoma [MCF7]) also generates off-target methylation

Overall, these findings provide some much-needed insight into the unique considerations of designing and interpreting epigenetic editing studies. The study also leaves us wondering whether the global off-target effects occur with designer DNA methylation systems, such as dCas9-Dnmt3a-Dnmt3L or dCas9-SunTag-DNMT3A, as well as the suite of other epigenetic effector domains that can be coupled with dCas9.

Set your sights off target over at Nature Communications, February 2018

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SunTag Casts Light on iPSC Reprogramming http://epigenie.com/suntag-helps-cast-light-ipsc-reprogramming/ http://epigenie.com/suntag-helps-cast-light-ipsc-reprogramming/#respond Tue, 06 Feb 2018 19:58:13 +0000 http://epigenie.com/?p=26796 While the DNA editing function of CRISPR/Cas9 systems may appear to hog the limelight, we believe that a new SunTag approach for CRISPR/Cas9-mediated induced pluripotent stem cell (iPSC) reprogramming via epigenome editing deserves its day in the sun!

The exciting reprogramming strategy utilizes an endonuclease dead Cas9 (dCas9) fused to a repetitive protein scaffold known as SunTag, which recruits multiple copies of effector domains fused to antibodies that recognize SunTag. Previous studies have employed this advanced strategy to edit the epigenome by promoting either DNA methylation or DNA demethylation via DNMT3A or TET1 effector domains, respectively.

Now, researchers from the lab of Sheng Ding (J. David Gladstone Institutes, San Francisco, USA) have promoted chromatin remodeling and gene expression of pluripotency-associated genes via the SunTag approach using the VP64 transcriptional activation domain or the core histone acetyltransferase (HAT) domain of p300 (p300core); a strategy known as “CRISPR activation”.

The team took to this approach to cast some light on the mechanisms controlling the reprogramming of somatic cells to iPSCs, but also in the hope of crafting a more efficient and effective reprogramming protocol. The classical methods employed to generate iPSCs exploit the forced expression of multiple transcription factors, which can obscure the sequential mechanisms at play during the acquisition of pluripotency.

Let´s delve into the highlights of this new study, which employed mouse embryonic fibroblasts (MEFs) as the target cell type:

  • CRISPR activation employing dCas9-SunTag-VP64 targeted and remodeled the endogenous Oct4 and Sox2 pluripotency-associated gene loci using single guide RNAs specific for regulatory sequences
    • Unexpectedly, the single act of remodeling the previously silenced Sox2 promoter triggered the expression of other pluripotency-associated genes in MEFS and permitted the establishment of the pluripotency network
    • Remodeling of the Oct4 promoter and enhancer also promoted the establishment of the pluripotency network in MEFs
    • Both these scenarios permitted the generation of karyotypically-normal fully pluripotent iPSC lines, as evidenced by the ability of iPSCs to contribute to chimeric animals
  • Excitingly, targeting dCas9-SunTag-p300core to the endogenous Oct4 gene promoter and enhancer promoted histone acetylation and the initiation of reprogramming
    • However, the authors noted a noticeable latency in transcriptional activation for the p300core domain when compared to VP64

Ding himself notes that “This is a new way to make induced pluripotent stem cells that is fundamentally different from how they’ve been created before. At the beginning of the study, we didn’t think this would work, but we wanted to at least try to answer the question: can you reprogram a cell just by unlocking a specific location of the genome? And the answer is yes.”

He continues, “Having different options to make iPSCs will be useful when scientists encounter challenges or difficulties with one approach. Our approach could lead to a simpler method of creating iPSCs or could be used to directly reprogram skin cells into other cell types, such as heart cells or brain cells. The fact that modulating one site is sufficient is very surprising. Now, we want to understand how this whole process spreads from a single location to the entire genome.”

Can SunTag shed some light on your iPSC research? Try switching on that table lamp and reading all the details concerning this new study over at Cell Stem Cell, February 2018.

