Fast genomic μChIP-chip from 1,000 cells

A new method for rapid genome-wide μChIP-chip from as few as 1,000 cells

Histone H3 Lysine 27 Methylation Asymmetry on Developmentally-Regulated Promoters Distinguish the First Two Lineages in Mouse Preimplantation Embryos

First lineage specification in the mammalian embryo leads to formation of the inner cell mass (ICM) and trophectoderm (TE), which respectively give rise to embryonic and extraembryonic tissues. We show here that this first differentiation event is accompanied by asymmetric distribution of trimethylated histone H3 lysine 27 (H3K27me3) on promoters of signaling and developmentally-regulated genes in the mouse ICM and TE. A genome-wide survey of promoter occupancy by H3K4me3 and H3K27me3 indicates that both compartments harbor promoters enriched in either modification, and promoters co-enriched in trimethylated H3K4 and H3K27 linked to developmental and signaling functions. The majority of H3K4/K27me3 co-enriched promoters are distinct between the two lineages, primarily due to differences in the distribution of H3K27me3. Derivation of embryonic stem cells leads to significant losses and gains of H3K4/K27me3 co-enriched promoters relative to the ICM, with distinct contributions of (de)methylation events on K4 and K27. Our results show histone trimethylation asymmetry on promoters in the first two developmental lineages, and highlight an epigenetic skewing associated with embryonic stem cell derivation

Parental vitamin deficiency affects the embryonic gene expression of immune-, lipid transport- and apolipoprotein genes

World Health Organization is concerned for parental vitamin deficiency and its effect on offspring health. This study examines the effect of a marginally dietary-induced parental one carbon (1-C) micronutrient deficiency on embryonic gene expression using zebrafish. Metabolic profiling revealed a reduced 1-C cycle efficiency in F(0) generation. Parental deficiency reduced the fecundity and a total of 364 genes were differentially expressed in the F(1) embryos. The upregulated genes (53%) in the deficient group were enriched in biological processes such as immune response and blood coagulation. Several genes encoding enzymes essential for the 1-C cycle and for lipid transport (especially apolipoproteins) were aberrantly expressed. We show that a parental diet deficient in micronutrients disturbs the expression in descendant embryos of genes associated with overall health, and result in inherited aberrations in the 1-C cycle and lipid metabolism. This emphasises the importance of parental micronutrient status for the health of the offspring

Screening bioactive food compounds in honey bees suggests curcumin blocks alcohol-induced damage to longevity and DNA methylation

publishedVersio

EWAS of post-COVID-19 patients shows methylation differences in the immune-response associated gene, IFI44L, three months after COVID-19 infection

Although substantial progress has been made in managing COVID-19, it is still difficult to predict a patient’s prognosis. We explored the epigenetic signatures of COVID-19 in peripheral blood using data from an ongoing prospective observational study of COVID-19 called the Norwegian Corona Cohort Study. A series of EWASs were performed to compare the DNA methylation profiles between COVID-19 cases and controls three months post-infection. We also investigated differences associated with severity and long-COVID. Three CpGs—cg22399236, cg03607951, and cg09829636—were significantly hypomethylated (FDR < 0.05) in COVID-19 positive individuals. cg03607951 is located in IFI44L which is involved in innate response to viral infection and several systemic autoimmune diseases. cg09829636 is located in ANKRD9, a gene implicated in a wide variety of cellular processes, including the degradation of IMPDH2. The link between ANKRD9 and IMPDH2 is striking given that IMPDHs are considered therapeutic targets for COVID-19. Furthermore, gene ontology analyses revealed pathways involved in response to viruses. The lack of significant differences associated with severity and long-COVID may be real or reflect limitations in sample size. Our findings support the involvement of interferon responsive genes in the pathophysiology of COVID-19 and indicate a possible link to systemic autoimmune diseases.publishedVersio

Parental micronutrient deficiency distorts liver DNA methylation and expression of lipid genes associated with a fatty-liver-like phenotype in offspring

