Chan-Zuckerberg Biohub

Nov 15, 2024 | cell.com | Chan-Zuckerberg Biohub

KeywordschromatinDNA replicationnucleosomestranscription factorsepigenomicsepigeneticsmolecular methodstranscriptiongenome architectureIntroductionNucleosomes are the linchpin of epigenetic inheritance.

Aug 14, 2024 | genomebiology.biomedcentral.com | Chan-Zuckerberg Biohub

Our E-P-INs’ architecture was composed using the Python [49] and R [50] programming languages. These languages enabled us to create comparable networks. Assembling an E-P-IN is contingent on the ABC model [8], which uses epigenetic datasets to define candidate enhancers and predict their interactions with promoters.

Apr 2, 2024 | genomebiology.biomedcentral.com | Chan-Zuckerberg Biohub

For the seqFISH + dataset, we limited the scope of our analysis to the set of genes for which at least 10 molecules were detected in at least one cell. This helped reduce sparsity in the data, resulting in 3726 genes remaining. Because pattern classification requires nuclear segmentation masks, we removed all cells lacking annotated nuclei for the remainder of 179 cells. Because the MERFISH data had a much higher number of molecules detected per gene, no gene needed to be removed.

Dec 7, 2023 | cell.com | Jovanka Gencel-Augusto |Trever G. Bivona |Chan-Zuckerberg Biohub

Although growth receptor pathways commonly activate similar pathways, Lv et al. show that EGF signaling represses m6A levels in contrast to induction by PDGF. EGFR blocks ALKBH5 nuclear export, increasing m6A eraser function and suppression of ferroptosis through glutathione production. ALKBH5 inhibitors enhance the anti-tumor efficacy of EGFR or glutathione inhibitors.

Sep 10, 2023 | biorxiv.org | Soorya Pradeep |Thomas A. Zangle |Chan-Zuckerberg Biohub

AbstractThe continuous balance of growth and degradation inside cells maintains homeostasis. Disturbance of the balance by internal or external factors cause state of disease. Effective disease treatments seek to restore this balance. Here, we present a method based on quantitative phase imaging (QPI) based measurements of cell mass and the velocity of mass transport to quantify the balance of growth and degradation within intracellular control volumes.