Tag: H3K9me3

Functional-metabolic coupling in distinct renal cell types coordinates organ-wide physiology and delays premature ageing

Preferential carbohydrate import and early metabolism in PCs (but not SCs) supports renal physiology independent of ATP production Drosophila renal (Malpighian, MpT) tubules consist of two major cell types, the larger PCs and smaller SCs which perform distinct roles in ion, solute and water transport (Fig. 1a, b)16. These functional differences…

Continue Reading Functional-metabolic coupling in distinct renal cell types coordinates organ-wide physiology and delays premature ageing

How does the table shows the following statement

How does the table shows the following statement please explain briefly in words. 1-The majority of the women were diagnosed with low histological grade (grade I/II: 73.3%), early clinical stage (stage I/II: 71.5%), ER-positive (73.1%), PR-positive (72.1%), or HER2-negative (66.8%) 2. ‘The optimal cut-off value of H3K9me3 H-score was 240.0…

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Solved How does the table shows the following statement

How does the table shows the following statement please explain briefly in words. 1-‘The level of H3K9me3 in adjacent tissues was available in 633 patients, and the median (P25, P75) in tumor tissues [160.0 (62.5, 255.0)] was significantly lower than that in adjacent tissues 255.0 (210.0, 270.0)] (p <0.001) 2….

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Primate-specific ZNF808 is essential for pancreatic development in humans

Subjects The study was conducted in accordance with the Declaration of Helsinki and all subjects or their parents/guardian gave informed written consent for genetic testing. DNA testing and storage in the Beta Cell Research Bank was approved by the Wales Research Ethics Committee 5 Bangor (REC 17/WA/0327, IRAS project ID…

Continue Reading Primate-specific ZNF808 is essential for pancreatic development in humans

How to trigger h3k9me3 at specific loci?

What are the advantages of polythene chromosomes? 5 answers What’s the role of Dpt gene? 5 answers What are the different stages of cleavage of Ascaris lumbricoides? 5 answers What is the human ortholog to SWR-C? 3 answers What are the key elements of a DRE contabilidade? 5 answers How…

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How to study h3k9me3 activators?

What are the latest advances in bioinformatics? 5 answers What agents can cause h3k9 methylation? 5 answers How are precursors to histone methylation measured? 5 answers How to trigger h3k9me3 at specific loci? 4 answers Does arginine have any effect on herpes virus? 5 answers What sirtuns deacetylate h2? 4…

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Asymmetric distribution of parental H3K9me3 in S phase silences L1 elements

doi: 10.1038/s41586-023-06711-3. Online ahead of print. Zhiming Li #  1   2   3   4 , Shoufu Duan #  1   2   3   4 , Xu Hua  1   2   3   4 , Xiaowei Xu  1   2   3   4 , Yinglu Li  4 , Demis Menolfi  1 , Hui Zhou …

Continue Reading Asymmetric distribution of parental H3K9me3 in S phase silences L1 elements

TNRC18 engages H3K9me3 to mediate silencing of endogenous retrotransposons

Padeken, J., Methot, S. P. & Gasser, S. M. Establishment of H3K9-methylated heterochromatin and its functions in tissue differentiation and maintenance. Nat. Rev. Mol. Cell Biol. 23, 623–640 (2022). Article  CAS  PubMed  PubMed Central  Google Scholar  Tchasovnikarova, I. A. et al. Epigenetic silencing by the HUSH complex mediates position-effect variegation…

Continue Reading TNRC18 engages H3K9me3 to mediate silencing of endogenous retrotransposons

Unzipped chromosome-level genomes reveal allopolyploid nematode origin pattern as unreduced gamete hybridization

Nematode materials and species identification Mi, Mj, and Mg were collected from farmlands in Wuhan city of Hubei province, Longyan city of Fujian province, and Changsha city of Hunan Provinces, respectively. Two Ma samples were collected from farmlands in Shenyang city of Liaoning province and Shiping city of Yunnan province….

