表观遗传学、干细胞和合成生物学新闻亚博赞助阿根廷亚博博彩 https://epienie.com网站 科学新闻、技术和产品信息亚博pc 2020年3月4日星期三07:03:06+0000 在美国 每小时 1个 https://wordpress.org/?v=5.3.2 dCas9-ROS1切断靶向DNA去甲基化的甲基化中间分子 //www.sogroupadmin.com/dcas9-ros1-cuts-out-the-methylation-middlemen-in-targeted-dna-demethylation/ //www.sogroupadmin.com/dcas9-ros1-cuts-out-the-methylation-middlemen-in-targeted-dna-demethylation/#应答 2020年3月3日星期二17:05:04+0000 凯瑟琳·维尔兰科特 DNA甲基化 表观遗传学 标题 5-羧胞嘧啶 5-甲酰胞嘧啶 5-羟甲基胞嘧啶 5立方厘米 5立方英尺 5立方厘米 5毫升 染色质 Crispr-cas9系列 去甲基化 表观基因组编辑 绿色荧光粉 HEK293型 荧光素酶 甲基化 罗斯1 泰特 http://epienie.com/?p=28318个 俗话说,从A到B的最短路径是一条直线,如果你在研究DNA去甲基化,你就知道从甲基化到非甲基化的胞嘧啶这条路有多么复杂。哺乳动物使用10-11个易位蛋白(TET)和#160;来氧化5mC,但是这个过程会产生可能是…;]

As the saying goes, the shortest path from A to B is a straight line and if you’re studying DNA demethylation, you know just how complicated things can get along the road from methylated to unmethylated cytosines. Mammals use Ten-Eleven Translocation proteins (TET)  to oxidize 5mC, but the process creates pit stops that may be independent epigenetic states of their own: 5-hydroxy-, -formyl- and –carboxycytosine (5hmC, 5fC, 5caC). Plants, on the other hand, have evolved a more direct route to demethylation with the DNA glycosylase REPRESSOR OF SILENCING 1 (ROS1), which directly targets 5mC for base excision repair (BER). New research is taking advantage of this epigenetic beeline, and the result is a more direct targeted demethylation tool.

The talented team from the lab of Teresa Roldán-Arjona (University of Cόrdoba, Spain) fused a deactivated Cas9 (dCAs9) protein to the active domain of ROS1 (dCas9-ROS1) and transfected it, along with a methylated reported construct, into HEK293 cells and found that:

  • dCas9-ROS1 is able to reactivate the expression of a methylation-silenced luciferase gene in a density dependent manner
    • However, it is unable to reactivate a plasmid that’s 100% methylated
  • dCas9-ROS1 also reactivates a methylation-silenced GFP construct, but is less efficient than traditional dCas9-p300 or dCas9-VP160 activators
    • All three constructs are unable to re-activate GFP constructs that are 90% methylated
  • Co-transfecting dCas9-ROS1 with other constructs actually decreases luciferase activity compared to transfecting each construct individually
  • Co-transfecting dCas9-ROS1 with additional, targeted downstream BER factors does not improve its ability to re-activate a methylated luciferase construct
  • Active dCas9-ROS1 transfection decreases methylation across multiple CpGs in and near the promoter of the luciferase expression construct

Interestingly, dCas9-ROS1 also increases the expression of an unmethylated luciferase construct, which means that even newly transfected constructs are subject to de novo methylation, or that dCas9-ROS1 may have activator activities outside its role as a demethylase. Either way, you’ll be happy to have this technique ride shotgun on your next mammalian demethylation experiment!

Head directly to the original article in the Journal of Molecular Biology, February 2020.

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表观遗传学研究表明,Vaping的安全性取决于烟雾 //www.sogroupadmin.com/epigenetic-study-suggestions-that-the-safety-of-vaping-is-running-on-magues/表观遗传学研究建议-安全性/ //www.sogroupadmin.com/epigenetic研究表明vaping的安全性是在烟雾中运行的/#respond 2020年3月3日星期二07:36:18+0000 斯图尔特·阿特金森 肿瘤表遗传学电子书 染色质 DNA甲基化 表观遗传学 标题 5-羟甲基胞嘧啶 5-甲基胞嘧啶 5立方厘米 5毫升 DNA羟甲基化 DNA甲基化 DNA甲基转移酶 第1行 长散布核苷酸元件1 吸烟 十一易位 吸血 http://epienie.com/?p=28315 由于有尽可能多的口味和表观遗传修饰,vaping作为一种安全的香烟替代品和一种戒烟的方法已经出现在现场。然而,与呼吸机相关的肺损伤的增加以及青少年对呼吸机的“不可预见的”大量摄入,促使科学家们进行了研究

With as many flavors as there are epigenetic modifications, vaping has arrived on the scene as a safer alternative to the smoking of cigarettes and a means to give up a rather unhealthy habit. However, the rise in vaping-related lung injuries and the “unforeseen” massive uptake of vaping by teenagers have prompted scientists to undertake detailed analyses regarding the relative safety of this alternative to traditional smoking. Is the promise of safety for vapers just smoke and mirrors?

