However, analyses of chromatin-associated RNAs (caRNAs) are often limited to one caRNA at a time. Here, we describe the iMARGI (in situ mapping of RNA-genome interactome) technique, which is used to discover caRNAs and reveal their respective genomic interaction loci. iMARGI starts with in ...
Exploring the Roles of RNAs in Chromatin Architecture Using Deep Learning We investigate the roles of chromatin-associated RNAs (caRNAs) in genome folding in HFFc6 cells by bioinformatics analyses and proposing a deep learning framework (AkitaR) that leverages both genome sequences and genome-wide ...
Here, we report that scaffold attachment factor A (SAF-A), originally identified as a structural nuclear protein, interacts with chromatin-associated RNAs (caRNAs) via its RGG domain to regulate human interphase chromatin structures in a transcription-dependent manner. Mechanistically, this is ...
Chromatin-associated RNAs play various roles in gene regulation and genome organization, yet they remain challenging to interrogate. Here the authors report a targeted DNA-associated RNA and RNA-RNA interaction mapping method and use it to identify caRNAs at DNA anchor regions associated with chromati...
Eukaryotic genomes are extensively transcribed into various types of RNAs, many of which are physically associated with chromatin incisat their transcription sites or in trans to other genomic loci. Emerging roles have been uncovered for these chromatin-associated RNAs (caRNAs) in gene regulation and ...
These data suggest a feedback loop where the 3D genome modulates the spatial distribution of RNA, which in turn affects the dynamic 3D genome organization.#How chromatin-associated RNAs (caRNAs) are spatially organized in the context of the multiscale genome architecture is unclear. Here the ...
The gist of this technology is to ligate chromatin-associated RNAs (caRNAs) with their target genomic sequences by proximity ligation, forming RNA-DNA chimeric sequences, which are converted to a sequencing library for paired-end sequencing. Using MARGI, we produced RNA-genome interaction maps for...
The gist of this technology is to ligate chromatin-associated RNAs (caRNAs) with their target genomic sequences by proximity ligation, forming RNA-DNA chimeric sequences, which are converted to a sequencing library for paired-end sequencing. Using MARGI, we produced RNA-genome interaction maps for...
Df31 is capable to tether a heterogeneous pool of short, single-stranded RNAs to chromatin. This class of chromatin-associated RNA (caRNA) is stably linked to chromatin and is largely composed of snoRNAs, which are preferentially bound by Df31. We suggest that the Df31-mediated linkage of ...
Here, we propose a deep learning framework, called AkitaR, that leverages both genome sequences and genome-wide RNA-DNA interactions to investigate the roles of chromatin-associated RNAs (caRNAs) on genome folding in HFFc6 cells. In order to disentangle the cis - and trans -regulatory roles ...