Continue Reading Unzipped chromosome-level genomes reveal allopolyploid nematode origin pattern as unreduced gamete hybridization

Characterization of H3K9me3 and DNA methylation co-marked CpG-rich regions during mouse development | BMC Genomics

CHMs are stable during mouse development To explore the co-localization between H3K9me3 and DNA methylation, we collected public H3K9me3 chromatin immunoprecipitation sequencing (ChIP-seq) and whole-genome bisulfite sequencing (WGBS) data during mouse pre-implantation embryogenesis [11], PGC development [12], spermatogenesis [13, 14], retina development [15], heart and liver development after gastrulation [16,17,18]…

Continue Reading Characterization of H3K9me3 and DNA methylation co-marked CpG-rich regions during mouse development | BMC Genomics

Decoupling the downstream effects of germline nuclear RNAi reveals that H3K9me3 is dispensable for heritable RNAi and the maintenance of endogenous siRNA-mediated transcriptional silencing in Caenorhabditis elegans

Decoupling the downstream effects of germline nuclear RNAi reveals that H3K9me3 is dispensable for heritable RNAi and the maintenance of endogenous siRNA-mediated transcriptional silencing in Caenorhabditis elegans – Fingerprint — Rutgers, The State University of New Jersey Sort by Weight Alphabetically Medicine & Life Sciences Caenorhabditis elegans 100% RNA Interference…

Continue Reading Decoupling the downstream effects of germline nuclear RNAi reveals that H3K9me3 is dispensable for heritable RNAi and the maintenance of endogenous siRNA-mediated transcriptional silencing in Caenorhabditis elegans

TET2 modulates spatial relocalization of heterochromatin in aged hematopoietic stem and progenitor cells

Animal models Animal studies were approved by the Institutional Animal Care Use Committee of the Institute of Biosciences and Technology, Texas A&M University (AUP 2020-0195). Most mouse strains bear a C57BL/6 genetic background unless otherwise noted. All the animals were housed in a certified animal facility with a standard dark/light…

Continue Reading TET2 modulates spatial relocalization of heterochromatin in aged hematopoietic stem and progenitor cells

DNA-binding protein PfAP2-P regulates parasite pathogenesis during malaria parasite blood stages

Parasite culture, maintenance, synchronization and transfection The DiCre-expressing P. falciparum clone II3 (ref. 10) was maintained in human A+ erythrocytes at 37 °C in Roswell Park Memorial Institute 1640 medium containing AlbumaxII (Invitrogen) supplemented with 2 mM l-glutamine. Parasites were either synchronized by sorbitol treatment or by purifying mature schizont stages using…

Continue Reading DNA-binding protein PfAP2-P regulates parasite pathogenesis during malaria parasite blood stages

DNA’s backup plan for genomic stability

The proper functioning of an important architectural component of our DNA, known as heterochromatin, is maintained by at least two pathways that can substitute for one another when either is lost, RIKEN researchers have found1. This finding provides a remarkable insight into how these complex biological systems include redundancy to…

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hiPSC Reprogramming Mimics hESCs

By Gail Dutton Although similar, the epigenomes of human induced pluripotent stem cells (hiPSCs) differ from those of the human embryonic stem cells (hESCs) they aim to replicate. These differences include epigenetic memory of their original specialized state and reprogramming aberrations that affect the cells’ functions, adding another challenge for…

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Human endogenous retroviruses as epigenetic therapeutic targets in TP53-mutated diffuse large B-cell lymphoma

TP53 mutation (TP53mut) occurs in 10-20% of diffuse large B-cell lymphoma (DLBCL) cases and serves as an unfavorable biomarker of DLBCL progression. It confers resistance to immunochemotherapy, high-dose chemotherapy, autologous stem cell transplantation, and anti-CD19 chimeric antigen receptor T-cell therapy. Therapeutic targeting of TP53mut remains a significant challenge in DLBCL…

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Chromatin aberration triggered by environmental cues

Download: H3K9me3 heatmap Megabase-sized H3K9me3 domains can be triggered by environmental cues (Type I-III). These domains are prominent in primary cultured cells, and likely reflect nuclear architecture changes. They are gene-poor regions that contact the nuclear lamina in certain cells. The knock-down of histone methyltransferase Suv39h1 and the inhibitions of…

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How-to: Profile the epigenome

The epigenome regulates the expression of genes without altering their underlying DNA sequence. Comprising a dynamic landscape of chemical modifications and structural changes to DNA and its associated histone proteins, the epigenome wields profound influence over cellular identity and function. Epigenetic mechanisms, such as DNA methylation and histone modifications, form…

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DNA Methylation Controls Verticillium Dahliae’s Virulence in Plants

This study is led by Dr Cheng-Guo Duan (Center of Excellence in Molecular Plant Sciences, Chinese Academy of Science). As a conserved epigenetic mark, DNA cytosine methylation at 5′ position (5-mC) plays important roles in multiple biological processes including plant immunity. While, it remains still elusive about the involvement of…

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Widespread loss of the silencing epigenetic mark H3K9me3 in astrocytes and neurons along with hippocampal-dependent cognitive impairment in C9orf72 BAC transgenic mice.