Intriguingly, a previous study from the laboratory of Ahmad Besaratinia (University of Southern California, Los Angeles, CA, USA) revealed that vapers exhibited similarly deregulated gene expression in the oral epithelium (a major target organ for smoking-associated cancer) as smokers. Given that carcinogens associated with vaping and cigarette smoking can induce epigenetic alterations, the team sought to extend their comparison to the epigenetic realm.

To compare and contrast the epigenetic consequences of smoking and vaping, Caliri and colleagues studied DNA methylation levels in leukocytes derived from peripheral blood samples of age-, gender-, and ethnicity- matched vapers, smokers, and control patients (non-vapers/non-smokers). Specifically, the team assessed 5-methylcytosine (5-mC) levels at Long Interspersed Nucleotide Element 1 (LINE-1) by employing a Global DNA Methylation LINE 1 Assay as a measure of global DNA methylation, and also global DNA hydroxymethylation (5-hmC) levels, the oxidation product of 5-mC.

What the authors discovered suggests that the idea that vaping represents a safe alternative to smoking may be running on fumes:

  • Exclusive vapers and smokers display significant reductions in both DNA methylation levels at LINE-1 repeat elements and global 5-hmC levels when compared to samples derived from non-smokers/vapers
    • However, vapers and smokers exhibit similar levels of these epigenetic modifications, suggesting that smoking and vaping affect peripheral blood in the same manner
    • A positive and statistically significant correlation exists between DNA methylation levels at LINE-1 repeat elements and global 5-hmC levels
  • Analyses of relevant enzyme levels reveal only modest changes in the transcription of factors that catalyze the addition (DNA methyltransferases 1, 3A, and 3B) or removal (ten-eleven translocation 1-3) of DNA methylation in both vapers and smokers
    • The discovered alterations do not reach statistical significance when compared to controls
  • Finally, the authors combined the vaping/smoking history of each participant with the verification of vaping/smoking status via measurements of plasma cotinine concentration (a prime metabolite of nicotine), exhaled carbon monoxide, and carboxyhemoglobin levels
    • This analysis revealed an inverse statistically significant correlation between both LINE-1 methylation and global 5-hmC levels and both the duration and intensity of vaping/smoking and levels of plasma cotinine

While the authors note certain limitations to their study, which include small size and the use of peripheral blood leukocytes as a surrogate for target organs where tumorigenesis can occur, these data do provide evidence that both vaping and smoking alike can foster tumorigenesis-associated epigenetic alterations. It seems like the safety of vaping may be quickly going up in smoke.

“Our new study adds an important piece to that puzzle by demonstrating that epigenetic mechanisms, specifically changes in chemical tags attached to the DNA, may contribute to the abnormal expression of genes in vapers and smokers alike,” Besaratinia said. “The epidemic of teen vaping and the recent outbreak of vaping-related severe lung injury and deaths in the U.S. underscore the importance of generating scientific evidence on which future regulations for electronic cigarette manufacturing, marketing, and distribution can be based.”

To find out if the safety profile of vaping is genuinely running on fumes, head over to Epigenetics, February 2020.

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不活跃的X染色体花时间隐藏在表观遗传的覆盖下 //www.sogroupadmin.com/inactive-x-chronoms-spend-time-tucked-under-the-epigenetic-covers(非活性x染色体-花时间-折叠-下-表观遗传-覆盖物)/ //www.sogroupadmin.com/inactive-x-choross-spend-time-tucked-under-the-epigenetic-coups/#回复 2020年2月25日星期二16:19:24+0000 凯瑟琳·维尔兰科特 表观遗传学 标题 非编码RNA 等位基因特异性 染色质 剪切和运行 胚胎干细胞 lncRNA公司 m6A型 鼠标 RNA测序 斯彭 干细胞 转录抑制 X染色体失活 存在 http://epienie.com/?p=28291个 当它是冬天的尽头,外面的世界是冰冻的固体,没有比在一堆温暖的毯子下面更好的地方了,就像在一团Xist长的非编码RNA下面的一个失活的X染色体。虽然我们已经知道Xist是X染色体失活(XCI)的必要条件,但其机制是

When it’s the dead of winter, and the world outside is frozen solid, there’s no better place to be than under a mountain of warm blankets, like an inactivated X chromosome under a cloud of Xist long-noncoding RNA. Although we’ve known for a while that Xist is necessary for X chromosome inactivation (XCI), the mechanisms behind its action have remained tightly under wraps.

