#GeneRegulation digest #4:
🧬 New role of histone tails in nucleosome remodelling https://academic.oup.com/nar/advance-article/doi/10.1093/nar/gkad079/7034407
🧬 TFBSs under accelerated #evolution in primates https://www.nature.com/articles/s41467-023-36421-3
🧬 Review of IDRs in #transcription regulators https://www.cell.com/trends/biochemical-sciences/fulltext/S0968-0004(23)00008-7
🧬 CpG islands & protection of genes from premature transcription termination https://www.nature.com/articles/s41467-023-36236-2
🧬 Regulation of #enhancers by DNA #methylation https://www.sciencedirect.com/science/article/pii/S1097276523000400
🧬 H2A-H2B & short-term memory of #chromatin states https://www.sciencedirect.com/science/article/pii/S0092867423000077
The MYB transcription factor (TF) family is among the largest TF families and plays an important role in plant growth and stress response. However, few studies have investigated the role of the MYB gene in drought resistance in cotton. In this study, we analysed the drought transcriptomic data of co …
Litsea cubeba, an aromatic species of the Lauraceae family, produces a diverse array of monoterpenes. The biosynthesis of monoterpenes is regulated by transcriptional factors (TFs), such as APETALA2/ethylene response factor (AP2/ERF). However, the regulatory mechanisms that control the AP2/ERF gene …
These novel findings provide a molecular mechanism for apo- and holo-Tf regulation of iron release from endothelial cells. They further demonstrate how hepcidin impacts these protein-protein interactions, and offer a model for how holo-Tf and hepcidin corporate to suppress iron release. We have esta …
Glucocorticoids (GCs; i.e., steroids) are important chemotherapeutic agents in the treatment of B-cell precursor acute lymphoblastic leukemia (B-ALL) and <i>de novo</i> GC resistance predicts relapse and poor clinical outcome in patients. Glucocorticoids induce B-ALL cell apoptosis through activatio …
<span><b>Background</b> : Apo- (iron free) and holo- (iron bound) transferrin (Tf) participate in precise regulation of brain iron uptake at endothelial cells of the blood-brain barrier. Apo-Tf indicates an iron deficient environment and stimulates iron release, while holo-Tf indicates an iron sufficient</span> …
It is well known that enhancers regulate the spatiotemporal expression of their target genes by recruiting transcription factors (TFs) to the cognate binding sites in the region. However, the role of multiple binding sites for the same TFs and their specific spatial arrangement in determining the ov …
Molecular and atomic level characterization of transcription factor (TF)-DNA complexes is critical for understanding DNA-binding specificity and potentially structural changes that may occur in protein and/or DNA upon complex formation. Often TFs are large, multidomain proteins or contain disordered …
Weekly #GeneRegulation digest 3:
🧬 Epigenomics of environmental influences (review) https://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1010567
🧬 Multi-scale cis-regulatory code (review) https://www.sciencedirect.com/science/article/pii/S1097276522012151
🧬 RNA-mediated CTCF binding https://genome.cshlp.org/content/early/2023/01/17/gr.276643.122.abstract
🧬 How Pol II, BAF and TFs evict nucleosomes https://www.biorxiv.org/content/10.1101/2023.01.22.525083v1
🧬 Centromeres as hotspots of DNA breakage https://www.cell.com/molecular-cell/fulltext/S1097-2765(23)00004-7
🧬 Atlas of lamina-associated chromatin https://genomebiology.biomedcentral.com/articles/10.1186/s13059-023-02849-5
🧬 Histone-organized chromatin in bacteria https://www.biorxiv.org/content/10.1101/2023.01.26.525422v1
It is a generally accepted model that environmental influences can exert their effects, at least in part, by changing the molecular regulators of transcription that are described as epigenetic. As there is biochemical evidence that some epigenetic regulators of transcription can maintain their states long term and through cell division, an epigenetic model encompasses the idea of maintenance of the effect of an exposure long after it is no longer present. The evidence supporting this model is mostly from the observation of alterations of molecular regulators of transcription following exposures. With the understanding that the interpretation of these associations is more complex than originally recognised, this model may be oversimplistic; therefore, adopting novel perspectives and experimental approaches when examining how environmental exposures are linked to phenotypes may prove worthwhile. In this review, we have chosen to use the example of nonalcoholic fatty liver disease (NAFLD), a common, complex human disease with strong environmental and genetic influences. We describe how epigenomic approaches combined with emerging functional genetic and single-cell genomic techniques are poised to generate new insights into the pathogenesis of environmentally influenced human disease phenotypes exemplified by NAFLD.
Gene Regulation