Abstract Abstract Background Hexanucleotide repeat expansions of the G4C2 motif in a non-coding region of the C9ORF72 gene are the most common genetic cause of amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). Tissues from C9ALS/FTD patients and from mouse models of ALS show RNA foci, dipeptide-repeat proteins, and notably,…

Continue Reading Widespread loss of the silencing epigenetic mark H3K9me3 in astrocytes and neurons along with hippocampal-dependent cognitive impairment in C9orf72 BAC transgenic mice.

HP1 Chromodomain: The perfect cap for H3K9me3 – 3D model by nhaw6452 [1027a5a]

Post translational modification of residues on histone protein tails are known to significantly affect gene expression. In particular, the methylation of lysine residues at position 9 on histone H3 proteins (H3K9) has proven to be a hallmark indicator of inactive genes. To stop the unwanted expression of certain genes in…

Continue Reading HP1 Chromodomain: The perfect cap for H3K9me3 – 3D model by nhaw6452 [1027a5a]

TNT Removes Epigenetic Memories from hiPSCs

While lingering memories can represent unwelcome guests, destroying them with the power of dynamite may seem like overkill! However, a volatile new study now describes TNT or transient-naïve-treatment as a simple means of ridding human induced pluripotent stem cells (hiPSC) of their epigenetic memories and improving their therapeutic potential. An…

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The spreading of facultative H3K9me3-heterochromatin drives congenital disease

Abstract Heterochromatin marked by trimethylated histone 3 at lysine 9 (H3K9me3) plays fundamental roles in reprogramming to direct cell fate determination in higher eukaryotes. However, the upstream factors that guide the establishment and spreading of H3K9me3-heterochromatin, leading to human developmental malformations, remain elusive. In this study, we found that Cdk13,…

Continue Reading The spreading of facultative H3K9me3-heterochromatin drives congenital disease

New Reprogramming Method Produces Naive Human Induced Pluripotent Stem Cells

Researchers from Monash University in Melbourne and The University of Western Australia have demonstrated how a reprogramming method imitates embryonic epigenetic reset. Transient naive treatment (TNT) reprogrammed human induced pluripotent stem (hiPS) cells that are molecularly and functionally more similar to human embryonic stem (hES) cells than primed hiPS cells,…

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A high-throughput screening assay for silencing established HIV-1 macrophage infection identifies nucleoside analogs that perturb H3K9me3 on proviral genomes

HIV-infected macrophages are long-lived cells that represent a barrier to functional cure. Additionally, low-level viral expression by central nervous system (CNS) macrophages contributes to neurocognitive deficits that develop despite antiretroviral therapy (ART). We recently identified H3K9me3 as an atypical epigenetic mark associated with chronic HIV infection in macrophages. Thus, strategies…

Continue Reading A high-throughput screening assay for silencing established HIV-1 macrophage infection identifies nucleoside analogs that perturb H3K9me3 on proviral genomes

Unreprogrammed H3K9me3 prevents minor zygotic genome activation and lineage commitment in SCNT embryos

doi: 10.1038/s41467-023-40496-3. Ruimin Xu #  1   2   3 , Qianshu Zhu #  3   4 , Yuyan Zhao  1 , Mo Chen  2   5 , Lingyue Yang  1   2 , Shijun Shen  3   4 , Guang Yang  3   4 , Zhifei Shi  1 , Xiaolei Zhang  1 , Qi Shi  1   2 , Xiaochen Kou …

Continue Reading Unreprogrammed H3K9me3 prevents minor zygotic genome activation and lineage commitment in SCNT embryos

Imaging-based study demonstrates how the DEK nanoscale distribution differentially correlates with epigenetic marks in a breast cancer model