Like any good blanket fort, XCI involves multiple layers of support, and a new study from the lab of Edith Heard (European Molecular Biology Laboratory, Heidelberg, Germany) uncovers how the transcriptional repressor SPEN connects multiple layers of epigenetic regulation. The well-rested researchers developed a line of mouse embryonic stem cells (ES cells) where they could induce Xist expression with doxycycline and get rid of endogenous SPEN with an auxin-inducible degron. By allowing Xist to be expressed, in the absence of SPEN, they found that:

  •  Xist still forms RNA clouds and localizes to the X chromosome but gene silencing is lost
  • 80% of X linked genes need SPEN in order to be silenced by Xist, according to allele-specific RNAs-seq
  • When HaloTagged SPEN is added to cells with fluorescence-labelled Xist, SPEN localizes with Xist immediately after Xist is induced
  • In neural progenitor cells, where one X chromosome is already stably inactivated, degrading SPEN has no impact on Xist, and doesn’t alter X chromosome gene expression, except for the few genes that already escape XCI

Next, the talented team introduced their cells to cDNA fragments coding for specific domains of the SPEN protein to narrow down which regions are the most important for XCI. They found that:

  • The RNA binding domains and the SPEN paralogue/orthologue C-terminal (SPOC) domain are necessary for SPEN to accumulate along the X chromosome
  • A truncated SPOC domain allows SPEN to localize to the X chromosome, but fails to rescue XCI
    • Mutating the SPOC domain in the endogenous Spen gene in mouse ES cells has the same effect
  • Guiding a BglG-tagged SPOC domain to Bgl stem-loops on Xist allows the peptide to inactivate genes on the underlying X chromosome
  • The SPOC domain binds to members of NCoR and SMRT repressor complexes, the HDAC3 histone deacetylase, and the RNA m6A reader YTHDC1 according to mass spectrometry

Finally, to understand where it normally binds to the genome, the savvy scientists used CUT&RUN to map SPEN binding sites when Xist was expressed, and found:

  • SPEN tends to bind to the promoters of actively expressed genes, 4 hours after Xist induction, and these sites overlap with RNAPII ChIP-seq peaks
  • SPEN also binds to enhancers that are deacetylated during XCI, and overlaps with enhancers that are enriched in HDAC3 from separate ChIP-seq data
  • Many promoters lose SPEN binding after 24 hours of Xist expression, especially those that belong to genes that are efficiently silenced

Underneath it all, it seems like SPEN’s job is to bring Xist and other epigenetic regulators together with the X chromosome to get cozy and wind things down for inactivation. Cuddle up with the original article in Nature, January 2020.

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SAXS成像到达了物质的(勇敢的)核心:一个长的非编码RNA的第一个全长结构 //www.sogroupadmin.com/saxs-imaging-gets-to-the-braveheart-of-matter-first-full-leng-structure-of-a-long-non-coding-rna/ //www.sogroupadmin.com/saxs-imaging-gets-to-the-braveheart-of-the-matter-first-full-length-structure-of-a-long-non-coding-rna/#respond 2020年2月18日星期二18:34:51+0000 利齐·特瑞尔 非编码RNA 技术 勇敢的心 细胞核酸结合蛋白 中国石油天然气集团公司 恩文 lncRNA公司 长非编码Rna 萨克斯 小角x射线散射 结构生物学 结构 http://epienie.com/?p=28280 现在是情人节,这意味着爱在空气中,心形的新奇事物丰富多彩。但是来自Trushar Patel(加拿大艾伯塔省莱斯布里奇大学)和Karissa Sanbonmatsu(美国新墨西哥州洛斯阿拉莫斯国家实验室)实验室的最新研究已经颠覆了这个剧本:他们给了我们勇敢的心的形状,一种长的非编码RNA

It’s Valentine’s season, which means love is in the air, and heart-shaped novelties are abundant. But new research from the labs of Trushar Patel (University of Lethbridge, Alberta, Canada) and Karissa Sanbonmatsu (Los Alamos National Laboratory, New Mexico, USA) has flipped the script: they are giving us the shape of Braveheart, a long non-coding RNA that is critical for heart cell lineage commitment.

For years, lncRNAs have been breaking hearts of structural biologists everywhere; their long and flexible configurations, low expression levels, and short half-lives make it difficult to determine 3-dimensional structure using crystallographic methods. This savvy team employed small-angle X-ray scattering (SAXS) to finally woo the Braveheart (Bvht) lncRNA, but the process they developed can be applied to other RNAs and RNA-based complexes.

Here’s the workflow that won our hearts:

  • Transcribe the RNA of interest in vitro; snap-cooling can be used to promote stable RNA folding
  • Isolate homogeneous, single-molecule RNAs using size-exclusion chromatography (SEC), which are then subjected to SAXS imaging
  • Assemble the SAXS data into a low-resolution model; this generated model represents an average of the conformations
  • Utilize ERNWIN software to predict the atomistic structure, using the SAXS data and known secondary structure elements as constraints

In this study, they report the Bvht SAXS-based structure at a resolution between 13.4 and 38.5 Å, and additionally generated a structure of Bvht bound to Cellular Nucleic acid Binding Protein (CNBP). They show that Bvht has well-structured domains connected by flexible regions and that this structure undergoes significant conformational change upon interaction with CNBP.

The authors were able to use the Bvht-CNBP model to identify structural features of Bvht that are required for CNBP binding, highlighting the importance of structure in understanding function. Senior author Karissa Sanbonmatsu shares, “Our work represents the first step in showing that these difficult-to-image RNAs do possess 3-D structures, and that these molecular structures may very well determine how they operate.”

Spread the love and read more in Nature Communications, January 2020, and make a date to get to know your favorite RNA more intimately.

