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标题：Differential and coherent processing patterns from small RNAs
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作者：Sachin Pundhir ; Jan Gorodkin
期刊名称：Scientific Reports
电子版ISSN：2045-2322
出版年度：2015
卷号：5
DOI：10.1038/srep12062
出版社：Springer Nature
摘要：Post-transcriptional processing events related to short RNAs are often reflected in their read profile patterns emerging from high-throughput sequencing data. MicroRNA arm switching across different tissues is a well-known example of what we define as differential processing. Here, short RNAs from the nine cell lines of the ENCODE project, irrespective of their annotation status, were analyzed for genomic loci representing differential or coherent processing. We observed differential processing predominantly in RNAs annotated as miRNA, snoRNA or tRNA. Four out of five known cases of differentially processed miRNAs that were in the input dataset were recovered and several novel cases were discovered. In contrast to differential processing, coherent processing is observed widespread in both annotated and unannotated regions. While the annotated loci predominantly consist of ~24nt short RNAs, the unannotated loci comparatively consist of ~17nt short RNAs. Furthermore, these ~17nt short RNAs are significantly enriched for overlap to transcription start sites and DNase I hypersensitive sites (p-value