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Like a Fine Wine, Histone Variant H2A.Z Represses Memories and Accumulates with Age! http://epigenie.com/like-fine-wine-histone-variant-h2a-z-represses-memories-accumulates-age/ http://epigenie.com/like-fine-wine-histone-variant-h2a-z-represses-memories-accumulates-age/#respond Tue, 06 Feb 2018 19:40:28 +0000 http://epigenie.com/?p=26793 While aging works wonders for the taste of our ever-accumulating wine collection, the passage of the years is not as kind to our memories! To fully decipher the processes underlying learning and memory differences in the aging brain, the lab of Iva Zovkic at the University of Toronto Mississauga (Canada) recently expanded on past work into the role of histone variant H2A.Z in the suppression of memories. In their latest report, the team examined the differences in H2A.Z deposition in a brain region critical to memory formation (hippocampus) between young (4 months) and “middle-aged” (15.5 months) mice.

Here’s what they learned about H2A.Z via ChIP-seq:

  • H2A.Z enrichment occurs at gene bodies and promoters, with a stronger enrichment at promoters
    • CpG islands that flank transcription start sites, and thus exhibit low levels of DNA methylation, display significant H2A.Z enrichment
  • Steady-state (basal) H2A.Z levels increase with age at genes involved in transcriptional regulation and the ubiquitin proteasome system
    • H2A.Z is a replication independent histone variant, which allows its levels to build up with age in the brain’s post-mitotic neurons
  • H2A.Z eviction occurs in response to learning via contextual fear conditioning, regardless of age
    • However, despite similar levels of memory formation, aged mice show a reduced H2A.Z eviction response
    • While there is a trend for the same genes to be affected, eviction is most prominent and significant at different genes between the ages
  • Integration of the H2A.Z peaks with RNA-seq gene expression data revealed a positive association between H2A.Z levels and basal transcription levels, but a negative association with learning induced transcription
    • H2A.Z removal induces gene expression
  • By employing an adeno-associated virus (AAV) to deliver an shRNA that depletes H2A.Z, the team observed an effect on the learning induced expression of select genes
    • There was only a minimal effect on basal gene expression levels

Zovkic shares, “We have thousands of experiences each day, but we only remember things that are in some way important to us. This experiment used a very straightforward learning experience to illustrate that H2A.Z apparently serves to suppress memory, and the removal of this protein appears to…allow long-lasting memories to form.”

“We’re always trying to find molecular bases for memory, and discovering how genes related to memory are turned on and off is a step in a positive direction. Identifying H2A.Z as a unique protein that is involved with memory and increases with aging could be a big deal for creating genetic or pharmaceutical therapies for age-related cognitive decline and dementia. H2A.Z is a relatively specific therapeutic target.”

Evict the rest of your brain’s H2A.Z over at Cell Reports, January 2018

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Epigenetic and Mitochondrial Clocks Synchronously Accelerate with Bipolar Disorder http://epigenie.com/epigenetic-mitochondrial-clocks-synchronously-accelerate-bipolar-disorder/ http://epigenie.com/epigenetic-mitochondrial-clocks-synchronously-accelerate-bipolar-disorder/#respond Thu, 18 Jan 2018 19:22:42 +0000 http://epigenie.com/?p=26783 A wise man once said that time is relative, and while physics was on his mind, it seems that biology should have been as well. For instance, patients with bipolar disorder suffer from accelerated aging. However, examinations of telomere length have given mixed results, and this inspired the lab of Joao Quevedo in the University of Texas Health Science Center at Houston to set their gaze on the epigenetic clock and mitochondrial DNA copy number.

The group recruited 22 patients with bipolar disorder, 16 of their siblings, and 20 matched controls and examined their peripheral blood. In addition to analyzing the epigenetic clock via the 450k DNA methylation array, the group also interrogated other biological clocks (telomere length and mitochondrial DNA copy number) via qPCR.

Here’s what they discovered:

  • Older (>33 years old) bipolar disorder patients display both accelerated epigenetic aging and increased mitochondrial DNA copy number
    • However, they did not observe the same pattern in younger patients
  • Epigenetic age correlates with mitochondrial DNA copy number in older patients
  • Telomere length shows no significant difference in bipolar patients
    • Telomere length also shows no correlation with the two other biological clocks

Epigenetic Clock Cross-Talk

First author Gabriel Fries shares, “The epigenetic acceleration correlated with the number of copies of mitochondrial DNA, suggesting that the cross-talk between the nucleus and the mitochondria might be underlying the premature aging in bipolar disorder.” Interestingly, this correlation may arise with a little help from the 5% (17 of 353) of the epigenetic clock’s CpGs that map to nuclear-encoded mitochondrial genes.

