Results 31 to 40 of about 3,719 (149)

High-resolution mapping of mitotic DNA synthesis under conditions of replication stress in cultured cells

STAR Protocols, 2023
Summary: Cells experiencing DNA replication stress enter mitosis with under-replicated DNA, which activates a repair mechanism known as mitotic DNA synthesis (MiDAS).
Florian J. Groelly, Rebecca A. Dagg, Jonathan Mailler, Thanos D. Halazonetis, Madalena Tarsounas   +4 more
doaj   +1 more source

H3K4me3 Histone ChIP-Seq Analysis Reveals Molecular Mechanisms Responsible for Neutrophil Dysfunction in HIV-Infected Individuals

Frontiers in Immunology, 2021
Peripheral neutrophils in HIV-infected individuals are characterized by impairment of chemotaxis, phagocytosis, bactericidal activity, and oxidative burst ability regardless of whether patients are receiving antiretroviral therapy or not.
Paweł Piatek, Maciej Tarkowski, Magdalena Namiecinska, Agostino Riva, Marek Wieczorek, Sylwia Michlewska, Justyna Dulska, Małgorzata Domowicz, Małgorzata Kulińska-Michalska, Natalia Lewkowicz, Przemysław Lewkowicz   +10 more
doaj   +1 more source

Protocol to target a promoter region in human embryonic kidney cells using the CRISPR-dCas9 system for single-locus proteomics

STAR Protocols
Summary: The unbiased identification of less-abundant transcription factors, which direct the expression of a target gene, is technically challenging. Here, we present a protocol to analyze the locus-specific chromatin-regulating proteome using in situ ...
Reem Alkhayer, Viviane Ponath, Elke Pogge von Strandmann   +2 more
doaj   +1 more source

Computer analysis of co-localization of transcription factor binding sites in genome by ChIP-seq data

Вавиловский журнал генетики и селекции, 2017
Statistical features of the distribution of transcription factor binding sites in the mouse genome that are obtained by ChIP-seq experiments in embryonic stem cells have been considered. Clusters of sites that contain four or more different transcription
A. I. Dergilev, A. M. Spitsina, I. V. Chadaeva, A. V. Svichkarev, F. M. Naumenko, E. V. Kulakova, E. R. Galieva, E. E. Vityaev, M. Chen, Y. L. Orlov   +9 more
doaj   +1 more source

Shape-based peak identification for ChIP-Seq

BMC Bioinformatics, 2011
Background The identification of binding targets for proteins using ChIP-Seq has gained popularity as an alternative to ChIP-chip. Sequencing can, in principle, eliminate artifacts associated with microarrays, and cheap sequencing offers the ability to ...
Evans Steven N, Hower Valerie, Pachter Lior   +2 more
doaj   +1 more source

Chromatin Immunoprecipitation dataset of H3ac and H3K27me3 histone marks followed by DNA sequencing of Medicago truncatula embryos during control and heat stress conditions to decipher epigenetic regulation of desiccation tolerance acquisition

Data in Brief, 2022
Desiccation tolerance (DT) is one of the most important processes that seeds need to acquire during seed maturation because it will ensure survival until seeds have favourable conditions for germinating.
Jaiana Malabarba, Zhijuan Chen, David Windels, Jerome Verdier   +3 more
doaj   +1 more source

Characterization of carABpyrB operon and role of pyrE in Francisella novicida biofilm

MicrobiologyOpen, Volume 15, Issue 5, October 2026.
Pyrimidine biosynthesis links metabolism to biofilm regulation in Francisella novicida. During nutrient limitation, reduced pyrimidine availability shifts metabolism from uracil salvage to de novo synthesis, increasing biofilm formation. Mutants in carABpyrB exhibit uracil‐dependent growth defects and elevated biofilm:growth ratios, revealing ...
Katie C. Sprinkel, Annika R. Geiger, Monique L. van Hoek   +2 more
wiley   +1 more source

Theoretical characterisation of strand cross-correlation in ChIP-seq

BMC Bioinformatics, 2020
Background Strand cross-correlation profiles are used for both peak calling pre-analysis and quality control (QC) in chromatin immunoprecipitation followed by sequencing (ChIP-seq) analysis.
Hayato Anzawa, Hitoshi Yamagata, Kengo Kinoshita   +2 more
doaj   +1 more source

ZNF865 (BLST) a Novel Regulator of DNA Damage and Cell Senescence in Back Pain

Aging Cell, Volume 25, Issue 10, October 2026.
ZNF865 (BLST) has previously been classified as part of the “unknome”, but here in the context of back pain, we demonstrate the first functional characterization of ZNF865. We demonstrate that it regulates genomic stability and subsequent senescence, and that downregulation in the intervertebral disc leads to pain behavior in rodent models.
Christian Lewis, Hunter Levis, Jonah Holbrook, Jacob T. Polaski, Timothy D. Jacobsen, Josh Mizels, Molly Czachor, Sarah E. Gullbrand, Brian Diekman, James C. Iatridis, Jason Gertz, Brandon Lawrence, Robby D. Bowles   +12 more
wiley   +1 more source

Circr, a Computational Tool to Identify miRNA:circRNA Associations

Frontiers in Bioinformatics, 2022
Circular RNAs (circRNAs) are known to act as important regulators of the microRNA (miRNA) activity. Yet, computational resources to identify miRNA:circRNA interactions are mostly limited to already annotated circRNAs or affected by high rates of false ...
Martina Dori, Jimmy Caroli, Jimmy Caroli, Mattia Forcato   +3 more
doaj   +1 more source