Cell culture Mammary epithelial, non-transformed MCF10A cells (ATCC CRL-10317) were grown in DMEM:F-12 (Dulbecco’s Modified Eagle Medium:Nutrient Mixture F-12) (1:1) medium (Gibco, 11330057) supplemented with 5% Horse Serum (HS), 2 mM l-glutamine and 1% penicillin/streptomycin (Sigma-Aldrich, G6784), 10 µg/ml insulin (Sigma-Aldrich, I9278) and 0.5 µg/ml hydrocortisone (Sigma-Aldrich, H0888). Human Epidermal Growth Factor (hEGF,…

Continue Reading Imaging-based study demonstrates how the DEK nanoscale distribution differentially correlates with epigenetic marks in a breast cancer model

Rapid gene content turnover on the germline-restricted chromosome in songbirds

This work was carried out in accordance with ethical animal research requirements of Poland according to Polish law (the Act On the Protection of Animals used for Scientific or Educational Purposes, 15.01.2015, item 266, implementing Directive 2010/63/EU of the European Parliament and of the European Council of 22.09.2010). Experiments on…

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Differential exon usage of developmental genes is associated with deregulated epigenetic marks

H3K36me3 mark is most relevant to AS events The first task was to prepare a suitable data set where differentially used exons (DEUs) can be clearly associated with individual genes. Hence, out of 19,240 clusters of protein coding genes generated for the DEXSeq analysis (see “Materials and methods” section), we…

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Single-molecule genome-wide mutation profiles of cell-free DNA for non-invasive detection of cancer

Genome-wide somatic mutation analyses of cancer tissues To develop this method, we examined whole-genome sequences of cancers from 2,511 individuals across 25 different cancers from the PCAWG study25,26, identifying distinct mutation frequencies across the genome in different tumor types (Extended Data Fig. 1). For example, analysis of lung tumor and…

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Zfp296 knockout enhances chromatin accessibility and induces a unique state of pluripotency in embryonic stem cells

Establishment of Zfp296-deficient ESCs The expression of Zfp296 during ESC differentiation into trophectoderm was examined using the ZHBTc4 ESC line, in which expression of Pou5f1 encoding Oct3/4 can be downregulated by tetracycline20. As shown in Supplementary Fig. 1a, Zfp296 expression rapidly decreased, suggesting that Zfp296 is downstream of Oct3/4. To generate…

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H3K9me3 signals significantly increase as oocytes become more proximal.

A. Wild-type, met-2 mutant, and set-25 mutant gonads were dissected, fixed, and stained for DNA (blue) and H3K9me3 (red). In N2s, an increase in H3K9me3 signal is observed at the -3 to -1 positions in comparison to more distal oocytes and pachytene nuclei from the same animal. Loss of MET-2…

Continue Reading H3K9me3 signals significantly increase as oocytes become more proximal.

Depletion of TOP-2 and condensin II does not alter H3K9me3 deposition in proximal gonads.

A. Gonads from N2 adults treated with either control or top-2/capg-2 RNAi were dissected, fixed, and stained for DNA (blue) and H3K9me3 (red). Treatment with top-2/capg-2 RNAi did not alter the deposition of H3K9me3 in proximal gonads. Scale bar represents a length of 2 μm. B. Quantification of signal density…

Continue Reading Depletion of TOP-2 and condensin II does not alter H3K9me3 deposition in proximal gonads.

Epigenetic silencing of OR and TAS2R genes expression in human orbitofrontal cortex at early stages of sporadic Alzheimer’s disease

doi: 10.1007/s00018-023-04845-1. Affiliations Expand Affiliations 1 Neurodegenerative Diseases Group, Hospital Universitario 12 de Octubre Research Institute (imas12), Madrid, Spain. vdacunhaalves@gmail.com. 2 Network Center for Biomedical Research, Neurodegenerative Diseases (CIBERNED), Madrid, Spain. vdacunhaalves@gmail.com. 3 PhD Program in Neuroscience, Autonoma de Madrid University, Madrid, Spain. vdacunhaalves@gmail.com. 4 Neurodegenerative Diseases Group, Hospital Universitario…

Continue Reading Epigenetic silencing of OR and TAS2R genes expression in human orbitofrontal cortex at early stages of sporadic Alzheimer’s disease

SMCHD1 and LRIF1 converge at the FSHD-associated D4Z4 repeat and LRIF1 promoter yet display different modes of action

