Dataset Information

Integrative Genomics Positions MKRN1 as a Novel Ribonucleoprotein within the Embryonic Stem Cell Gene Regulatory Network

ABSTRACT: For identification of proteins that associate with Makorin1 (MKRN1) in RNA-dependent and RNA-independent manners, we affinity purified FLAG-tagged Makorin1 (MKRN1) from mouse embryonic stem cells constitutively expressing FLAG:MKRN1. Anti-FLAG control immunoprecipitations were performed from a FLAG vectrol control (FLAG:Ctrl) mouse embryonic stem cell line that did not express FLAG:MKRN1. Following FLAG immunoprecipitation, anti-FLAG beads from FLAG:MKRN1 and FLAG:Ctrl immunoprecipitations were split into separate tubes such that half of the beads were digested with 200Ã∞â≈ Ã≠Âµg/mL RNase A while the other half of the beads were undigested. RNase A-digested and undigested immunoprecipitates were subjected to LC-MS/MS analysis. Of the 48 RNA-related proteins previously identified to associate with FLAG:MKRN1, L1TD1, PABPC1, PABPC4, YBX1, IGF2BP1 and UPF1 were found to remain associated with FLAG:MKRN1 in the presence of RNase A.

OTHER RELATED OMICS DATASETS IN: PRJNA255236GSE59394PRJNA255235PRJNA255234

INSTRUMENT(S): LTQ Orbitrap Velos

ORGANISM(S): Mus Musculus (mouse)

TISSUE(S): Embryonic Stem Cell

SUBMITTER: Gareth Palidwor

LAB HEAD: Dr. William L. Stanford

PROVIDER: PXD001291 | Pride | 2015-07-21

REPOSITORIES: Pride

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Dataset's files

Source:

			Action	DRS
	Exp1_FLAG_Ctrl_-RNase.mzXML	Mzxml
	Exp1_FLAG_Ctrl_-RNase.raw	Raw
	Exp1_FLAG_Ctrl_RNase.mzXML	Mzxml
	Exp1_FLAG_Ctrl_RNase.raw	Raw
	Exp1_FLAG_MKRN1_-RNase.mzXML	Mzxml

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Publications

Integrative genomics positions MKRN1 as a novel ribonucleoprotein within the embryonic stem cell gene regulatory network.

Cassar Paul A PA Carpenedo Richard L RL Samavarchi-Tehrani Payman P Olsen Jonathan B JB Park Chang Jun CJ Chang Wing Y WY Chen Zhaoyi Z Choey Chandarong C Delaney Sean S Guo Huishan H Guo Hongbo H Tanner R Matthew RM Perkins Theodore J TJ Tenenbaum Scott A SA Emili Andrew A Wrana Jeffrey L JL Gibbings Derrick D Stanford William L WL

EMBO reports 20150811 10

In embryonic stem cells (ESCs), gene regulatory networks (GRNs) coordinate gene expression to maintain ESC identity; however, the complete repertoire of factors regulating the ESC state is not fully understood. Our previous temporal microarray analysis of ESC commitment identified the E3 ubiquitin ligase protein Makorin-1 (MKRN1) as a potential novel component of the ESC GRN. Here, using multilayered systems-level analyses, we compiled a MKRN1-centered interactome in undifferentiated ESCs at the ...[more]

PMID: 26265008

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