RNA splicing is prevalent in mammalian transcriptome, and alternative splicing on pre-mRNAs is believed to be one of the major sources for protein divergence.However, it remains largely uncharacterized of the splicings in long noncoding RNAs, particularly of the trans-splicings.To identify trans-splicing events, we composed a pipeline to look up chimeric RNA-seq reads.The reads with sequencing errors or low quality mappings were excluded to minimal the experimental artifacts.In total, thousands of chimeric RNAs were identified.We experimentally verified many of them by RT-PCR and genomic PCR.The data from GRO-seq experiment and sequence analysis further supported that the chimeric RNAs we identified were indeed generated from trans-splicing.By comparing the trans-splicing patterns with the 3D genome structure, we found that the events are enriched in the spatially-approximated loci in nuclear 3D space.Thus, we proposed that the physical approximation may induce RNA trans-splicing with further evidence from 1000 genome data.Taken together, our findings provide important insights into characteristics of trans-splicing process in the long noncoding RNAs, and facilitate future studies in understanding of the regulations of trans-splicing.