Somatic loss of LRIF1 or SMCHD1 in control myocytes leads to insufficient DUX4 derepression We have previously shown that SMCHD1 and LRIF1L aid in transcriptional repression of the D4Z4 repeat as short-term depletion of either LRIF1L or SMCHD1 in muscle cells having a D4Z4 repeat of <20 units on a…

Continue Reading SMCHD1 and LRIF1 converge at the FSHD-associated D4Z4 repeat and LRIF1 promoter yet display different modes of action

CD147 Facilitates the Pathogenesis of Psoriasis through Glycolysis and H3K9me3 Modification in Keratinocytes

doi: 10.34133/research.0167. eCollection 2023. Chao Chen  1   2   3   4   5 , Xiaoqing Yi  1   2   3   4   5 , Panpan Liu  1   2   3   4   5 , Jie Li  1   2   3   4   5 , Bei Yan …

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Solved 11. If a chromatin remodeler removes the nucleosomes

In the case of H3K9me3, this specific histone modification involves the addition of three methyl groups to the lysine 9 residue of histone H3. H3K9me3 is associated with heterochromatin formation and typically leads to the compaction of chromatin and transcriptional repression. The presence of H3K9me3 marks the chromatin region as…

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Anti-H3K9me3 Antibody – Kerafast

This H3K9me3 rabbit polyclonal antibody was raised against a modified branched peptide and specifically recognizes histone H3 tri-methylated on lysine 9 (H3K9me3). Highlights: Detects a single protein of approximately 14 kDa by western blot using acid extracted histones Suitable for chromatin immunoprecipitation (ChIP) assays H3K9me3 indicates the addition of a…

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mES H3K9me3 enrichment of MMERGLN repeat instances

mES H3K9me3 enrichment of MMERGLN repeat instances ES H3K9me3 enrichment of MMERGLN repeat instances The repeat phylogeny was determined ES H3K9me3 reads mapped to instances of the MMERGLN repeats. The branch coloring shows enrichment in H3K9me3 relative to ES H3. [download] Does the applet not display properly? Archaeopteryx requires at…

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PhaeoEpiView: an epigenome browser of the newly assembled genome of the model diatom Phaeodactylum tricornutum

Despite being an established model, the genome and annotation of P. tricornutum are not concordant and the existing epigenetic resources generated so far lack a well-defined framework for accurate and user friendly utilization. To address this limitation, we sought to establish a coherent resource rendering the multiple genomic and epigenomic…

Continue Reading PhaeoEpiView: an epigenome browser of the newly assembled genome of the model diatom Phaeodactylum tricornutum

Gluconeogenic enzyme PCK1 supports S-adenosylmethionine biosynthesis and promotes H3K9me3 modification to suppress hepatocellular carcinoma progression

doi: 10.1172/JCI161713. Online ahead of print. Dongmei Gou  1 , Rui Liu  1 , Xiaoqun Shan  1 , Haijun Deng  1 , Chang Chen  2 , Jin Xiang  1 , Yi Liu  1 , Qingzhu Gao  1 , Zhi Li  3 , Ailong Huang  4 , Kai Wang  4 , Ni Tang  1 Affiliations Expand Affiliations 1 Institute for Viral Hepatitis,…

Continue Reading Gluconeogenic enzyme PCK1 supports S-adenosylmethionine biosynthesis and promotes H3K9me3 modification to suppress hepatocellular carcinoma progression

Mobile element variation contributes to population-specific genome diversification, gene regulation and disease risk

Development and benchmarking of MEGAnE Accurate variant genotyping is required for statistical genetics. To enable both discovery and accurate MEV genotyping from genomes studied using short reads, we developed a new bioinformatic tool, mobile element genotype analysis environment (MEGAnE; Supplementary Note). Compared to SVs resolved by long reads, MEGAnE discovers…

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Solved E F Histone H3 (tri methyl K9 Histone H3

Abstract Background: Intrahepatic cholangiocarcinoma (ICC) is a malignant tumor, which poses a serious threat to human health. Histone 3 lysine 9 trimethylation (H3K9me3) is a post-translational modification involved in regulating a broad range of biological processes and has been considered as potential therapeutic target in types of cancer. However, there…

