keyword
https://read.qxmd.com/read/37289591/investigating-pioneer-factor-activity-and-its-coordination-with-chromatin-remodelers-using-integrated-synthetic-oligo-assay
#21
JOURNAL ARTICLE
Hengye Chen, Chao Yan, Archana Dhasarathy, Michael Kladde, Lu Bai
Chromatin accessibility is regulated by pioneer factors (PFs) and chromatin remodelers (CRs). Here, we present a protocol, based on integrated synthetic oligonucleotide libraries in yeast, to systematically interrogate the nucleosome-displacing activities of PFs and their coordination with CRs. We describe steps for designing oligonucleotide sequences, constructing yeast libraries, measuring nucleosome configurations, and data analyses. This approach potentially can be adapted for use in higher eukaryotes to investigate the activities of many types of chromatin-associated factors...
June 7, 2023: STAR protocols
https://read.qxmd.com/read/37236433/methods-to-investigate-nucleosome-structure-and-dynamics-with-single-molecule-fret
#22
JOURNAL ARTICLE
Subhra K Das, Mai T Huynh, Jia Gao, Bhaswati Sengupta, Satya P Yadav, Tae-Hee Lee
The nucleosome is the fundamental building block of chromatin. Changes taking place at the nucleosome level are the molecular basis of chromatin transactions with various enzymes and factors. These changes are directly and indirectly regulated by chromatin modifications such as DNA methylation and histone post-translational modifications including acetylation, methylation, and ubiquitylation. Nucleosomal changes are often stochastic, unsynchronized, and heterogeneous, making it very difficult to monitor with traditional ensemble averaging methods...
May 24, 2023: Methods: a Companion to Methods in Enzymology
https://read.qxmd.com/read/37221952/super-resolution-imaging-of-linearized-chromatin-in-tunable-nanochannels
#23
JOURNAL ARTICLE
Ji-Hoon Lee, Joyce Han-Ching Chiu, Nicholas J Ginga, Tasdiq Ahmed, M D Thouless, Yifan Liu, Shuichi Takayama
Nanofluidic linearization and optical mapping of naked DNA have been reported in the research literature, and implemented in commercial instruments. However, the resolution with which DNA features can be resolved is still inherently limited by both Brownian motion and diffraction-limited optics. Direct analysis of native chromatin is further hampered by difficulty in electrophoretic manipulation, which is routinely used for DNA analysis. This paper describes the development of a three-layer, tunable, nanochannel system that enables non-electrophoretic linearization and immobilization of native chromatin...
May 24, 2023: Nanoscale Horizons: the Home for Rapid Reports of Exceptional Significance in Nanoscience and Nanotechnolgy
https://read.qxmd.com/read/37217032/histone-variant-h2b-z-acetylation-is-necessary-for-maintenance-of-toxoplasma-gondii-biological-fitness
#24
JOURNAL ARTICLE
Laura Vanagas, Daniela Muñoz, Constanza Cristaldi, Agustina Ganuza, Rosario Nájera, Mabel C Bonardi, Valeria R Turowski, Fanny Guzman, Bin Deng, Kami Kim, William J Sullivan, Sergio O Angel
Through regulation of DNA packaging, histone proteins are fundamental to a wide array of biological processes. A variety of post-translational modifications (PTMs), including acetylation, constitute a proposed histone code that is interpreted by "reader" proteins to modulate chromatin structure. Canonical histones can be replaced with variant versions that add an additional layer of regulatory complexity. The protozoan parasite Toxoplasma gondii is unique among eukaryotes in possessing a novel variant of H2B designated H2B...
May 20, 2023: Biochimica et Biophysica Acta. Gene Regulatory Mechanisms
https://read.qxmd.com/read/37184694/using-synthetic-dna-libraries-to-investigate-chromatin-and-gene-regulation
#25
REVIEW
Holly Kleinschmidt, Cheng Xu, Lu Bai
Despite the recent explosion in genome-wide studies in chromatin and gene regulation, we are still far from extracting a set of genetic rules that can predict the function of the regulatory genome. One major reason for this deficiency is that gene regulation is a multi-layered process that involves an enormous variable space, which cannot be fully explored using native genomes. This problem can be partially solved by introducing synthetic DNA libraries into cells, a method that can test the regulatory roles of thousands to millions of sequences with limited variables...