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达尔文选择作用于DNA甲基化:没有从头甲基转移酶的5mC持续存在 //www.sogroupadmin.com/darwinian-selection-acts-on-dna-methylization-persistence-of-5mc-without-a-de-novo-甲基转移酶/ //www.sogroupadmin.com/darwinian-selection-acts-on-dna-methylization-persistence-of-5mc-without-a-de-novo-methyltransfer/#respond公司 2020年2月18日星期二16:53:47+0000 埃里克·迪尔 DNA甲基化 新生隐球菌 DNA甲基化 DNA甲基转移酶 dnmt公司 进化 医学院 选择 工作组 http://epienie.com/?p=28276 坚持新年决心保持健康有困难吗?然后你可能想向一个酵母寻求一些建议:他们的一些进化适应性与数百万年来用甲基转移酶维持DNA甲基化有关。DNA甲基化是一种常见的基因组修饰,存在于所有生命中,并且普遍存在

Having trouble maintaining that New Year’s resolution to stay fit? Then you might want to ask a yeast for some advice: it turns out some of their evolutionary fitness is tied to maintaining DNA methylation with a methyltransferase for millions of years. DNA methylation is a common genomic modification, present in all life and prevalent in vertebrates and plants. The regulation of cytosine methylation (5mC) in vertebrates and plants is divided between its deposition and maintenance enzymes. In mammals, de novo methyltransferases such as DNMT3A/B lay down 5mC early in development, then the maintenance methyltransferase DNMT1 passes it through cell division. One would assume that 5mC cannot exist without both of these types of enzymes; but there are some species of yeasts that have only one. How these methyltransferases function has been completely unknown.

The lab of Hiten Madhani at the University of California, San Francisco wanted to study the yeast Cryptococcus neoformans, which only has one DNMT enzyme: DNMT5. They were uncertain as to how C. neoformans was maintaining 5mC in its genome without a pair of DNMTs. They used various cloning approaches, whole-genome bisulfite sequencing (WGBS), and methylated DNA immunoprecipitation sequencing (MeDIP-seq) to explore the function of DNMT5 and the regulation of 5mC in C. neoformans  

  • Using methyltransferase assays in S. cerevisiae, they found that DNMT5 efficiently methylates hemimethylated DNA in a manner comparable to human DNMT1 rates, and it does not methylate unmodified DNA. They conclude that DNMT5 is a maintenance DNMT.  
    • They confirmed this by removing DNMT5 expression using a GAL-inducible promoter as well as genetic deletion and reintroduction of the gene. In both experiments, after DNMT5 removal, 5mC is lost; reintroduction of DNMT5 does not restore 5mC even after 90 generations.
    • They also showed that 5mC is not able to spread to new sites in vivo or in intro
  •   To determine how 5mC was established, they examined relatives of C. neoformans
    • Close relatives only have DMNT5, while more distant ones have an uncharacterized DNMT: DNMTX
    • They found that DNMTX is a de novo DNMT by cloning into C. neoformans and observing de novo 5mC accumulation
    • The de novo DNMTX was lost from a C. neoformans ancestor 50-150 million years ago
  • Using whole-genome bisulfite sequencing, they found that all closely related strains still have 5mC, and the marks were in analogous genomic regions (ex. transposons), suggesting they serve an important function that is being selected for. 

Senior author Hiten Madhani shares, “Natural selection is maintaining methylation at much higher levels than would be expected from a neutral process of random gains and losses. This is the epigenetic equivalent of Darwinian evolution. Previously, there was no evidence of this kind of selection happening over these time scales. This is an entirely novel concept. But now the big question is ‘Is this happening outside of this exceptional circumstance, and if so, how do we find it?’”

Catch this multi-million year story in Cell, January 2020

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ATAC Me:一个表观遗传的一二连击击中增强子的标记 //www.sogroupadmin.com/atac-me-an-epigenetic-one-two-combo-hits-the-mark-at-enhancers(表观遗传学一双复合点击标记增强剂)/ //www.sogroupadmin.com/atac me一个表观遗传一二组合在增强子处击中标记/#应答 太阳,2020年2月16日11:25:18+0000 斯图尔特·阿特金森 染色质 表观遗传学 标题 ATAC我 细胞命运 染色质 染色质可及性 区别 DNA甲基化 增强 基因表达 Tn5号 Tn5转置 从天然染色质无障碍片段的转座辅助富集 工作组 全基因组亚硫酸氢盐测序 http://epienie.com/?p=28270 有很多方法可以“攻击”一个问题–;正面,侧面,非常小心,或迅速和突然,但正如许多拳击手可能告诉你的那样,经典的一二连击通常是一种款待。现在,在一项新的研究中,一个疯狂的准备好戒指的研究人员最近成功了

There are many ways to “attack” a problem – head-on, from the side, with great care, or swiftly and suddenly, but as many a boxer may tell you, the classic one-two combo usually works a treat. Now, in a slugfest of a new study, a rambunctious rabble of ring-ready researchers recently hit the mark and “knocked out” a vexing problem related to gene regulation during cell fate decisions by throwing their very own epigenetic one-two combo – the new “ATAC-Me” technique.

