Biology subjects

Xintao Wei

Publications and source records attributed to Xintao Wei.

2 recordsLinked to original sources

bioRxiv2015

Resources for the comprehensive discovery of functional RNA elements

Transcriptome-wide maps of RNA binding protein (RBP)-RNA interactions by immunoprecipitation (IP)-based methods such as RNA IP (RIP) and crosslinking and IP (CLIP) are key starting points for evaluating the molecular roles of the thousands of human RBPs. A significant bottleneck to the application of these methods in diverse cell-lines, tissues and developmental stages, is the availability of validated IP-quality antibodies. Using IP followed by immunoblot assays, we have developed a validated repository of 438 commercially available antibodies that interrogate 365 unique RBPs. In parallel, 362 short-hairpin RNA (shRNA) constructs against 276 unique RBPs were also used to confirm specificity of these antibodies. These antibodies can characterize subcellular RBP localization. With the burgeoning interest in the roles of RBPs in cancer, neurobiology and development, these resources are invaluable to the broad scientific community. Detailed information about these resources is publicly available at the ENCODE portal (https://www.encodeproject.org/).\n\nHighlightsO_LIAntibodies against 365 unique RBPs successfully immunoprecipitate the RBPs\nC_LIO_LIShort-hairpin RNAs against 276 unique RBPs confirm the specificity of RBP antibodies\nC_LIO_LIAntibodies characterize subcellular localization of RBPs\nC_LIO_LIAntibody and hairpin RNA information are provided at https://www.encodeproject.org/\nC_LI

Genomics↗

bioRxiv2014

Genome-wide Identification of Zero Nucleotide Recursive Splicing in Drosophila

Recursive splicing is a process in which large introns are removed in multiple steps by resplicing at ratchet points - 5 splice sites recreated after splicing1. Recursive splicing was first identified in the Drosophila Ultrabithorax (Ubx) gene1 and only three additional Drosophila genes have since been experimentally shown to undergo recursive splicing2,3. Here, we identify 196 zero nucleotide exon ratchet points in 130 introns of 115 Drosophila genes from total RNA sequencing data generated from developmental time points, dissected tissues, and cultured cells. Recursive splicing events were identified by splice junctions that map to annotated 5 splice sites and unannotated intronic 3 splice sites, the presence of the sequence AG/GT at the 3 splice site, and a 5 to 3 gradient of decreasing RNA-Seq read density indicative of co-transcriptional splicing. The sequential nature of recursive splicing was confirmed by identification of lariat introns generated by splicing to and from the ratchet points. We also show that recursive splicing is a constitutive process, and that the sequence and function of ratchet points are evolutionarily conserved. Together these results indicate that recursive splicing is commonly used in Drosophila and provides insight into the mechanisms by which some introns are removed.

Genomics↗