Tag: Nucleosome

Read the Full Video Transcript Andrea Miyahira: Welcome. I’m Andrea Miyahira and I’m the senior director of Global Research and Scientific Communications at the Prostate Cancer Foundation. Today I’m joined by Dr. Gavin Ha, an assistant professor at Fred Hutchinson Cancer Center and the PCF 2019 Young Investigator. Dr. Ha’s…

We present a protocol for assay for transposase-accessible chromatin with high-throughput sequencing (ATAC-seq) specifically on adipocytes using nucleus sorting with adipose tissues isolated from transgenic reporter mice with nuclear fluorescence labeling. ATAC-seq is a powerful technique to understand gene expression regulatory mechanisms. However, adipose tissue is difficult using this technique…

Protein expression, mutagenesis and purification Xenopus laevis histones for nucleosome assembly were overexpressed in the Escherichia coli BL21(DE3) pLysS strain and purified from inclusion body as previously described48. The cells were grown in LB medium at 37 °C and induced with 1 mM IPTG when OD600 reached 0.6. After 3 h of expression,…

Overview of sample sequencing We compared the transcriptomes of BZ-resistant (17LER) and wild-type (17WTS) T. cruzi populations. cDNA libraries were constructed, sequenced and analysed for identifying the DE transcripts associated with resistance to BZ. The following parameters were evaluated using the read-quality analysis: (i) quantity of the sequenced reads; (ii)…

Description Genes encoding 45S ribosomal RNA (rDNA) are known for their abundance within eukaryotic genomes and for their unstable copy numbers in response to changes in various genetic and epigenetic factors. Commonly, we understand as epigenetic factors (affecting gene expression without a change in DNA sequence), namely…

Research by MIT scientists was published in normal genetics, indicating that many genes interact with dozens of different regulators. Identification of the regulatory elements that influence genes can help unravel the mysteries of the development of specific diseases, as well as develop approaches to treat them. The genome is 100…

In this section, we derive a simplified expression for the proportionality constant \(\alpha\) that enables quantitative ChIP-seq and we introduce some consequences for track building. This new expression is more intuitive to understand, easier to evaluate, and more accurate to sequencing outcomes than the previous expression. While values derived from…

1. Introduction Pyropia is a representative genus in the rhodophyte order Bangiales. It is of fundamental commercial and social importance as the edible seaweed “nori” [1]. Pyropia species, particularly Pyropia yezoensis (also referred to as Neopyropia yezoensis) and Pyropia haitanensis (also referred to as Neoporphyra haitanensis), are widely cultivated in…

Science has moved on since William Shakespeare put quill to parchment around 1600 to write the Tragedy of Hamlet, Prince of Denmark, but his legacy has survived to influence a new manuscript that describes the quest to discover histone modifications that better distinguish active enhancers. “H2B, or not H2B, that…

PENNSYLVANIA: New research by the research team at Penn State sheds light on how an enzyme that aids in the regulation of ageing and other metabolic processes accesses our genetic material to modify gene expression within the cell. A team led by Penn State researchers created images of a sirtuin…

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…

ATAC-seq peak calling with MACS 3 I am trying to call peaks in ATAC-seq data. Not surprisingly, MACS is a popular option. According to the MACS documentation: To find enriched cutting sites such as some DNAse-Seq datasets. In this case, all 5′ ends of sequenced reads should be extended in…

Bell, S. P. & Labib, K. Chromosome duplication in Saccharomyces cerevisiae. Genetics 203, 1027–1067 (2016). Article  CAS  PubMed  PubMed Central  Google Scholar  Eaton, M. L., Galani, K., Kang, S., Bell, S. P. & MacAlpine, D. M. Conserved nucleosome positioning defines replication origins. Genes Dev. 24, 748–753 (2010). Article  CAS  PubMed …

Which ATAC-seq SAM/BAM fields are required for bigwig generation by deeptools bamCoverage? 0 Hi, I plan to convert SAM file into BED file using bedops sam2bed tool and perform “chr start and end coordinates” data points manipulation to break di-nucleosome and tri-nucleosome data points into mono-nucleosome data points, then convert…

In a recent article published in Nature Genetics, researchers showed that mammalian SWItch/Sucrose Non-Fermentable (mSWI/SNF) chromatin remodeling complexes represent a potential class of host-directed broad-acting severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) therapeutic target. Study: Pharmacological disruption of mSWI/SNF complex activity restricts SARS-CoV-2 infection. Image Credit: Kateryna Kon/Shutterstock Background Chromatin…

Objective: The aim of this study was to define the clinical, histopathologic, and prognostic features associated with simultaneous positivity for anti-dsDNA, -nucleosome, and -histone antibodies (3-pos) in Korean patients with biopsy-proven lupus nephritis (LN). Methods: The 102 patients included in the study had undergone kidney biopsy prior to the start…

