Nucleosome footprinting in plasma cell-free DNA for the pre-surgical diagnosis of ovarian cancer
npj Genomic Medicine, 2022 Fragmentation patterns of plasma cell-free DNA (cfDNA) are known to reflect nucleosome positions of cell types contributing to cfDNA. Based on cfDNA fragmentation patterns, the deviation in nucleosome footprints was quantified between diagnosed ovarian ...
Adriaan Vanderstichele +20 more
doaj +1 more source
PuFFIN--a parameter-free method to build nucleosome maps from paired-end reads. [PDF]
, 2014 BackgroundWe introduce a novel method, called PuFFIN, that takes advantage of paired-end short reads to build genome-wide nucleosome maps with larger numbers of detected nucleosomes and higher accuracy than existing tools. In contrast to other approaches
Bunnik, Evelien M +3 more
core +4 more sources
Nucleosome structural studies [PDF]
Current Opinion in Structural Biology, 2011 Chromatin plays a fundamental role in eukaryotic genomic regulation, and the increasing awareness of the importance of epigenetic processes in human health and disease emphasizes the need for understanding the structure and function of the nucleosome.
Song, Tan, Curt A, Davey
openaire +2 more sources
Paternal Circadian Disruption Impairs Offspring Cognition via Sperm microRNAs
Advanced Science, EarlyView.Paternal circadian disruption remodels the sperm small RNA payload, elevating miR‐92a‐3p/miR‐25‐3p levels and perturbing early embryonic gene regulatory programs. Microinjection experiments and single‐embryo transcriptomics reveal sex‐specific developmental vulnerabilities, ultimately impairing offspring hippocampal synaptic plasticity and cognition ...
Kexin Zou +22 more
wiley +1 more source
Genomic sequence is highly predictive of local nucleosome depletion. [PDF]
PLoS Computational Biology, 2008 The regulation of DNA accessibility through nucleosome positioning is important for transcription control. Computational models have been developed to predict genome-wide nucleosome positions from DNA sequences, but these models consider only nucleosome ...
Guo-Cheng Yuan, Jun S Liu
doaj +1 more source
Embedded CRISPRi Enhances Gene‐Silencing Efficiency in Drosophila
Advanced Science, EarlyView.Current CRISPR interference (CRISPRi) technology in Drosophila has limited efficiency. This study introduces the emCRISPRi platform, which significantly enhances transcriptional silencing efficacy by embedding inhibitory domains within the dCas9 architecture.
Pengchong Fu +7 more
wiley +1 more source
FACT, the Bur kinase pathway, and the histone co-repressor HirC have overlapping nucleosome-related roles in yeast transcription elongation. [PDF]
PLoS ONE, 2011 Gene transcription is constrained by the nucleosomal nature of chromosomal DNA. This nucleosomal barrier is modulated by FACT, a conserved histone-binding heterodimer.
Jennifer R Stevens +6 more
doaj +1 more source
An organometallic compound which exhibits a DNA topology-dependent one-stranded intercalation mode [PDF]
, 2016 Understanding how small molecules interact with DNA is essential since it underlies a multitude of pathological conditions and therapeutic interventions.
Adhireksan +16 more
core +3 more sources
Promotion of DFU Wound Healing via BRG1–COL16A1 Axis in Fibroblasts
Advanced Science, EarlyView.In normal wound healing, transcription factor BRG1 is upregulated and binds the COL16A1 promoter to enhance its expression, promoting fibroblast proliferation, migration, contraction, extracellular matrix deposition, and granulation tissue formation, thus accelerating wound closure.
Penghui Wang +10 more
wiley +1 more source
The interaction landscape between transcription factors and the nucleosome
Nature, 2017 Nucleosomes cover most of the genome and are thought to be displaced by transcription factors in regions that direct gene expression. However, the modes of interaction between transcription factors and nucleosomal DNA remain largely unknown.
F. Zhu +11 more
semanticscholar +1 more source