However, the mechanistic potential doesn’t end there. 24% (85) of the epigenetic clock’s CpGs locate to glucocorticoid response elements, which are critical to stress response. Fries concludes, “We believe a difference wasn’t detected in younger patients because they haven’t had as much exposure to stressful events. This gave us a hint that cumulative chronic exposure to stress would relate to accelerated aging. We would see it more in older people who have experienced a lifetime of stress in dealing with the disease.”

Catch all the epigenetic cross-talk over at Translational Psychiatry, December 2017

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H3K4 Mono-Methylation Means More at Most Enhancers http://epigenie.com/h3k4-mono-methylation-means-enhancers/ http://epigenie.com/h3k4-mono-methylation-means-enhancers/#respond Tue, 16 Jan 2018 23:36:00 +0000 http://epigenie.com/?p=26778 People can have some pretty strange tastes. From mayonnaise on fries to syrup on spaghetti, there’s no accounting for personal preference. Proteins can have some interesting preferences too, where some regions of the genome look better than others. To get at these preferences, a recent publication from the Laboratory of Bing Ren at UC San Diego sought to find the histone modification tastes of proteins that prefer to bind enhancers.

Enhancers upregulate specific genes during development, but we’re still unclear on exactly how they work. Mono-methylation of lysine 4 on histone H3 (H3K4me1) is a dynamic modification that specifically marks both active and primed enhancers, while trimethylation (H3K4me3) marks promoters. The presence of H3K4me1 has been used to generate enhancer maps. However, the actual mechanistic role of H3K4me1 at enhancers remains unclear. H3K4me1/3 are both suspected to recruit chromatin modifiers/transcription factors, but identifying enhancer-specific proteins preferring H3K4me1 over H3K4me3 is no easy task.

With that goal in mind, the talented team sought to identify H3K4me1-associated proteins and their binding characteristics at enhancers. The group used SILAC (Stable Isotope Labeling by Amino acids in Cell culture) to label all proteins in HeLa cell nuclear extract prior to pull down with either H3K4me1- or H3K4me3-marked nucleosomes. By using heavy isotopes for one methylation state and light for the other, they were able to identify putative H3K4me1-prefering proteins with differential abundance in each pull down.. They also used various ChIP-seq and X-ray crystallography experiments in mouse embryonic stem cells (mESCs) to validate their findings.

Using these approaches, they found that:

  • A subset of proteins prefer binding to H3K4me1 over H3K4me3, including known enhancer-associated chromatin modifiers such as BAF (SWI/SNF) complex members
  • Knockout of the H3K4me1-specific methyltransferases KMT2C and KMT2D in mESCs result in dramatic reduction of H3K4me1 and several known chromatin modifiers at the same loci, but not H3K4me3
  • Catalytic inactivation of KMT2C/2D results in fewer changes in H3K4me1, but regions that do lose methylation also lose specific chromatin modifiers
  • Using a nucleosome remodeling assay, they found that H3K4me1-marked nucleosomes were more efficiently remodeled by the BAF complex
  • After solving the crystal structure of a specific BAF protein (BAF45C), they found that it may prefer H3K4me1 over H3K4me3 due to a small binding pocket that could not accommodate H3K4 tri- or di-methylation.

Overall, this work suggests that H3K4me1, but not H3K4me3, has an active role in recruiting the BAF complex and other chromatin modifiers to enhancers. This binding is likely important during development and differentiation. Follow up on the other proteins identified in this paper may provide further insight into enhancer function, which is still not well understood. So just like people, finding out a protein’s preferences can really help you get to know them.

Check out the full article at Nature Genetics, January 2018

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Single-Cell DNA Methylomes Reveal the Reprograming Secrets of Early Human Embryos http://epigenie.com/single-cell-dna-methylomes-reveal-reprograming-secrets-early-human-embryos/ http://epigenie.com/single-cell-dna-methylomes-reveal-reprograming-secrets-early-human-embryos/#respond Tue, 16 Jan 2018 19:05:24 +0000 http://epigenie.com/?p=26774 You’ve heard before that timing is everything, and this is doubly true in developmental biology. New research out of Fuchou Tang’s lab (Peking University, Beijing) singles in on the timing of methylation changes during embryonic development, and exposes the delicate epigenetic dance of global demethylation and targeted remethylation.