Micronutrient status of parents can affect long term health of their progeny. Around 2 billion humans are affected by chronic micronutrient deficiency. In this study we use zebrafish as a model system to examine morphological, molecular and epigenetic changes in mature offspring of parents that experienced a one-carbon (1-C) micronutrient deficiency. Zebrafish were fed a diet sufficient, or marginally deficient in 1-C nutrients (folate, vitamin B12, vitamin B6, methionine, choline), and then mated. Offspring livers underwent histological examination, RNA sequencing and genome-wide DNA methylation analysis. Parental 1-C micronutrient deficiency resulted in increased lipid inclusion and we identified 686 differentially expressed genes in offspring liver, the majority of which were downregulated. Downregulated genes were enriched for functional categories related to sterol, steroid and lipid biosynthesis, as well as mitochondrial protein synthesis. Differential DNA methylation was found at 2869 CpG sites, enriched in promoter regions and permutation analyses confirmed the association with parental feed. Our data indicate that parental 1-C nutrient status can persist as locus specific DNA methylation marks in descendants and suggest an effect on lipid utilization and mitochondrial protein translation in F1 livers. This points toward parental micronutrients status as an important factor for offspring health and welfare.publishedVersio

μChIP—a rapid micro chromatin immunoprecipitation assay for small cell samples and biopsies

Chromatin immunoprecipitation (ChIP) is a powerful technique for studying protein–DNA interactions. Drawbacks of current ChIP assays however are a requirement for large cell numbers, which limits applicability of ChIP to rare cell samples, and/or lengthy procedures with limited applications. There are to date no protocols for fast and parallel ChIPs of post-translationally modified histones from small cell numbers or biopsies, and importantly, no protocol allowing for investigations of transcription factor binding in small cell numbers. We report here the development of a micro (μ) ChIP assay suitable for up to nine parallel quantitative ChIPs of modified histones or RNA polymerase II from a single batch of 1000 cells. μChIP can also be downscaled to monitor the association of one protein with multiple genomic sites in as few as 100 cells. μChIP is applicable to small fresh tissue biopsies, and a cross-link-while-thawing procedure makes the assay suitable for frozen biopsies. Using μChIP, we characterize transcriptionally permissive and repressive histone H3 modifications on developmentally regulated promoters in human embryonal carcinoma cells and in osteosarcoma biopsies. μChIP creates possibilities for multiple parallel and rapid transcription factor binding and epigenetic analyses of rare cell and tissue samples

Breakthrough infections with the omicron and delta variants of SARS-CoV-2 result in similar re-activation of vaccine-induced immunity

Background: Results showing that sera from double vaccinated individuals have minimal neutralizing activity against Omicron have been interpreted as indicating the need for a third vaccine dose for protection. However, there is little information about early immune responses to Omicron infection in double vaccinated individuals. Methods: We measured inflammatory mediators, antibodies to the SARS-CoV-2 spike and nucleocapsid proteins, and spike peptide-induced release of interferon gamma in whole blood in 51 double-vaccinated individuals infected with Omicron, in 14 infected with Delta, and in 18 healthy controls. The median time points for the first and second samples were 7 and 14 days after symptom onset, respectively. Findings: Infection with Omicron or Delta led to a rapid and similar increase in antibodies to the receptor-binding domain (RBD) of Omicron protein and spike peptide-induced interferon gamma in whole blood. Both the Omicron- and the Delta-infected patients had a mild and transient increase in inflammatory parameters. <p<Interpretation: The results suggest that two vaccine doses are sufficient to mount a rapid and potent immune response upon infection in healthy individuals of with the Omicron variant

Positioning Europe for the EPITRANSCRIPTOMICS challenge

The genetic alphabet consists of the four letters: C, A, G, and T in DNA and C,A,G, and U in RNA. Triplets of these four letters jointly encode 20 different amino acids out of which proteins of all organisms are built. This system is universal and is found in all kingdoms of life. However, bases in DNA and RNA can be chemically modified. In DNA, around 10 different modifications are known, and those have been studied intensively over the past 20 years. Scientific studies on DNA modifications and proteins that recognize them gave rise to the large field of epigenetic and epigenomic research. The outcome of this intense research field is the discovery that development, ageing, and stem-cell dependent regeneration but also several diseases including cancer are largely controlled by the epigenetic state of cells. Consequently, this research has already led to the first FDA approved drugs that exploit the gained knowledge to combat disease. In recent years, the ~150 modifications found in RNA have come to the focus of intense research. Here we provide a perspective on necessary and expected developments in the fast expanding area of RNA modifications, termed epitranscriptomics.SCOPUS: no.jinfo:eu-repo/semantics/publishe