The noted problem relates to a previous study led by Emily Hodges (Vanderbilt University School of Medicine, Tennessee, USA) that provided evidence of methylated DNA occurring alongside high chromatin accessibility at gene enhancers in pluripotent stem cells. However, in somatic cells, these sites seem to resolve via the loss of DNA methylation at active enhancers and loss of chromatin accessibility at repressed enhancers (similar to what occurs at bivalent chromatin domains) to allow for the establishment or stabilization of cell identity.

Confirming this hard-hitting hypothesis requires the ability to measure spatiotemporal relationships within the context of chromatin at high resolution on a genome-wide scale – that’s no mean feat. Luckily, the luchadores from the Hodges lab never thought about throwing in the towel, and they now report on their “ATAC-Me” protocol – a novel one-two combo of transposase-assisted enrichment of chromatin accessibility fragments from native chromatin and subsequent sodium bisulfite conversion and deep sequencing as a knockout strategy to take down this formidable scientific foe.

Ding-ding: here are the top hits from this scientific skirmish (in which the Tn5 transposase again features at the top of the bill) where the induced differentiation of monocytes into macrophages served as a model system to understand the role of DNA methylation at enhancer regions:

  • ATAC-Me analysis of single DNA libraries corroborates previous findings by establishing the persistent hypermethylation of thousands of myeloid enhancers during monocyte-to-macrophage differentiation that also display high chromatin accessibility
    • These findings also corroborate the idea of a bivalent epigenetic state at enhancer regions, which perhaps represents an intermediate state along a continuum of enhancer activation
  • At early stages of monocyte-to-macrophage differentiation, chromatin accessibility changes correlate with the transcriptional responses of neighboring genes
    • Chromatin accessibility at myeloid enhancers increases rapidly before plateauing at around 24 hours
    • However, DNA methylation status fails to track with chromatin accessibility/gene expression
    • Overall, these findings imply that DNA methylation at enhancers does not influence gene transcription or transcription factor binding on its own and in isolation has minimal influence on cell fate decisions
  • Even at later time points, the authors only observe minimal reductions in DNA methylation levels
    • These data suggest a secondary role for DNA methylation removal at gene-regulatory elements

Overall, the knockout hit from this pugilistic paper is the existence of a significant enhancer-specific “disconnect” between chromatin accessibility, DNA methylation, and gene expression; however, the authors also highlight the value of ATAC-Me in “attacking” further epigenetic problems and expanding our understanding of DNA methylation in gene regulation.

For all the round-by-round highlights of the development of this one-two combo technique and the top shots from the subsequent scientific sparring session, see Molecular Cell, Jan 2020.

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一种新型的lncRNA播放猫MAOS与攻击行为 //www.sogroupadmin.com/a-novel-lncrna-plays-cat-and-maos-with-aggressive-behaviors网站/ //www.sogroupadmin.com/a-novel-lncrna-plays-cat-and-maos-with-aggressive-behaviors/#回应 2020年2月4日星期二17:13:37+0000 凯瑟琳·维尔兰科特 表观遗传学 标题 非编码RNA 侵略 染色质 脆皮的 齿状回 DNA甲基化 海马 冲动性 lncRNA公司 长非编码Rna 荧光素酶 毛亚 微阵列 神经祖细胞 神经元 精神病学 自杀 http://epienie.com/?p=28246 这是一个典型的两难选择——你是现在就吃那份美味的奶酪,还是留着待会儿吃?如果你缺乏自制力,你可能会有更高的冲动或攻击性行为障碍的风险,这些都与单胺氧化酶(MAO)家族的基因有关。实验室的一项新研究

It’s the classic dilemma — do you eat that delectable morsel of cheese now or save it for later? If you tend to lack self-control, you might be at higher risk of impulsive or aggressive behavioral disorders, which have been linked to genes in the monoamine oxidase (MAO) family. A new study from the lab of Gustavo Turecki (McGill University, Quebec, Canada) toys with the idea that dysregulation of MAOA is guided by a previously unknown lncRNA in the brain. 

Using brain (dentate gyrus) tissue from people who died by suicide, and a custom DNA methylation microarray, the talented team explored the epigenetic profile of two MAO genes (A and B) and the noncoding region between them and found that:

  • An intergenic region (IGR) containing 12 CpGs is less methylated in the brains of impulsive-aggressive suicides compared to controls
  • Hypomethylation is specific to neuronal nuclei separated by fluorescence activated cell sorting (FACS)
  • Expression of the MAOA gene is lower in the suicide group, as measured by qPCR

The clever crew noticed that the pattern of methylation in the IGR was similar to what is usually found in promoters, and hypothesized that a non-coding RNA might be expressed nearby. They used 5’ and 3’ rapid amplification of cDNA ends (RACE) to identify a novel transcript that they called MAALIN, which was more expressed in the suicide group. They decided to take a deep dive into MAALIN regulation and function and found that:

  • The differentially methylated sequence can drive MAALIN expression in luciferase assays, but only when it is not methylated
  • There is less H3K27me3 present at the promoter in dentate gyrus tissue from suicides compared to controls
  • Viral overexpression of MAALIN decreases MAOA expression in neural progenitor cells
  • On the other hand, CRISPR/Cas9 knockout of MAALIN increases MAOA

Next, the brainy bunch decided to pounce on their hypothesis that MAALIN regulates aggressive behaviors, and injected HSV-MAALIN vectors into the dentate gyrus of mice. The overexpression decreased MAOA expression in the same brain area and decreased the amount of time it took the mice to attack an intruder in their home cage.

