Mapping genome-wide RNA-RNA and RNA-DNA interactions in nuclear hubs of male and female Drosophila cells

The human RNA-DNA interactome is cell type-specific and dynamic

The RNA-DNA interactome is established as a new genome regulatory layer that defines and maintains cellular identity and behavior and is shown to be highly dynamic yet reproducibly organized in cell-type specific networks.

Long-distance RNA–RNA interactions shape dynamic RNA architectures and functional states in plant positive-strand RNA viruses

The genomes of positive-strand RNA [(+)ssRNA] viruses function as dynamic RNA molecules that participate in multiple, sometimes competing, processes during infection, including translation, genome replication, subgenomic RNA (sgRNA) transcription, and genome packaging. These distinct processes require viral RNAs to ado...

Target-Site Selection by Transcription Factors: Roles of DNA, Chromatin, and Cofactor-Mediated Regulation.

This review outlines how DNA/chromatin features and TF-centered mechanisms contribute to target-site selection and highlights DNA-binding domain-directed cofactor regulation as an underappreciated mechanism that modulates TF-DNA binding and may help explain selective genomic occupancy.

Formation of an RNA-mediated nuclear compartment

Mammalian nuclei are spatially compartmentalized so that active and inactive segments of the genome occupy separate sub-nuclear neighborhoods. Compartments are often found in association with nuclear structures such as the nuclear lamina, nucleoli, and nuclear speckles (speckles), suggesting links between them. The mol...

RBM25 exhibits distinct RNA- and chromatin-associated target programs in human embryonic stem cells

RNA-binding proteins (RBPs) are increasingly recognized to perform chromatin-associated functions in addition to their canonical roles in RNA regulation, yet how these activities are coordinated in human embryonic stem cells (hESCs) remain poorly understood. Here, we characterize distinct RNA- and chromatin-associated...

Dual-Binding Scaffold RRsS1 Bridges Pol IV Transcripts and DNA Templates for Robust Reproductive siRNA Biogenesis