biostudies-literatureDiffendall GMERC AdG PlasmoSilencingAgence Nationale de RechercheERC StG PlasmoEpiRNAe202201577https://www.ebi.ac.uk/biostudies/studies/S-EPMC9670795biostudies-literatureUnknown6(1)Non-coding RNAs (ncRNAs) are emerging regulators of immune evasion and transmission of <i>Plasmodium falciparum</i> RUF6 is an ncRNA gene family that is transcribed by RNA polymerase III but actively regulates the Pol II-transcribed <i>var</i> virulence gene family. Understanding how RUF6 ncRNA connects to downstream effectors is lacking. We developed an RNA-directed proteomic discovery (ChIRP-MS) protocol to identify in vivo RUF6 ncRNA-protein interactions. The RUF6 ncRNA interactome was purified with biotinylated antisense oligonucleotides. Quantitative label-free mass spectrometry identified several unique proteins linked to gene transcription including RNA Pol II subunits, nucleosome assembly proteins, and a homologue of DEAD box helicase 5 (DDX5). Affinity purification of Pf-DDX5 idenLife science allianceDiscovery of RUF6 ncRNA-interacting proteins involved in <i>P. falciparum</i> immune evasion.PMC9670795ANR-11 LabEx -0024-01Dingli FLoew DScherf ABaumgarten SBarcons-Simon ADiffendall GMfalseDiscovery of RUF6 ncRNA-interacting proteins involved in <i>P. falciparum</i> immune evasion.Non-coding RNAs (ncRNAs) are emerging regulators of immune evasion and transmission of <i>Plasmodium falciparum</i> RUF6 is an ncRNA gene family that is transcribed by RNA polymerase III but actively regulates the Pol II-transcribed <i>var</i> virulence gene family. Understanding how RUF6 ncRNA connects to downstream effectors is lacking. We developed an RNA-directed proteomic discovery (ChIRP-MS) protocol to identify in vivo RUF6 ncRNA-protein interactions. The RUF6 ncRNA interactome was purified with biotinylated antisense oligonucleotides. Quantitative label-free mass spectrometry identified several unique proteins linked to gene transcription including RNA Pol II subunits, nucleosome assembly proteins, and a homologue of DEAD box helicase 5 (DDX5). Affinity purification of Pf-DDX5 iden2023-01-01T00:00:00Z2023 Jan2026-05-28T00:51:40.94Z2024-11-14T23:18:57.648ZS-EPMC96707953637966910.26508/lsa.202201577