PERANAN PELUKIS ADE MOELYANA DALAM MENGEMBANGKAN SENI LUKIS DARI LIMBAH PELEPAH PISANG DI CIMAHI: (Kajian historis dari tahun 1969-2010)

Skripsi ini berjudul “Peranan Pelukis Ade Moelyana Dalam Mengembangkan Seni Lukis Pelepah Pisang di Cimahi Kajian Historis Tahun 1969-2010”. Permasalahan pokok yang dikaji dalam skripsi ini adalah bagaimana perkembangan seni lukis dari limbah pelepah pisang di Cimahi dari tahun 1969-2010 dan keterkaitannya dengan potensi ekonomi dari seni lukis pelepah pisang yang terabaikan. Metode yang digunakan adalah metode historis yang melalui empat tahap yaitu pengumpulan sumber lisan maupun sumber tertulis, kritik, interpretasi, dan historiografi. Untuk memperdalam analisis, penulis menggunakan pendekatan interdisipliner melalui kajian ilmu sosial dan ilmu ekonomi dengan memakai konsep-konsep seperti interaksi sosial, distribusi, ekonomi kreatif, kewirausahaan, dll. Teknik penelitian yang digunakan dalam penelitian ini adalah dengan menggunakan teknik wawancara. Hal ini dilakukan karena terbatasnya sumber tertulis yang mengkaji secara langsung mengenai permasalahan di atas. Berdasarkan hasil temuan di lapangan, seni lukis dari limbah pelepah pisang ini telah ada sejak tahun 1969. Seni lukis ini merupakan seni lukis yang unik karena menggunakan limbah dari pelepah pisang. Pada awal perkembangannya seni lukis ini tidak serta merta dapat diterima oleh masyarakat sekitar, dan barulah pada tahun 2002 seni lukis dari limbah pelepah pisang ini mengalami puncak perkembangan. Pasalnya seni lukis ini tidak hanya dipasarkan di Cimahi saja, melainkan sampai ke mancanegara. Seni lukis dari limbah pelepah pisang ini dapat dijadikan sebagai sektor ekonomi kreatif dan dapat dijadikan sebagai lahan lapangan pekerjaan. Banyak upaya yang dilakukan oleh pelukis untuk mengembangkan seni lukis dari limbah pelepah pisang, selain itu pula pemerintah turut serta dalam mengembangkan seni lukis pelepah pisang. Kata kunci : Seni Lukis Pelepah Pisang, Ekonomi Kreatif, Pemasaran This skripsi titled Ade Moelyama role in developing the art painting of wasted banana leaves in Cimahi of historical studies from 1969 to 2010. The main issue studied in this skripsi was “How Development Art Painting of Wasted Banana Leaves in Cimahi from 1969 to 2010 and linkages with economic potential of art painting of banana leaves neglected. The method used is the historical method through four phases of heuristics, criticism, interpretation and historiography. To deepen the analysis, the author use the approach interdisciplinary through the study of social and economic by using concepts such as social interaction, distribution, creative economy, entrepreneurship, and other. A research technique used in this research is to use interview techniques. This is done because of the limited resources that examines written directly on the above problems. Based on the research results, the art painting of wasted banana leaves has existed since 1969. This painting is a painting that is unique because it uses waste form banan leaves. In the early development of art is not necessarily acceptable to the local community, and then in 2002 the art painting of wasted banana leaves is experiencing the peak development. This is because not only do marketing painting around Cimahi but abroad as well. Painting of wasted banana stalks can be used as a creative economic sector and creates jobs. Lack of awareness of the various parties to make this painting became dormant. Many attempts were made by the painter to develop the art of waste banana leaves, in addition the goverment also participated in the development the art of painting banana leaves. Keywords : Art Painting of Banana Leaves, Creative Economy, Marketin