SELEX and ChIP/CLIP-Seq identification of nucleic acid sequences bound by the DDX43 KH domain (89 aa)

SELEX (systematic evolution of ligands by exponential enrichment), chromatin immunoprecipitation (ChIP)-seq, and crosslinking immunoprecipitation (CLIP)-seq showed that the DDX43 KH domain binds C/T rich DNA and U rich RNA. Overall design: Using purified recombinant DDX43-KH-89 protein to pull down ssDNA from a oligonucleotides library (TriLink Biotechnologies, O-32001-20), the bound DNA was Illumina sequenced. DDX43 KH domain (89 aa) was overexpressed in HEK293T cells, bound DNA and RNA were pulled down by Co-IP, and isolated, and illumina sequenced.