Bergwerk, M. et al. Covid-19 breakthrough infections in vaccinated health care workers. N. Engl. J. Med. 385, 1474–1484 (2021). Article  CAS  PubMed  Google Scholar  V’Kovski, P., Kratzel, A., Steiner, S., Stalder, H. & Thiel, V. Coronavirus biology and replication: implications for SARS-CoV-2. Nat. Rev. Microbiol. 19, 155–170 (2021). Article  PubMed …

doi: 10.1007/978-1-0716-3084-6_12. Affiliations Expand Affiliation 1 Department of Life Sciences, Pohang University of Science and Technology (POSTECH), Pohang, South Korea. tyroh@postech.edu. Item in Clipboard Tae-Young Roh. Methods Mol Biol. 2023. Show details Display options Display options Format AbstractPubMedPMID doi: 10.1007/978-1-0716-3084-6_12. Affiliation 1 Department of Life Sciences, Pohang University of Science…

What gets hyped, and what remains neglected, often depends on good storytelling. When the Human Genome Project began, in 1990, it had a simple story, well told. From a standing start, American taxpayers would pay for an exhaustive map of the DNA that makes up the 24 sorts of chromosomes…

Received: 24 January 2023 / Revised: 2 March 2023 / Accepted: 4 March 2023 / Published: 7 March 2023 Round 1 Reviewer 1 Report In this manuscript, Staneva et al. study mitochondrial dynamics of ageing in budding yeast chromatin mutants. In particular, the authors investigated arp4, hho1 and double mutants….

Ludwig, L. S. et al. Transcriptional states and chromatin accessibility underlying human erythropoiesis. Cell Rep. 27, 3228–3240.e7 (2019). Article  CAS  PubMed  PubMed Central  Google Scholar  Argelaguet, R. et al. Multi-omics profiling of mouse gastrulation at single-cell resolution. Nature 576, 487–491 (2019). Article  CAS  PubMed  PubMed Central  Google Scholar  Pawlak, M….

Early detection (pancreatic cancer) cfMeDIP-seq, 5hmC sequencing LR elastic-net Hierarchical clustering, t-SNE, LR with elastic-net penalization Methylation (5mC-5hmC) 208 (72/136) 24-feature 5mC, 27-features 5hmC, 51-features combined model SML, UML Combined 5mC and 5hmC AUC of 0.997 (sensitivity 0.938, specificity 0.955) Median total reads: 17.4 M, 0.8 nonduplicate mapping rate pms.cd120.com/PDAC/index.html…

DOI: 10.18129/B9.bioc.NuPoP     This is the development version of NuPoP; for the stable release version, see NuPoP. An R package for nucleosome positioning prediction Bioconductor version: Development (3.17) NuPoP is an R package for Nucleosome Positioning Prediction.This package is built upon a duration hidden Markov model proposed in Xi…

Citation: Kaimeng Huang*, Xiaobai Zhang*, Jiejun Shi*, Mingze Yao, Jiannan Lin, Jiao Li, He Liu, Huanhuan Li, Guang Shi, Zhibin Wang, Biliang Zhang, Jiekai Chen, Guangjin Pan, Cizhong Jiang, Duanqing Pei, and Hongjie Yao. 12/7/2015. “Dynamically reorganized chromatin is the key for the reprogramming of somatic cells to pluripotent cells.”…

image: DNA bits view more  Credit: alengo Cancer has many faces – no wonder, then, that the range of cancer-causing mutations is huge as well. The totality of such genomic alterations in an individual is what experts call a “mutational landscape.” These landscapes differ from one another depending on the type…

Finzi, D. Identification of a reservoir for HIV-1 in patients on highly active antiretroviral therapy. Science 278, 1295–1300 (1997). Article  CAS  Google Scholar  Wong, J. K. Recovery of replication-competent HIV despite prolonged suppression of plasma viremia. Science 278, 1291–1295 (1997). Article  CAS  Google Scholar  Joos, B. et al. HIV rebounds…

Griffin: Getting more information from cell-free DNA Early liquid biopsy strategies focused on the sequence of the fragments of cell-free DNA released by tumors. The DNA of cancer cells can be rearranged or mutated in characteristic ways, allowing scientists to detect the presence of cancer or important mutations that could…

NEW YORK – A University of Wisconsin at Madison-led team has tapped into tumor DNA fragment and nucleotide frequency profiles in blood samples to come up with an approach that could be used to detect or monitor early-stage cancer. “Genome-wide fragmentation patterns in cell-free DNA (cfDNA) in plasma are strongly…

1 Bomi8228 Probetacellulin Q9TTC5 2 Bomi5121 Dimethylaniline monooxygenase [N-oxide-forming] 3/Dimethylaniline oxidase 3/Hepatic flavin-containing monooxygenase 3/Trimethylamine monooxygenase Q8HYJ9 3 Bomi10437 Uterine milk protein P46201 4 Bomi9179 Signal transducer and activator of transcription 5A/Mammary gland factor Q95115 5 Bomi9003 Selenoprotein P P49907 6 Bomi3613 Acetyl-CoA carboxylase 1 Q9TTS3 7 Bomi5003 Cytoskeleton-associated protein…

