Teo, W. W. | bioRxiv Science

bioRxiv2020

RNA LEVER Mediates Long-Range Regulation of ε-globin by Keeping PRC2 in Check

Polycomb Repressive Complex 2 (PRC2) is an epigenetic regulator required for gene silencing during embryonic development. Previous studies have reported that PRC2 interacts with RNA in a promiscuous manner, but the biological functions of such interaction are unknown. Here we present a seesaw mechanism for the regulation of {varepsilon}-globin through inactivating EZH2 by an upstream non-coding RNA (LEVER). We show that LEVER, a non-coding RNA identified by RNA immunoprecipitation sequencing (RIP-seq) of the PRC2 core subunit EZH2 and Nanopore sequencing, binds PRC2 and thereby prevents the accumulation of H3K27 methylation along the genomic region where LEVER RNA is transcribed. The open chromatin within the LEVER locus in turn competes for the chromatin interaction between the {varepsilon}-globin promoter and the Locus Control Region (LCR), working as a negative regulatory element of {varepsilon}-globin expression. Hence, LEVER RNA negatively regulates {varepsilon}-globin by sequestering PRC2 from repressing the LEVER locus, which is a competitor of the {varepsilon}-globin-LCR interaction.

molecular biology↗

bioRxiv2019

Widespread interaction between ADAR1 and transcriptional byproducts

BackgroundADAR1, an adenosine-to-inosine (A-to-I) RNA editing enzyme, has an emerging role in cancer immunotherapy. ADAR1 presumably works by suppressing cellular innate immunity response to endogenously generated double-stranded RNAs through RNA editing. However, RNA species that are directly regulated by ADAR1 mediated RNA editing processes remain poorly defined. ResultsIn this study, we used a novel bioinformatics approach to track ADAR1-RNA interactions. By integrating DNA-seq, RNA-seq, and ADAR1 RNA immunoprecipitation sequencing (fRIP-seq) data of K562 cell line, we provided the first in-situ landscape profiling of ADAR1 RNA binding and editing activities. With long RNA fragments captured by ADAR1 immunoprecipitation, we were able to identify exon junctions and genomic boundaries used by ADAR1-associated RNAs and thus we could possibly trace pre-RNA processing steps that had been acting on them. Our methodology allowed us to acquire the knowledge of transcriptome-wide scenario of ADAR1 activities. Intriguingly, we found that ADAR1 had a tendency to interact with transcriptional byproducts originated from obscure regions such as introns and intergenic regions. ConclusionsOur observation might shed light on the dual role of ADAR1 proteins not only in diversifying the transcriptome, but also in reigning RNA debris from obscure regions. Moreover, as the functional potential of seemly transcriptional byproducts is just beginning to emerge, this study would bridge ADAR1 with other fields of RNA biology.

genomics↗