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Chromatin immunoprecipitation (ChIP) is a technique for identifying DNA sequences associated with specific proteins in vivo. The association of DNA fragments with a binding protein, such as a transcription factor or modified histone, can be assessed by sequencing, microarrays or PCR after precipitation with an antibody that recognizes the protein.
In aging mouse livers, 40% of elongating RNA polymerases are stalled, biasing transcriptional output dependent on gene length. This transcriptional stress appears to be caused by endogenous DNA damage.
Introduction of hereditary persistence of fetal hemoglobin variants into the γ-globin promoter by using CRISPR mutagenesis and editing provides insights into transcription factor interplay, with implications for gene therapies targeting this element.
Meiotic recombination in yeast is not only initiated by single break sites, but also caused by closely spaced Spo11-dependent double-stranded DNA breaks that create chromosomal gaps.
Glucocorticoid receptors (GR) are thought to bind DNA as dimers or monomers, to regulate different transcription pathways. Here, the authors perform genome-wide studies on GRs with mutations that impair dimerization and provide evidence that monomeric GRs do not play a significant physiologic role.
BPNet is an interpretable deep learning tool that predicts transcription-factor binding profiles from DNA sequence at base-pair resolution, enabling the identification of motifs and the regulatory syntax underlying transcription-factor binding.
Neuronal differentiation requires rearrangement of the transcriptional and chromatin landscapes of neural cells. Here, the authors study in-vitro neuronal differentiation of murine embryonic stem cells (ESCs) to show that this process is modulated by DOT1L activity, which regulates H3K79me2 accumulation, and preserves accessibility of SOX2-bound enhancers.
The development of an epigenetics-focused, CRISPR-based high-content functional genomics screening platform provides insight into chromatin regulation and uncovers a potential strategy to treat an aggressive type of leukemia.
Here we report Droplet Paired-Tag, a rapid and robust method to simultaneously profile histone modifications and gene expression in single cells at scale. The new procedure provides researchers with a tool for studying the epigenome and gene regulation in complex tissues and disease pathogenesis.
A study in Nature Methods describes a light-activated dynamic looping (LADL) system, which consists of a synthetic architectural protein that rapidly induces long-range chromatin interactions in response to blue light.