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ChIP-Seq experiment, MACS2 bdgpeakcall 0 fold-change, pvalue and qvalue

Hello, I’m currently following this paper Myc Regulates Chromatin Decompaction and Nuclear Architecture during B Cell Activation. It is a ChIP-Seq to generate genome-wide maps of 34 chromatin modifications (17 acetylation marks, and 17 methylation marks) and the histone variant H2AZ. B cells were either naïve (G0) or activated for…

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A multi-omics integrative analysis based on CRISPR screens re-defines the pluripotency regulatory network in ESCs

Genome-scale CRISPR screen to identify regulators that maintain mESC pluripotency To establish a function-based PGRN, we first performed a CRISPR-Cas9 mediated genome-wide screen to detect genes essential for self-renewal. mESCs were cultured under Leukaemia inhibitory factors (LIF)/serum condition (L/S), which was commonly used in similar tasks and confer a naïve…

Continue Reading A multi-omics integrative analysis based on CRISPR screens re-defines the pluripotency regulatory network in ESCs

Whole-genome doubling perturbs the 3D genome

Whole-genome doubling (WGD) is a cancer hallmark, but its functional consequences during tumorigenesis are unclear. Lambuta et al. chemically induce WGD in three TP53-mutant cell line models and examine its effects on the 3D genome using single-cell and bulk genomic methods including Hi-C. Cells with WGD show a loss of…

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Setdb1 is required for germline development and silencing of H3K9me3-marked endogenous retroviruses in primordial germ cells

Sheng Liu1,6, Julie Brind’Amour1,6, Mohammad M. Karimi1,2, Kenjiro Shirane3, Aaron Bogutz1, Louis Lefebvre1, Hiroyuki Sasaki3,4, Yoichi Shinkai4,5 and Matthew C. Lorincz1 1Department of Medical Genetics, Life Sciences Institute, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canadan; 2Biomedical Research Centre, University of British Columbia, Vancouver, British Columbia V6T 1Z3,…

Continue Reading Setdb1 is required for germline development and silencing of H3K9me3-marked endogenous retroviruses in primordial germ cells

SUV39H1 is a prognosis and immune microenvironment-related biomarker in diffuse large B-cell lymphoma

Background: The tumor microenvironment plays a crucial role in the oncogenesis and treatment of diffuse large B-cell lymphoma (DLBCL). The H3K9me3-specific histone methyltransferase Suppressor of variegation 3-9 homolog 1 (SUV39H1) is a significant gene that promotes the progression of various malignancies. However, the specific expression of SUV39H1 in DLBCL remains…

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4/7/2023 BMG Feinberg Fellow Candidate, Dr. Nazerke Atinbayeva

When: Friday, April 7, 202310:00 AM – 11:00 AM Central Where: Robert H Lurie Medical Research Center, Searle Seminar Room, 303 E. Superior, Chicago, IL 60611 map it Audience: Faculty/Staff – Student – Post Docs/Docs – Graduate Students Contact: Beverly Kirk   (312) 503-5217 Group: Biochemistry & Molecular Genetics Invited Lectures…

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SARS-CoV-2 rewires host chromatin | Nature Reviews Microbiology

The conformation of the mammalian 3D genome is highly regulated and has a key role in various biological processes, such as transcription, DNA replication or repair, cell division or cell differentiation. By high-throughput chromosome conformation capture (Hi-C) and analysis, chromatin architecture is structured into A compartments (transcriptionally active euchromatin) and B compartments…

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H3K9 trimethylation dictates neuronal ferroptosis through repressing Tfr1

. 2023 Mar 24;271678X231165653. doi: 10.1177/0271678X231165653. Online ahead of print. Ting Lan  1 , Liye Hu  1 , Tingting Sun  1 , Xuechun Wang  2 , Zhongnan Xiao  1 , Danmin Shen  1 , Weihua Wu  1 , Zhaoli Luo  1 , Chao Wei  3 , Xiaotong Wang  3 , Meng Liu  3 , Yi Guo  2 , Liyong Wang  4 , Yamei…

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Writing the Rules on CRISPR Activation

Researchers from the Wellcome Sanger Institute and collaborators used human stem cells and neurons to investigate what features influence how well CRISPR activation works for different sets of genes. Their study “Massively parallel characterization of CRISPR activator efficacy in human induced pluripotent stem cells and neurons,” which appears in Molecular…

