Nuclear Structure and Function Research Group

This page provides data supporting:
Melnik, S., et al. (2011). 'Proteomes of factories containing RNA polymerases I, II, or III '. Nature Methods 8, 962-968. [PubMed] [pdf]

Overview/Abstract
Human nuclei contain three RNA polymerases (I, II and III) that transcribe different groups of genes; the active forms of all three are difficult to isolate because they are bound to the substructure. Here we describe a purification approach for isolating active RNA polymerase complexes from mammalian cells. After isolation, we analyzed their protein content by mass spectrometry. Each complex represents part of the core of a transcription factory. For example, the RNA polymerase II complex contains subunits unique to RNA polymerase II plus various transcription factors but shares a number of ribonucleoproteins with the other polymerase complexes; it is also rich in polymerase II transcripts. We also describe a native chromosome conformation capture method to confirm that the complexes remain attached to the same pairs of DNA templates found in vivo.

Three experiments were described; the paper concentrates on the first but data for all are given here.

• Read-me file

Comparing complexes I, II, and III (seen in all three experiments)
    ► Shared and unique components (.xls format)

Experiment 1
• Complex I
    ► Output from CPFP; FDR = 0.84% (.xls format)
    ► Relative abundancies; spectral indices (.xls format)
    ► Output from "Protein Centre" (.csv format)
    ► RAW files (.mzXML and .RAW format)
• Complex II
    ► Output from CPFP; FDR = 0.8% (.xls format)
    ► Relative abundancies; spectral indices (.xls format)
    ► Output from "Protein Centre" (.csv format)
    ► RAW files (.mzXML and .RAW format)
• Complex III
    ► Output from CPFP; FDR = 0.82% (.xls format)
    ► Relative abundancies; spectral indices (.xls format)
    ► Output from "Protein Centre" (.csv format)
    ► RAW files (.mzXML and .RAW format)

Experiment 2
• Complex I
    ► Output from CPFP; FDR = 0.8% (.xls format)
    ► Output from "Protein Centre" (.csv format)
    ► RAW files (.mzXML and .RAW format)
• Complex II
    ► Output from CPFP; FDR = 0.8% (.xls format)
    ► Output from "Protein Centre" (.csv format)
    ► RAW files (.mzXML and .RAW format)
• Complex III
    ► Output from CPFP; FDR = 0.8% (.xls format)
    ► Output from "Protein Centre" (.csv format)
    ► RAW files (.mzXML and .RAW format)

Experiment 3
• Complex II
    ► Output from CPFP; FDR = 0.75% (.xls format)
    ► Relative abundancies; spectral indices (.xls format)
    ► Output from "Protein Centre" (.csv format)
    ► RAW files (.mzXML and .RAW format)
• Complex III
    ► Output from CPFP; FDR = 0.65% (.xls format)
    ► Relative abundancies; spectral indices (.xls format)
    ► Output from "Protein Centre" (.csv format)
    ► RAW files (.mzXML and .RAW format)

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