Interactome Profiling (RIME)
identify protein interactions by mass spec
RIME (Rapid Immunoprecipitation Mass spectrometry of Endogenous proteins) is a recently developed technique ideally suited for the identification of transcriptional co-factors and chromatin associated proteins.
RIME was originally described in this Cell Reports publication.
The RIME Service includes:
- Nuclear isolation and sonication.
- Purification of proteins and tryptic digestion.
- Mass spectrometry.
- Data analysis.
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The RIME methodology was originally described in this Cell Reports publication.
With RIME, mass spectrometry is used, along with immunoprecipitation of a target protein, to detect endogenous-interacting proteins in formaldehyde cross-linked cells.
Advantages of cell cross-linking include:
- Preserves bona fide interactions allowing for more stringent washes and minimizing the detection of non-specific interactions.
- Captures low-affinity interactions that are typically lost during washing.
- Captures adjacent DNA binding proteins that participate in gene regulation but do not function through direct interaction with the targeted protein.
Benefits of RIME include:
- Identify transcriptional co-factors/co-regulators.
- Identify proteins complexed with epigenetic modifiers.
- Detect low-affinity interactions.
- Map protein interaction networks.
- Validate identified proteins by ChIP-Seq and map global co-occupancy with the RIME target protein.
- Understand how co-factors participate in differential gene regulation.
- Identify the prominent co-occurrence of transcription factor binding at adjacent sites.
Figure 1: Venn Diagram of RIME treated MCF7 cells