Gene regulatory network inference in the era of single-cell multi-omics
The interplay between chromatin, transcription factors and genes generates complex
regulatory circuits that can be represented as gene regulatory networks (GRNs). The study …
regulatory circuits that can be represented as gene regulatory networks (GRNs). The study …
The spatial organization of transcriptional control
In animals, the sequences for controlling gene expression do not concentrate just at the
transcription start site of genes, but are frequently thousands to millions of base pairs distal …
transcription start site of genes, but are frequently thousands to millions of base pairs distal …
Nuclear compartmentalization as a mechanism of quantitative control of gene expression
Gene regulation requires the dynamic coordination of hundreds of regulatory factors at
precise genomic and RNA targets. Although many regulatory factors have specific affinity for …
precise genomic and RNA targets. Although many regulatory factors have specific affinity for …
Enhancer–promoter interactions and transcription are largely maintained upon acute loss of CTCF, cohesin, WAPL or YY1
It remains unclear why acute depletion of CTCF (CCCTC-binding factor) and cohesin only
marginally affects expression of most genes despite substantially perturbing three …
marginally affects expression of most genes despite substantially perturbing three …
Advances and opportunities in RNA structure experimental determination and computational modeling
Beyond transferring genetic information, RNAs are molecules with diverse functions that
include catalyzing biochemical reactions and regulating gene expression. Most of these …
include catalyzing biochemical reactions and regulating gene expression. Most of these …
[HTML][HTML] Spatial and temporal organization of the genome: Current state and future aims of the 4D nucleome project
The four-dimensional nucleome (4DN) consortium studies the architecture of the genome
and the nucleus in space and time. We summarize progress by the consortium and highlight …
and the nucleus in space and time. We summarize progress by the consortium and highlight …
Mechanisms of Polycomb group protein function in cancer
V Parreno, AM Martinez, G Cavalli - Cell research, 2022 - nature.com
Cancer arises from a multitude of disorders resulting in loss of differentiation and a stem cell-
like phenotype characterized by uncontrolled growth. Polycomb Group (PcG) proteins are …
like phenotype characterized by uncontrolled growth. Polycomb Group (PcG) proteins are …
New insights into genome folding by loop extrusion from inducible degron technologies
Chromatin folds into dynamic loops that often span hundreds of kilobases and physically
wire distant loci together for gene regulation. These loops are continuously created …
wire distant loci together for gene regulation. These loops are continuously created …
Multiscale reorganization of the genome following DNA damage facilitates chromosome translocations via nuclear actin polymerization
Nuclear actin-based movements have been shown to orchestrate clustering of DNA double-
strand breaks (DSBs) into homology-directed repair domains. Here we describe multiscale …
strand breaks (DSBs) into homology-directed repair domains. Here we describe multiscale …
Cell-type-specific prediction of 3D chromatin organization enables high-throughput in silico genetic screening
Investigating how chromatin organization determines cell-type-specific gene expression
remains challenging. Experimental methods for measuring three-dimensional chromatin …
remains challenging. Experimental methods for measuring three-dimensional chromatin …