May 15, 2023: Chromosoma
https://read.qxmd.com/read/37162994/chromatin-structure-and-context-dependent-sequence-features-control-prime-editing-efficiency
#26
Somang Kim, Jimmy B Yuan, Wendy S Woods, Destry A Newton, Pablo Perez-Pinera, Jun S Song
Prime editor (PE) is a highly versatile CRISPR-Cas9 genome editing technique. The current constructs, however, have variable efficiency and may require laborious experimental optimization. This study presents statistical models for learning the salient epigenomic and sequence features of target sites modulating the editing efficiency and provides guidelines for designing optimal PEs. We found that both regional constitutive heterochromatin and local nucleosome occlusion of target sites impede editing, while position-specific G/C nucleotides in the primer binding site (PBS) and reverse transcription (RT) template regions of PE guide-RNA (pegRNA) yield high editing efficiency, especially for short PBS designs...
April 15, 2023: bioRxiv
https://read.qxmd.com/read/37116493/complementary-strategies-for-directing-in-vivo-transcription-factor-binding-through-dna-binding-domains-and-intrinsically-disordered-regions
#27
JOURNAL ARTICLE
Divya Krishna Kumar, Felix Jonas, Tamar Jana, Sagie Brodsky, Miri Carmi, Naama Barkai
DNA binding domains (DBDs) of transcription factors (TFs) recognize DNA sequence motifs that are highly abundant in genomes. Within cells, TFs bind a subset of motif-containing sites as directed by either their DBDs or DBD-external (nonDBD) sequences. To define the relative roles of DBDs and nonDBDs in directing binding preferences, we compared the genome-wide binding of 48 (∼30%) budding yeast TFs with their DBD-only, nonDBD-truncated, and nonDBD-only mutants. With a few exceptions, binding locations differed between DBDs and TFs, resulting from the cumulative action of multiple determinants mapped mostly to disordered nonDBD regions...
May 4, 2023: Molecular Cell
https://read.qxmd.com/read/37107631/an-update-of-epigenetic-drugs-for-the-treatment-of-cancers-and-brain-diseases-a-comprehensive-review
#28
REVIEW
Zahra Sahafnejad, Shahin Ramazi, Abdollah Allahverdi
Epigenetics has long been recognized as a significant field in biology and is defined as the investigation of any alteration in gene expression patterns that is not attributed to changes in the DNA sequences. Epigenetic marks, including histone modifications, non-coding RNAs, and DNA methylation, play crucial roles in gene regulation. Numerous studies in humans have been carried out on single-nucleotide resolution of DNA methylation, the CpG island, new histone modifications, and genome-wide nucleosome positioning...
April 6, 2023: Genes
https://read.qxmd.com/read/37059093/the-magic-of-unraveling-genome-architecture-and-function
#29
REVIEW
Maria Pia Cosma, Maria Victoria Neguembor
Over the last decades, technological breakthroughs in super-resolution microscopy have allowed us to reach molecular resolution and design experiments of unprecedented complexity. Investigating how chromatin is folded in 3D, from the nucleosome level up to the entire genome, is becoming possible by "magic" (imaging genomic), i.e., the combination of imaging and genomic approaches. This offers endless opportunities to delve into the relationship between genome structure and function. Here, we review recently achieved objectives and the conceptual and technical challenges the field of genome architecture is currently undertaking...
April 8, 2023: Cell Reports
https://read.qxmd.com/read/36972316/an-associative-memory-hamiltonian-model-for-dna-and-nucleosomes
#30
JOURNAL ARTICLE
Weiqi Lu, José N Onuchic, Michele Di Pierro
A model for DNA and nucleosomes is introduced with the goal of studying chromosomes from a single base level all the way to higher-order chromatin structures. This model, dubbed the Widely Editable Chromatin Model (WEChroM), reproduces the complex mechanics of the double helix including its bending persistence length and twisting persistence length, and their respective temperature dependence. The WEChroM Hamiltonian is composed of chain connectivity, steric interactions, and associative memory terms representing all remaining interactions leading to the structure, dynamics, and mechanical characteristics of the B-DNA...
March 27, 2023: PLoS Computational Biology
https://read.qxmd.com/read/36824796/histone-variant-h2b-z-acetylation-is-necessary-for-maintenance-of-toxoplasma-gondii-biological-fitness
#31
Laura Vanagas, Daniela Muñoz, Constanza Cristaldi, Agustina Ganuza, Rosario Nájera, Mabel C Bonardi, Valeria R Turowski, Fanny Guzman, Bin Deng, Kami Kim, William J Sullivan, Sergio O Angel
Through regulation of DNA packaging, histone proteins are fundamental to a wide array of biological processes. A variety of post-translational modifications (PTMs), including acetylation, constitute a proposed histone code that is interpreted by "reader" proteins to modulate chromatin structure. Canonical histones can be replaced with variant versions that add an additional layer of regulatory complexity. The protozoan parasite Toxoplasma gondii is unique among eukaryotes in possessing a novel variant of H2B designated H2B...
