Tag: H3K9me3

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…

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…

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…

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,…

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…

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…

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…

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…

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…

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,…

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…

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…

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…

. 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…

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…

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…

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…

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…

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…

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…

. 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…

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/)…

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 …

. 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…

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…

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…

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…

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…

. 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…

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…

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…

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…

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…