Senior author Gustavo Turecki shares, “While aggressive behavior is part of our normal repertoire of behavioral responses, when pathological, it becomes a major problem for which we do not have efficient intervention tools.” Benoit Labonté, the first author on the study, adds “By identifying this novel gene, one could think of using it as a diagnostic tool for people with high impulsivity levels to develop suicidal behaviours. We can also consider for future research developing pharmacological agents acting on this pathway to treat patients with impulsivity issues often observed in addition including alcoholism, drug of abuse or gambling.”

Take a squeak peek at the original article in Molecular Psychiatry, January 2020.

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动态表观遗传学编辑组合:突变DNMT3A和SunTag联合减少非靶甲基化 //www.sogroupadmin.com/a-dynamic-epigenetic-editing-duo-variant-dnmt3a-and-suntag-team-up-to-reduce-off-target-methylation/ //www.sogroupadmin.com/a-dynamic-epigenetic-editing-duo-variant-dnmt3a-and-suntag-team-up-to-reduce-off-target-methylation/#respond/回应 2020年2月4日星期二14:18:36+0000 利齐·特瑞尔 DNA甲基化 基因组编辑 标题 技术 dcas9号 Dnmt3a级 DNMT3L型 表观编辑 甲基化 偏离目标 桑塔格 http://epienie.com/?p=28238 一些优秀的超级英雄是从一个变异事件中诞生的。彼得·帕克是如何成为蜘蛛侠的,布鲁斯·班纳是如何变成令人难以置信的绿巨人的,X战警是如何获得力量的。它只是表明突变并不总是件坏事——这一点可以从新的超级英雄团队在[…;]

Some of the best superheroes are born out of a mutational event. It’s how Peter Parker became Spiderman, how Bruce Banner turned into the Incredible Hulk, and where the X-Men derive their powers. It just goes to show that mutations aren’t always a bad thing — a point exemplified by the new superhero team in town: mutant DNMT3A alongside the SunTag system. Assembled together, they have the superpower of highly efficient epigenetic editing with reduced off-target effects.

Deep in their secret lair, a team led by Albert Jeltsch and Pavel Bashtrykov (Stuttgart University, Germany) set out to improve upon the current epigenetic editing systems that use targeted methylation to modify chromatin and silence genes. Just like with other epigenetic editing systems, they employed catalytically dead Cas9 (dCas9) and a guide RNA to direct a DNA methyltransferase to a target gene. Then they modified the system in three major ways. First, rather than just using the standard DNMT3A DNA methyltransferase, they used a DNMT3A/DNMT3L fusion that has a higher methyltransferase activity. Second, they combined this feature with the 10XSunTag system: dCas9 is fused to a SunTag, which acts as a scaffold for the recruitment of up to ten tagged DNMT3A/DNMT3L subunits. Finally, they also set out to further engineer the system to reduce off-target effects.

Using bisulfite sequencing, they measured methylation at the guide RNA-targeted ISG15 locus, as well as at an off-target site (VEGFA).

Here’s what they found:

  • The SunTag system methylates the ISG15 locus efficiently (84% of CpG sites) but also methylates the off-target VEGFA locus (53% of sites)
  • The crystal structure of DNMT3A bound to DNA revealed four critical residues that, when mutated, decrease the affinity of DNMT3A for DNA
    • All four mutations decrease the off-target activity of DNMT3A/DNMT3L but also cause a decrease in the on-target methylation efficiency
  • Combing mutant DNMT3A/DNMT3L with the SunTag system minimizes the off-target effects while retaining the most on-target activity
    • The most promising mutation, R887E, retained 76% of the wild-type activity at ISG15 and had an 88% reduction in off-target VEGFA methylation
    • In a genome-wide screen (MBD-seq), the R887E mutant has a 7.8 fold reduction in off-target methylation compared to the wild-type

By incorporating a mutation into DNMT3A, they created a more precise mechanism for programmable gene methylation. Although the addition of the SunTag system helps overcome some loss of activity by recruiting more effectors, more is not necessarily better. A longer SunTag that can recruit 24 effectors actually decreased the methylation efficiency.

So is this more precise system the hero we need in the epigenetic editing world? Will they be invited to join the Justice League? Read the full article and decide for yourself in the International Journal of Molecular Science, January 2020.

