Tag: Systems Biochemistry

An epigenome editing toolkit to dissect the mechanisms of gene regulation

AI SummaryThe article discusses a recent study that has developed an epigenome editing toolkit that allows for precise programming of chromatin modifications at specific positions in the genome. This technology will help researchers understand the causal role of these modifications in transcription regulation and investigate their impact on various biological processes. Additionally, the toolkit may… Continue reading An epigenome editing toolkit to dissect the mechanisms of gene regulation

A CTCF-binding site in the Mdm1-Il22-Ifng locus shapes cytokine expression profiles and plays a critical role in early Th1 cell fate specification

Multilayered gene regulation orchestrates cell-type-specific cytokine expression. Liu et al. examine the impact of chromatin loop formation on the expression of IFN-γ and IL-22, which are cytokine loci closely located in the genome, and identify an inducible topologically associating domain required for proper IFN-γ production in Th1 cells. Deleting a CTCF-binding site within this domain leads to lineage-specific cytokine dysregulation and increased susceptibility to pathogens.

Enhancer-gene mapping with SCENT method offers insights into disease mechanisms

AI SummaryThe article discusses the development of a statistical method called SCENT (single-cell enhancer target gene mapping) that allows for the mapping of enhancer-gene interactions in various cell types to identify potential causal loci for common and rare diseases. The researchers applied this method to various human tissues and found important insights for immune diseases… Continue reading Enhancer-gene mapping with SCENT method offers insights into disease mechanisms

Deciphering protein interaction network dynamics with a machine learning-based framework

AI SummaryThe content describes the development of Tapioca, a machine learning-based framework, that accurately predicts protein-protein interaction network dynamics. The framework was used to study host regulation during the reactivation of an oncogenic virus from latency. Through an interactome homology analysis method, a proviral host factor with broad relevance for herpesviruses was identified. This research… Continue reading Deciphering protein interaction network dynamics with a machine learning-based framework

Breakthrough technique unveils secrets of “backtracking” in gene regulation

AI SummarySummary: A new technique has been developed that can determine the frequency and location of a molecular event called “backtracking” in the genome of any species. This event is believed to be a form of gene regulation that influences many human genes involved in basic life processes. The technique was developed by researchers at… Continue reading Breakthrough technique unveils secrets of “backtracking” in gene regulation

Study throws our understanding of gene regulation for a loop

AI SummaryScientists are studying how loop structures in genetic material can repress or silence gene activity, which could impact human health.To function properly, the genetic material is highly organized into loop structures that often bring together widely separated sections of the genome critical to the regulation of gene activity. Scientists now address how these loops… Continue reading Study throws our understanding of gene regulation for a loop

Small molecule WDR5 inhibitors down-regulate lncRNA expression

WD Repeat Domain 5 (WDR5) plays an important role as a scaffold protein in both protein-protein and RNA-protein complexes involved in epigenetic gene regulation. In particular, some of these lncRNAs were reported to regulate the expression of genes in cis as well as themselves through binding WDR5. In this report, we investigate the two known… Continue reading Small molecule WDR5 inhibitors down-regulate lncRNA expression

New study reveals crucial ‘housekeeping’ genetic elements and their potent role to fight cancer

AI SummaryA recent study discovered 11,000 gene regulators present in every cell type, called housekeeping cis-regulatory elements (HK-CREs). These regulators are important for maintaining cellular stability and have reduced activity in certain cancers, indicating their potential as tumor suppressors.A recent study in genetic control elements revealed around 11,000 gene regulators active in every cell type,… Continue reading New study reveals crucial ‘housekeeping’ genetic elements and their potent role to fight cancer