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New research writes the rules on CRISPR activ

New research writes the rules on CRISPR activation  New research starts to write the rulebook on how to effectively use CRISPR activation technology. Researchers, from the Wellcome Sanger Institute and collaborators, used human stem cells and neurons to investigate what features influence how well CRISPR activation works for different sets…

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New research explores the rules of CRISPR activation

Credit: Molecular Cell (2023). DOI: 10.1016/j.molcel.2023.02.011 New research is starting to write the rulebook on how to effectively use CRISPR activation technology. Researchers from the Wellcome Sanger Institute and collaborators have used human stem cells and neurons to investigate the features that influence how well CRISPR activation works for different…

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Sci-Hub | Contrasting roles of H3K4me3 and H3K9me3 in regulation of apoptosis and gemcitabine resistance in human pancreatic cancer cells. BMC Cancer, 18(1)

Sci-Hub | Contrasting roles of H3K4me3 and H3K9me3 in regulation of apoptosis and gemcitabine resistance in human pancreatic cancer cells. BMC Cancer, 18(1) | 10.1186/s12885-018-4061-y ◂ ↓ save Lu, C., Yang, D., Sabbatini, M. E., Colby, A. H., Grinstaff, M. W., Oberlies, N. H., … Liu, K. (2018). Contrasting roles…

Continue Reading Sci-Hub | Contrasting roles of H3K4me3 and H3K9me3 in regulation of apoptosis and gemcitabine resistance in human pancreatic cancer cells. BMC Cancer, 18(1)

Segmentation

Segmentation Segmentation algorithms partition the genome into regions with distinct epigenomic profiles. These are genomic regions of similar signal pattern over a selected number of assays. To segment the genome for each cell type we currently use either ChromHMM (Ernst et al., 2011) or Segway (Hoffman et al., 2011). These…

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Using Entrez to download Supplementary files in GEO entry via command line?

Suppose I’m looking at a GEO entry like so: www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM946533 Notice at the bottom is a table of ‘Supplementary files’, containing broadpeak and bigwig files. I’m wondering how to download these using Entrez. I’ve tried a variety of approaches, the “closest” I’ve gotten is the following: esearch -db gds -query…

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Remodeling of H3K9me3 during the pluripotent to totipotent-like state transition

. 2022 Dec 25;S2213-6711(22)00595-1. doi: 10.1016/j.stemcr.2022.12.006. Online ahead of print. Hu Li  1 , Jiatong Sun  2 , Yu Dong  2 , Yixin Huang  2 , Li Wu  2 , Chenxiang Xi  2 , Zhongqu Su  3 , Yihan Xiao  2 , Chuyu Zhang  2 , Yuwei Liang  2 , Yujun Li  2 , Zhiyi Lin  2 , Lu Shen  2 , Yixing…

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Any good tools for biological annotation of ChIP-seq broadpeak (H3K9me3, H3K27me3)?

Any good tools for biological annotation of ChIP-seq broadpeak (H3K9me3, H3K27me3)? 0 Hi, I have called ChIP-seq broadpeak (H3K9me3, H3K27me3) using SICER2 in mm10. The peak looks good and consistent with the IGV findings. Is there any good tools to annotate these broad peaks to coding genes? I know GREAT(great.stanford.edu/public/html/)…

Continue Reading Any good tools for biological annotation of ChIP-seq broadpeak (H3K9me3, H3K27me3)?

Differential enrichment of H3K9me3 in intrahepatic cholangiocarcinoma | BMC Medical Genomics

Sia D, Tovar V, Moeini A, Llovet JM. Intrahepatic cholangiocarcinoma: pathogenesis and rationale for molecular therapies. Oncogene. 2013;32(41):4861–70. CAS  Article  Google Scholar  Sungwan P, Lert-Itthiporn W, Silsirivanit A, Klinhom-On N, Okada S, Wongkham S, Seubwai W. Bioinformatics analysis identified CDC20 as a potential drug target for cholangiocarcinoma. PeerJ. 2021;9:e11067. Article …

Continue Reading Differential enrichment of H3K9me3 in intrahepatic cholangiocarcinoma | BMC Medical Genomics

Allele-specific H3K9me3 and DNA methylation co-marked CpG-rich regions serve as potential imprinting control regions in pre-implantation embryo