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N6-甲基腺苷修饰的CarRNAs对转录的表观遗传抑制作用 //www.sogroupadmin.com/n6-甲基腺苷修饰-carrnas-hit-the-epigenetic-brake-on-transcription/ //www.sogroupadmin.com/n6-methyladenosine-modified-carrnas-hit-the-epigenetic-brake-on-transcription/#respond 2020年2月3日星期一09:27:47+0000 斯图尔特·阿特金森 染色质 标题 亚博赞助曼联 卡拉纳斯 芯片序列 芯片测序 染色质 染色体与调控RNA 胚胎干细胞亚博赞助曼联 表观遗传学 H3K27ac型 H3K4me3型 m6A型 哺乳动物自然伸长转录序列测定 质谱法 梅里普序列 小鼠胚胎干细胞 甲基化RNA免疫沉淀测序 METTL3号 mNET序列 小鼠胚胎干细胞亚博赞助曼联 N6甲基腺苷 多能性 多能干细胞亚博赞助曼联 RNA甲基化 RNA修饰 YTHDC1号 http://epienie.com/?p=28233 亚硝基系统,改进的空气动力学,以及光滑的轮胎在你的车上可能都有助于解决你需要的速度,当你回到方向盘;然而,需要减速是同样重要的世界基因调控。最近,一个研究小组描述了如何修改一个racy子集 <图中类= “WP-块的图像尺寸大”> “”类=
M6A充当后生制动carRNAs

氧化亚氮系统,改进的空气动力学,以及在您的汽车光面轮胎可能都有助于解渴你需要速度,当你后面的车轮;然而,慢下来,需要的是就像在基因调控的世界都至关重要。最近,一个研究小组已描述了如何被称为染色体相关的调节 的RNA carRNAs 诱导基因间RNA的一个活泼子集的修改转录减速变化到底层表观遗传状态可以修改下游基因的表达。

在生物学高速公路的表观遗传学车道时,N6甲基腺苷( M6A )-modification of pluripotency-related mRNAs by Mettl3 puts a brake on their transcription by “speeding up” their Ythdf2-driven decay in the cytoplasm of pluripotent stem cells; however, studies have suggested that m6A may also play a nucleus-specific Ythdc1-mediated function in transcriptional regulation. These findings drove a car-pooling research team led by Yawei Gao (Tongji University, Shanghai), Dali Han (Chinese Academy of Sciences, Beijing, China), and Chuan He (University of Chicago, Illinois, USA) to “hit the brakes” on other projects, shift gears, and accelerate an investigation into the transcriptional consequences of m6A in the nucleus of mouse embryonic stem cells (mESCs). Fascinatingly, the team now reports that m6A acts as an epigenetic brake for carRNAs, which include promoter-associated, enhancer, and repeats RNAs, in a mechanism that also impedes downstream gene expression via alterations at the chromatin level.

So, let’s allow Liu, Dou, Chen, and colleagues to take us for an epigenetic ride through their car-efully compiled data:

  • Mass spectrometry and methylated RNA immunoprecipitation sequencing (MeRIP-seq) of wild type, Ythdc1 conditional knockout, and Mettl3 knockout mESCs established that Mettl3 deposits m6A modifications on carRNAs located in intergenic regions and Ythdc1 recognizes said RNAs (but not Ythdc2)
    • m6A levels negatively correlate with carRNA expression, suggesting that m6A acts to destabilize these RNAs
    • Ythdc1 promotes the decay of modified RNA via the nuclear exosome targeting (NEXT) complex, with LINE1 repeat elements constituting the greatest proportion of Mettl3-modified carRNAs affected by Ythdc1
  • Time-course RNA-seq of both nascent transcripts and total nuclear RNAs and mammalian native elongating transcript sequencing (mNET-seq) also established that the loss of the m6A-modified carRNAs by Mettl3 depletion leads to a general upregulation of gene expression and transcription rate
    • Genes with m6A-modified upstream carRNAs display higher increases in transcription rate than those with non-m6A-modified upstream carRNAs, indicating that loss of m6A activates the transcription of genes downstream of the carRNAs
  • As a mechanism for this observation, the authors found that the loss of m6A on carRNAs enhances chromatin accessibility (by DNase I-TUNEL assays), increases the binding of transcription factors (Ep300 and Yy1 by ChIP-seq), and increases the levels of active histone marks (H3K4me3 and H3K27ac by ChIP-seq) at carRNA loci
    • Genes affected include epigenetic regulators (e.g., the Prdm9 and Kmt2d H3K4me3 methyltransferases) and differentiation-associated factors (e.g., Esrrb and Ranbp17), which could set off further chromatin opening in a positive feedback loop

Overall, these data support the existence of direct crosstalk between the m6A modification of carRNA and the underlying chromatin state, which supposes an additional layer of transcriptional regulation.

“This has major implications in basic biology,” study leader He said. “It directly affects gene transcriptions, and not just a few of them. It could induce global chromatin change and affects transcription of 6,000 genes in the cell line we studied.” He continues, “I believe this represents a conceptual change. Barriers like these are hard to crack, but once you do, everything flows from there.”

To wheel-y get what we this fascinating new study is driving at, why not take a ride over to Science, January 2020.