February 14, 2023: bioRxiv
https://read.qxmd.com/read/36610392/nucleosome-dyad-determines-the-h1-c-terminus-collapse-on-distinct-dna-arms
#32
JOURNAL ARTICLE
Jaime Alegrio Louro, Ramachandran Boopathi, Brice Beinsteiner, Abdul Kareem Mohideen Patel, Tat Cheung Cheng, Dimitar Angelov, Ali Hamiche, Jan Bendar, Seyit Kale, Bruno P Klaholz, Stefan Dimitrov
Nucleosomes are symmetric structures. However, binding of linker histones generates an inherently asymmetric H1-nucleosome complex, and whether this asymmetry is transmitted to the overall nucleosome structure, and therefore also to chromatin, is unclear. Efforts to investigate potential asymmetry due to H1s have been hampered by the DNA sequence, which naturally differs in each gyre. To overcome this issue, we designed and analyzed by cryo-EM a nucleosome reconstituted with a palindromic (601L) 197-bp DNA...
December 26, 2022: Structure
https://read.qxmd.com/read/36573457/ethanol-induced-condensation-and-decondensation-in-dna-linked-nanoparticles-a-nucleosome-like-model-for-the-condensed-state
#33
JOURNAL ARTICLE
Qinsi Xiong, One-Sun Lee, Chad A Mirkin, George Schatz
Inspired by the conventional use of ethanol to induce DNA precipitation, ethanol condensation has been applied as a routine method to dynamically tune "bond" lengths (i.e., the surface-to-surface distances between adjacent nanoparticles that are linked by DNA) and thermal stabilities of colloidal crystals involving DNA-linked nanoparticles. However, the underlying mechanism of how the DNA bond that links gold nanoparticles changes in this class of colloidal crystals in response to ethanol remains unclear. Here, we conducted a series of all-atom molecular dynamic (MD) simulations to explore the free energy landscape for DNA condensation and decondensation...
December 27, 2022: Journal of the American Chemical Society
https://read.qxmd.com/read/36544209/characterizing-chromatin-interactions-of-regulatory-elements-and-nucleosome-positions-using-hi-c-micro-c-and-promoter-capture-micro-c
#34
JOURNAL ARTICLE
Beoung Hun Lee, Zexun Wu, Suhn K Rhie
BACKGROUND: Regulatory elements such as promoters, enhancers, and insulators interact each other to mediate molecular processes. To capture chromatin interactions of regulatory elements, 3C-derived methods such as Hi-C and Micro-C are developed. Here, we generated and analyzed Hi-C, Micro-C, and promoter capture Micro-C datasets with different sequencing depths to study chromatin interactions of regulatory elements and nucleosome positions in human prostate cancer cells. RESULTS: Compared to Hi-C, Micro-C identifies more high-resolution loops, including ones around structural variants...
December 21, 2022: Epigenetics & Chromatin
https://read.qxmd.com/read/36269766/the-rearing-environment-persistently-modulates-mouse-phenotypes-from-the-molecular-to-the-behavioural-level
#35
MULTICENTER STUDY
Ivana Jaric, Bernhard Voelkl, Melanie Clerc, Marc W Schmid, Janja Novak, Marianna Rosso, Reto Rufener, Vanessa Tabea von Kortzfleisch, S Helene Richter, Manuela Buettner, André Bleich, Irmgard Amrein, David P Wolfer, Chadi Touma, Shinichi Sunagawa, Hanno Würbel
The phenotype of an organism results from its genotype and the influence of the environment throughout development. Even when using animals of the same genotype, independent studies may test animals of different phenotypes, resulting in poor replicability due to genotype-by-environment interactions. Thus, genetically defined strains of mice may respond differently to experimental treatments depending on their rearing environment. However, the extent of such phenotypic plasticity and its implications for the replicability of research findings have remained unknown...
October 2022: PLoS Biology
https://read.qxmd.com/read/36232624/the-structural-effects-of-phosphorylation-of-protein-arginine-methyltransferase-5-on-its-binding-to-histone-h4
#36
JOURNAL ARTICLE
Rita Börzsei, Bayartsetseg Bayarsaikhan, Balázs Zoltán Zsidó, Beáta Lontay, Csaba Hetényi
The protein arginine methyltransferase 5 (PRMT5) enzyme is responsible for arginine methylation on various proteins, including histone H4. PRMT5 is a promising drug target, playing a role in the pathomechanism of several diseases, especially in the progression of certain types of cancer. It was recently proved that the phosphorylation of PRMT5 on T80 residue increases its methyltransferase activity; furthermore, elevated levels of the enzyme were measured in the case of human hepatocellular carcinoma and other types of tumours...