Zhang H., Qin C., An C., Zheng X., Wen S., Chen W., Liu X., Lv Z., Yang P., Xu W., Gao W., Wu Y. 2021. Application of the CRISPR/Cas9-based gene editing technique in basic research, diagnosis, and therapy of cancer. Mol. Cancer. 20 (1), 126. doi.org/10.1186/s12943-021-01431-6 Article  CAS  Google Scholar …

Amiel, D., Frank, C., Harwood, F., Fronek, J. & Akeson, W. Tendons and ligaments: a morphological and biochemical comparison. J. Orthop. Res. 1, 257–265 (1984). PubMed  CAS  Google Scholar  Lipps, D. B., Wojtys, E. M. & Ashton-Miller, J. A. Anterior cruciate ligament fatigue failures in knees subjected to repeated simulated…

The incidence of lung adenocarcinoma (LUAD), the most common subtype of lung cancer, continues to make lung cancer the largest cause of cancer-related deaths worldwide. Long noncoding RNAs (lncRNAs) have been shown to have a significant role in both the onset and progression of lung cancer. In this study, we…

Baylin, S. B. & Jones, P. A. A decade of exploring the cancer epigenome – biological and translational implications. Nat. Rev. Cancer 11, 726–734 (2011). CAS  PubMed  PubMed Central  Article  Google Scholar  Greenberg, M. V. C. & Bourc’his, D. The diverse roles of DNA methylation in mammalian development and disease….

Martincorena, I. et al. Somatic mutant clones colonize the human esophagus with age. Science 362, 911–917 (2018). CAS  PubMed  PubMed Central  Google Scholar  Yizhak, K. et al. RNA sequence analysis reveals macroscopic somatic clonal expansion across normal tissues. Science 364, eaaw0726 (2019). CAS  PubMed  PubMed Central  Google Scholar  Yokoyama, A….

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 …

Clapier, C. R., Iwasa, J., Cairns, B. R. & Peterson, C. L. Mechanisms of action and regulation of ATP-dependent chromatin-remodelling complexes. Nat. Rev. Mol. Cell Biol. 18, 407–422 (2017). CAS  PubMed  PubMed Central  Article  Google Scholar  Mashtalir, N. et al. Modular organization and assembly of SWI/SNF family chromatin remodeling complexes….

Allfrey, V. G., Faulkner, R. & Mirsky, A. E. Acetylation and methylation of histones and their possible role in the regulation of RNA synthesis. Proc. Natl Acad. Sci. USA 51, 786–794 (1964). CAS  PubMed  PubMed Central  Google Scholar  Ho, J. W. K. et al. Comparative analysis of metazoan chromatin organization….

Showing result 1 – 5 of 34 swedish dissertations containing the word ChIP-Seq. Author : Ola Wallerman; Claes Wadelius; Jussi Taipale; Uppsala universitet; []Keywords : MEDICAL AND HEALTH SCIENCES; MEDICIN OCH HÄLSOVETENSKAP; MEDICIN OCH HÄLSOVETENSKAP; MEDICAL AND HEALTH SCIENCES; ChIP; ChIP-chip; ChIP-seq; transcription factors; motif discovery; nucleosome positioning; HepG2; genome-wide;…

Cryo-Em structure of the hexameric RUVBL1-RUVBL2 in complex with ZNHIT2 HeteromerQ9Y230; 3×ADP; 7p6x SMTL PDBe PDBe-KB PDBj PDBsum RCSB 1-456 Assess Truncated human R2TP complex, structure 3 (ADP-filled) HeteromerQ9Y230; 6×ADP; 6qi8 SMTL PDBe PDBe-KB PDBj PDBsum RCSB 2-456 Assess Truncated human R2TP complex, structure 4 (ADP-empty) HeteromerQ9Y230; 5×ADP; 6qi9 SMTL…

Significance Hairpin pyrrole-imidazole (Py-Im) polyamides can be programmed to bind a broad repertoire of DNA sequences. Py-Im small molecules can be used to target cancer-specific coding regions and block transcription elongation. This transcription blockage by Py-Im cannot be rescued by transcription elongation factors, such as TFIIS. The mechanism by which…

Conflicting results suggest a missing variant In order to narrow down candidates for the causal genetic variant, we performed genome-wide association mapping separately in individual lake populations (previously, association mapping was only performed across the whole species flock5). Interestingly, despite clear association peaks in the crater lakes (Fig. 1a, b), the…

Sept. 22, Louisiana Tech University will host a multiscale genome organization research webinar in which graduate students and postdoctoral researchers will share their work in the field. The webinar, which will begin at 10 a.m. Central Standard Time, will feature five speakers from universities around the world: Stephanie Protillo, a…

3D-Beacons Network acts as a one-stop shop for protein structures by combining and standardising data from several providers Cryo-EM structure of the BRCA1-UbcH5c/BARD1 E3-E2 module bound to a nucleosome. Image obtained from PDBe A new platform called 3D-Beacons Network brings together experimentally determined and predicted protein structure models and related…

INTRODUCTION Genomic instability often refers to the existence of a variety of DNA alterations, ranging from single nucleotide changes (such as base substitution, deletion, and insertion) to chromosomal rearrangements (e.g., gain or loss of a segment or the whole chromosome) (1). Loss of genome stability can lead to early onset…