. 2022 May;24(5):783-792. doi: 10.1038/s41556-022-00900-4. Epub 2022 Apr 28. Affiliations Expand Affiliations 1 Institute for Regenerative Medicine, Shanghai East Hospital, Shanghai Key Laboratory of Signaling and Disease Research, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, Shanghai, China. 2 Shanghai Institute of Stem…

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Figure – PMC

Early-life FGF2 alters the association of H3K9me3 at FGF2 and GR promoters. (A and B) The association of H3K9me3 at FGF2 decreased significantly in HC and NAcc bLR rats following neonatal FGF2 exposure (***P < 0.001, n = 6 per group). (A and C) However, the association of H3K9me3 at…

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Single-Cell Technology Measures Epigenetic States and Gene Expression in One Go

Advances in single-cell technologies have not only made it possible to analyze multiple molecular families in individual cells, they have also enabled scientists to parse through limitations in data analysis arising from the intercellular diversity of measured parameters. Although single-cell sequencing is now widely available, techniques to detect epigenetic markers…

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A new technique to unravel gene regulation

Zebrafish notochord nuclei at 15-somite stage. Grey: nuclear DNA (DAPI). Color: histone H3K9me3. Credit: Phong Nguyen, Franka Rang & Kim de Luca. How is the activity of genes regulated by the packaging of DNA? To answer this question, a technique to measure both gene expression and DNA packaging at the…

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ATF7ip Targets Transposable Elements for H3K9me3 Deposition to Modify CD8+ T Cell Effector and Memory Responses

Key Points ATF7ip is a critical regulator of CD8+ T cell effector and memory responses. Deletion of ATF7ip in CD8+ T cells results in enhanced Il2 and Il7r expression. ATF7ip targets transposable elements to modulate Il7r and Il2 expression. Abstract CD8+ T cells are critical for the immune response to…

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SETDB1/NSD-dependent H3K9me3/H3K36me3 dual heterochromatin maintains gene expression profiles by bookmarking poised enhancers

. 2022 Jan 17;S1097-2765(21)01142-4. doi: 10.1016/j.molcel.2021.12.037. Online ahead of print. Affiliations Expand Affiliations 1 DNA Repeat Lab, Institute of Human Genetics CNRS-Université de Montpellier UMR 9002, 141 rue de la Cardonille, 34000 Montpellier, France. 2 Chromatin and Cell Biology Lab, Institute of Human Genetics CNRS-Université de Montpellier UMR 9002, 141…

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Lead exposure induces dysregulation of constitutive heterochromatin hallmarks in live cells

This article was originally published here Curr Res Toxicol. 2021 Dec 11;3:100061. doi: 10.1016/j.crtox.2021.12.001. eCollection 2022. ABSTRACT Lead (Pb) is a heavy metal contaminant commonly found in air, soil, and drinking water due to legacy uses. Excretion of ingested Pb can result in extensive kidney damages due to elevated oxidative…

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Exercise Reduces H3K9me3 and Regulates Brain Derived Neurotrophic Factor and GABRA2 in an Age Dependent Manner

FIGURE 6 H3K9me3 repression of BDNF and GABA receptors decreases with age. Comparison of ChIP%… FIGURE 6 H3K9me3 repression of BDNF and GABA receptors decreases with age. Comparison of ChIP% input data from young and aged mice. (A) H3K9me3 levels at the BDNF 1 promoter were significantly greater in young…

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Figure 5 | One-Two Punch Therapy for the Treatment of T-Cell Malignancies Involving p53-Dependent Cellular Senescence

Wogonin induced senescence-associated heterochromatin foci in senescent cells. (a) Hut-102 and Jurkat cells were treated with or without 20 μM wogonin for 5 d; then, the cells were fixed and permeabilized, and nuclei were stained with DAPI (blue). SAHF formed in wogonin-treated Hut-102 and Jurkat cells. Representative confocal images for wogonin-induced SAHF…

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Early male and female germ cells regulate their gene expression differently

13 December 2021 Gene expression during early development of primordial germ cells (PGCs) is sex-specific. Research led by Professor Petra Hajkova from the Reprogramming and Chromatin research group at the Medical Research Council London Institute of Medical Sciences has shown for the first time that germ cells, which give rise…

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