Identification of nucleolin-targeted RNA transcripts

Although Rrp6 contains a helicase and RNase D domain at the C-terminus, it is not involved in stable RNA interactions. We thus hypothesized that mRrp6-mediated nucleolar inflammatory RNA degradation may depend on the pre-mRNA substrate that is delivered to the mRrp6-exosome complex by nucleolin as a guide factor. To demonstrate this possibility, we examined nucleoplasmic RNAs which were bound to nucleolin through RNA-IP-sequencing at the late time points of LPS stimulation. Overall design: Nucleoplasimc RNAs were immunoprecipiated with anti-nucleolin antibodies during LPS stimulation and then analyzed by Illumina Hiseq 2000