//www.sogroupadmin.com/n6-甲基腺苷修饰-carrnas-hit-the-epigenetic-brake-on-transcription/feed/ 0个 胚层改良剂中单细胞多OMIC地图 - 小鼠破译最完美的车身计划和也许男人? //www.sogroupadmin.com/single-cell-multi-omic-maps-of-germ-layer-enhancers-decriphing-the-best-layed-body-plans-of-mice-and-may-men(单细胞-多组分-图-胚芽层-增强子-破译-最好的-铺位-身体-计划-小鼠-/ //www.sogroupadmin.com/single-cell-multi-omic-maps-of-germ-layer-enhancers-deciphering-the-best-laid-body-plans-of-mice-and-perhaps-men/#comments 2020年1月22日星期三11:24:33+0000 斯图尔特·阿特金森 染色质 DNA甲基化 标题 亚博赞助曼联 和转录组测序 细胞命运 染色质可及性 Dna去甲基化 DNA甲基化 胚胎发育 胚胎学 增强 表观遗传学 表基因组 表观基因组学 甲基化谱 财政部 鼠标发展 多组分分析 多组分因子分析 多能性 scNMT序列 单细胞分析 单细胞核小体 http://epienie.com/?p=28224 一个周末,带着一本诗集,一个骑山地车的假期,或者也许是一次大胆的珠宝抢劫……不管你对一个有趣的周末有什么想法,一套周密的、精确的说明通常都会有帮助;总之,你需要一个计划!在原肠胚中,精确的表观基因组和转录组指令决定了多能性的分化

一个周末离开以诗歌,一个山地自行车假期,或者一个大胆的珠宝抢劫案......无论你的一个有趣的周末的想法是,一个铺设好了,精确的指令集通常帮助的书;总之,你需要一个计划!在 gastrulating小鼠胚胎,精确表观和转录的指令支配多能细胞分化成三个胚层(内胚层,中胚层和外胚层)的细胞,从而在建立脊椎动物“身体计划”的帮助。虽然我们在这个发展阶段具有这一计划的转录部分的一个大致的了解,我们还缺乏有关知识如何以及何时后天改变决定基因的表达或抑制,因此细胞命运的选择和身体的规划编制。

Fully exploring these biological instructions requires multilevel analyses on a vanishingly small number of cells and researchers from the Babraham Institute, EMBL’s European Bioinformatics Institute, the CRUK Cambridge Institute, and the Wellcome-MRC Cambridge Stem Cell Institute led by the dream team of Oliver Stegle, John C. Marioni, and Wolf Reik recently took on this daunting task in gastrulating mouse embryos.

Argelaguet and colleagues employed single-cell nucleosome, methylome, and transcriptome sequencing (scNMT-seq) to profile over one thousand single cells isolated from mouse embryos as they exit the pluripotent state and move through germ-layer specification. To help with linking epigenetic “edicts” to transcriptional profiles and subsequent cell-fate choice, the authors also employed multi-omics factor analysis (MOFA), which integrates gene expression data from RNA-sequencing with regulatory element data from the  DNA methylation and chromatin accessibility assays and then performs unsupervised dimensionality reduction to capture global sources of cell-to-cell variability via a small number of inferred factors.

So, what did this well thought out set of experiments tell us regarding the epigenetic instructions that form an integral part of the best-laid “body” plans of mice, and perhaps even men?

  • Cells exit from pluripotency during the establishment of a repressive epigenetic landscape, which is driven by a global increase in DNA methylation through a wave of de novo methylation, and a gradual decline in global chromatin accessibility in embryonic and extra-embryonic tissues
    • Of the 5,000 genes evaluated, the expression of 125 and 52 genes display a significant correlation with promoter DNA methylation and chromatin accessibility, respectively, and mainly comprise repressed early pluripotency and germ cell markers
    • Fascinatingly, only a small number of upregulated genes display epigenetic alterations at promoter sequences, suggesting the involvement of different regulatory elements
  • Subsequent characterization of germ-layer epigenomes by employing MOFA suggests that early embryonic cells become epigenetically primed at enhancer regions towards an ectodermal fate as soon as cells exit the pluripotent state, a finding that supports the existence of a ‘default’ differentiation pathway (as observed in many pluripotent stem cells)
    • MOFA links increases in gene expression during mesodermal and endoderm commitment to DNA methylation alterations (driven by ten-eleven translocation (TET)-mediated demethylation) and increased chromatin accessibility at lineage-specific enhancers
    • These enhancer-associated epigenetic changes drive the formation of mesodermal and endoderm transcriptional profiles that drive cells away from the default ectoderm pathway

Overall, the authors provide evidence for the definition of the germ-layer epigenome during gastrulation by a hierarchical or asymmetric epigenetic model; germ-layer specific epigenetic alterations at enhancer elements provide the instructions for cell-fate decisions, the emergence of the distinct germ layers, and formation of the vertebrate body plan.

Co-first author Stephen J. Clark shares, “Through analysing the timeline of events, we identified that the diversification of the three gastrulation layers was mainly driven by epigenetic events affecting germ layer specific enhancers. We found that the epigenome of the ectoderm layer was established much earlier in development than the other two, even though all three cell types arise at a similar time.”

Co-senior author Wolf Reik continues, “Our findings develop our understanding of the role of the epigenome in defining cell fate commitments at different stages of development, with important implications for stem cell biology and medicine. It is very enjoyable to see how the multidisciplinary research community that has come together in this project is now sharing the success of their efforts.”

So, what are your big plans for today? If you have space for a little “light” reading alongside your poetry, see Nature, December 2019, for how epigenetic alterations at enhancers form part of the best-laid body plan of mice, and perhaps men!

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