September 26, 2022: International Journal of Molecular Sciences
https://read.qxmd.com/read/36163372/modelling-clinical-dna-fragmentation-in-the-development-of-universal-pcr-based-assays-for-bisulfite-converted-formalin-fixed-and-cell-free-dna-sample-analysis
#37
JOURNAL ARTICLE
Andrew D Johnston, Jennifer Lu, Darren Korbie, Matt Trau
In fragmented DNA, PCR-based methods quantify the number of intact regions at a specific amplicon length. However, the relationship between the population of DNA fragments within a sample and the likelihood they will amplify has not been fully described. To address this, we have derived a mathematical equation that relates the distribution profile of a stochastically fragmented DNA sample to the probability that a DNA fragment within that sample can be amplified by any PCR assay of arbitrary length. Two panels of multiplex PCR assays for quantifying fragmented DNA were then developed: a four-plex panel that can be applied to any human DNA sample and used to estimate the percentage of regions that are intact at any length; and a two-plex panel optimized for quantifying circulating cell-free DNA (cfDNA)...
September 26, 2022: Scientific Reports
https://read.qxmd.com/read/36063975/modeling-g4s-in-chromatin-context-confirms-partial-nucleosome-exclusion-and-reveals-nucleosome-disrupting-effects-of-the-least-selective-g4-ligands
#38
JOURNAL ARTICLE
Iuliia Pavlova, Nikolay Barinov, Roman Novikov, Vjacheslav Severov, Mikhail Iudin, Tatiana Vedekhina, Andrey Larin, Vladislav Babenko, Andrey Aralov, Evgeny Gnuchikh, Makar Sardushkin, Dmitry Klinov, Vladimir Tsvetkov, Anna Varizhuk
G-quadruplexes (G4s) are gaining increasing attention as possible regulators of chromatin packaging, and robust approaches to their studies in pseudo-native context are much needed. Here, we designed a simple in vitro model of G4-prone genomic DNA and employed it to elucidate the impact of G4s and G4-stabilizing ligands on nucleosome occupancy. We obtained two 226-bp dsDNA constructs composed of the strong nucleosome positioning sequence and an internucleosomal DNA-imitating tail. The tail was G4-free in the control construct and harbored a "strong" (stable) G4 motif in the construct of interest...
September 3, 2022: Biochimie
https://read.qxmd.com/read/36033287/minerva-a-cubesat-for-demonstrating-dna-damage-mitigation-against-space-radiation-in-c-elegans-by-using-genetic-modification
#39
JOURNAL ARTICLE
Sumeth Klomchitcharoen, Tanchanok Tangwattanasirikun, Sean Gallup, Noparin Smerwong, Peetimon Arunwiriyakit, Pisitchai Tachavises, Jin Tangkijngamwong, Pichamon Phatthanaanukun, Benjamard Jirapanyalerd, Siripak Chattanupakorn, Visarut Rungpongvanich, Norawit Nangsue, Krai Meemon, Patompon Wongtrakoonkate, Suradej Hongeng, Yodchanan Wongsawat
The ideas of deep-space human exploration, interplanetary travel, and space civilizations are becoming a reality. However, numerous hindrances remain standing in the way of accomplishing these feats, one of which is space ionizing radiation. Space ionizing radiation has become the most hazardous health risk for long-term human space exploration, as it can induce chromosomal damage and epigenetic changes. The Minerva mission aims to demonstrate cutting-edge technology to inhibit DNA damage against deep-space radiation exposure by using genetic modification...
August 2022: Heliyon
https://read.qxmd.com/read/36015053/localization-of-epigenetic-markers-in-leishmania-chromatin
#40
JOURNAL ARTICLE
Jacquelyn R McDonald, Bryan C Jensen, Aakash Sur, Iris L K Wong, Stephen M Beverley, Peter J Myler
Eukaryotes use histone variants and post-translation modifications (PTMs), as well as DNA base modifications, to regulate DNA replication/repair, chromosome condensation, and gene expression. Despite the unusual organization of their protein-coding genes into large polycistronic transcription units (PTUs), trypanosomatid parasites also employ a "histone code" to control these processes, but the details of this epigenetic code are poorly understood. Here, we present the results of experiments designed to elucidate the distribution of histone variants and PTMs over the chromatin landscape of Leishmania tarentolae ...
August 18, 2022: Pathogens
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