Zhang, X.-Q. | Search bioRxiv

bioRxiv2017

The roles of Conserved Domains in DEMETER-Mediated Active DNA Demethylation in planta

DNA methylation plays critical roles in maintaining genome stability, genomic imprinting, transposon silencing, and development. In Arabidopsis genomic imprinting is established in the central cell by DEMETER (DME)-mediated active DNA demethylation, and is essential for seed viability. DME is a large polypeptide with multiple poorly characterized conserved domains. Here we show that the C-terminal enzymatic core of DME is sufficient to complement dme associated developmental defects. When targeted by a native DME promoter, nuclear-localized DME C-terminal region rescues dme seed abortion and pollen germination defects, and ameliorates CG hypermethylation phenotype in dme-2 endosperm. Furthermore, targeted expression of the DME N-terminal region in wild-type central cell induces dme-like seed abortion phenotype. Our results support a bipartite organization for DME protein, and suggest that the N-terminal region might have regulatory function such as assisting in DNA binding and enhancing the processivity of active DNA demethylation in heterochromatin targets.

plant biology↗

bioRxiv2017

Discovering the Interactions between Circular RNAs and RNA-binding Proteins from CLIP-seq Data using circScan

Although tens of thousands of circular RNAs (circRNAs) have been identified in mammalian genomes, only few of them have been characterized with biological functions. Here, we report a new approach, circScan, to identify regulatory interactions between circRNAs and RNA-binding proteins (RBPs) by discovering back-splicing reads from Cross-Linking and Immunoprecipitation followed by high-throughput sequencing (CLIP-seq) data. By using our method, we have systematically scanned ~1500 CLIP-seq datasets, and identified ~12540 and ~1090 novel circRNA-RBP interactions in human and mouse genomes, respectively, which include all known interactions between circRNAs and Argonaute (AGO) proteins. More than twenty novel interactions were further experimentally confirmed by RNA Immunoprecipitation quantitative PCR (RIP-qPCR). Importantly, we uncovered that some natural circRNAs interacted with cap-independent translation factors eukaryotic initiation factor 3 (eIF3) and N6-Methyladenosine (m6A), indicating they can be translated into proteins. These findings demonstrate that circRNAs are regulated by various RBPs, suggesting they may play important roles in diverse biological processes.

molecular biology↗