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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 Method
RIME was originally described in this Cell Reports publication.


The RIME Service includes:

  1. Nuclear isolation and sonication.
  2. Immunoprecipitation.
  3. Purification of proteins and tryptic digestion.
  4. Mass spectrometry.
  5. Data analysis.

To learn more, please give us a call or send us an Epigenetic Services Information Request. You can also download Active Motif’s Epigenetic Services Profile.

The RIME methodology was originally described in this Cell Reports publication.

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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:

  1. Preserves bona fide interactions allowing for more stringent washes and minimizing the detection of non-specific interactions.
  2. Captures low-affinity interactions that are typically lost during washing.
  3. 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:

  1. Identify transcriptional co-factors/co-regulators.
  2. Identify proteins complexed with epigenetic modifiers.
  3. Detect low-affinity interactions.
  4. Map protein interaction networks.
  5. Validate identified proteins by ChIP-Seq and map global co-occupancy with the RIME target protein.
  6. Understand how co-factors participate in differential gene regulation.
  7. Identify the prominent co-occurrence of transcription factor binding at adjacent sites.
RIME Venn Data
Figure 1: Venn Diagram of RIME treated MCF7 cells

RIME was performed to identify proteins that interact with the RNA polymerase machinery. Immunoprecipitations were performed with an antibody against POLR2A and two different amounts of cross-linked chromatin from MCF7 cells. Immunoprecipitated proteins were measured by mass spectrometry. The Venn diagram shows strong overlap of the detected proteins even in experiments using a 10 fold difference in starting material.

RIME POLR2A Coverage

RIME GO data