Tang’s lab is no stranger to embryonic epigenetics, previously reporting on the DNA methylation landscape in early embryos. Now this talented lab team made use of post-bisulfite adaptor tagging (PBAT) to perform whole-genome bisulfite sequencing of individual cells in human preimplantation embryos. Using this technique in euploid embryos, they interrogated changes in the genome-wide methylation status throughout pre-implantation development and early post-implantation. Additionally, they compared methylation patterns of the maternal and paternal genomes from the sperm and oocyte stages onward.

These ambitious authors analyzed over 6.5 Tb of sequencing data covering 10.8 million CpG sites to reveal the following:

  • In the preimplantation embryo, there are three major demethylation waves interspersed with two periods of de novo methylation
    • Extensive global demethylation occurs at 10-12 hours post-fertilization, the late zygote to two-cell stage, and the eight-cell to morula stage. While the first wave of demethylation occurs mostly at enhancer and gene body regions, the second two waves are primarily at introns and SINEs
    • Widespread de novo methylation occurs at the male pro-nuclear stage and the four-cell to eight-cell stage; these sites are enriched for families of repetitive elements (SINEs, LINEs, LTRs)
    • Sites of de novo methylation sites are often demethylated in subsequent developmental stages
  • Throughout the global methylation changes, the paternal genome is demethylated faster and more completely than the maternal genome
    • This does not appear to be related to genomic imprinting
  • Differentially methylated regions (DMRs) in oocytes are enriched at CpG islands, gene promoters, and SINEs, whereas the sperm DMRs are enriched in somatic-cell-specific enhancers and SINEs
  • DNA methylation is asymmetrically inherited during cell division, allowing blastomeres at the four-cell stage to be traced back to the parental cell

Overall, this work highlights the epigenetic intricacies in a developing embryo: the balance between demethylation of inherited parental sites and de novo methylation, as well as a unique timing component.

To see how the story develops further, check out Nature Genetics, January 2018

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YY1 Drives Enhancers and Promoters Loopy! http://epigenie.com/yy1-drives-enhancers-promoters-loopy/ http://epigenie.com/yy1-drives-enhancers-promoters-loopy/#respond Mon, 15 Jan 2018 09:01:54 +0000 http://epigenie.com/?p=26771 Cell culture hood in disarray? Favorite coffee cup missing? Internet running slow? What exactly drives you loopy in the laboratory?! Recently, the lab of Richard A. Young (Whitehead Institute for Biomedical Research, Cambridge, USA) has been driven round the bend in their quest to understand what controls the DNA looping process that brings together enhancers and promoters for gene regulation purposes. Thankfully (for them!), their new findings bring some much-needed harmony that firmly establishes the Yin Yang 1 (YY1) GLI-Kruppel zinc finger transcription factor as a driving force behind the loopy behavior of genes in mammalian cells!

Luckily, Weintraub and colleagues intended to keep us all in the loop:

  • Chromatin immunoprecipitation mass spectrometry (ChIP-MS) with antibodies for specific histone modifications (H3K27ac for active enhancers, H3K4me3 for active promoters) first identified YY1 as a potential mediator of DNA looping
    • CRISPR cell-essentiality screens and chromatin interaction analysis by paired-end tag sequencing (ChIA-PET) confirmed a role for YY1 in DNA looping
    • YY1 is expressed in the majority of tissues and YY1 enhancer/promoter occupation occurs in all cell types examined
    • HiChIP analysis (a protein-centric chromatin conformation method) demonstrated that YY1 occupies sites of enhancer-promoter interactions
  • YY1 structurally regulates enhancer-promoter interaction by binding to hypomethylated DNA and then preferentially forming YY1 homodimers to generate DNA loops
    • YY1-mediated looping facilitates the expression of associated genes
    • The process appears similar to CTCF-mediated DNA looping, although CTCF binds to sites distal from enhancers and promoters to form larger loops involved in chromatin insulation
    • YY1 mediated enhancer-promoter loops tend to take shape within the larger CTCF-mediated loops
  • CRISPR-mediated deletion of YY1 binding sites or depletion of YY1 protein disrupted enhancer-promoter contact and associated gene expression
    • Previous reports combined with these findings establish a requirement for YY1 for embryonic and adult cell viability

Overall, the authors suggest that this newly discovered role for YY1 accounts for previously reported diverse functions (including gene expression changes in cancer) and almost certainly represents a general feature of mammalian gene control.

Have you been driven crazy by this exciting new study? Then keep yourself “in the loop” over at Cell, December 2017.

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