Clontech Laboratories, Inc.

Panomics, Inc.

Affymetrix, Inc.

University of California

Pandmics, Inc.

Xianqiang Li

Xin Jiang

Steve Kain

Philip Coffino

A method is provided for identifying complexes between a transcription factor and another protein, the method comprising: isolating from a biological sample transcription factor complexes based on whether the transcription factor complexes comprise a particular type of transcription factor; and identifying which of a plurality of different proteins are present in the isolated transcription factor complexes.

Method for detecting transcription factor-protein interactions

A method is provided for screening for agents that affect protein degradation rates, the method comprising: taking a library of cells, the cells expressing a fusion protein comprising a reporter protein and a protein encoded by a sequence from a cDNA library derived from a sample of cells, the sequence from the cDNA library varying within the cell library; contacting the library of cells with a plurality of agents which may affect protein degradation rates; for each agent, selecting cells in the library which express short-lived proteins based on whether the cells have different reporter signal intensities than other cells in the library, the difference being indicative of the selected cells expressing shorter lived fusion proteins than the fusion proteins expressed by the other cells in the library; and characterizing the fusion proteins expressed by the selected cells for each agent.

Screening methods involving the detection of short-lived proteins

A method is provided for identifying complexes between a transcription factor and another protein, such as another different transcription factor. The method includes the steps of isolating from a biological sample transcription factor complexes based on whether the transcription factor complexes include a particular type of transcription factor; and identifying which of the multiple different proteins are present in the isolated transcription factor complexes.

Green fluorescent protein (GFP) is widely used as a reporter in determining gene expression and protein localization. The present invention provides fusion proteins with a half life of ten hours or less with several embodiments having half lives of 4 hours or less. Such proteins may be constructed by fusing C-terminal amino acids of the degradation domain of mouse ornithine decarboxylase (MODC), which contains a PEST sequence, to the C-terminal end of an enhanced variant of GFP (EGFP). Fluorescence intensity of the fusion protein in transfected cells is similar to that of EGFP, but the fusion protein, unlike EGFP, is unstable in the presence of cycloheximide. Specific mutations in the MODC region have resulted in mutants with varying half lives, useful for a variety of purposes.

Rapidly degrading GFP-fusion proteins and methods of use

Methods, arrays and kits are provided for rapidly and efficiently identifying and quantifying multiple different activated transcription factors in a biological sample at the same time. In one aspect, a method is provided for isolating DNA probes which bind to activated transcription factors, including the step of mixing a library of double stranded DNA probes with a sample containing activated transcription factors. The transcription factor probes that have bound to the activated transcription factors are isolated from the mixture via an agarose gel separation. The bound probes can be identified, for example, by using an array of hybridization probes.

Method and kit for isolating DNA probes that bind to activated transcription factors

Method and kits are provided for screening for transcription factor modulators efficiently. In one aspect, the method can be employed to profile multiple, different transcription factors activated in a sample in the presence of each of the transcription factor modulators. Comparison of the activated transcription factor profiles in the presence and absence of the modulator identifies the transcription factor modulator that modulates the activation of specific transcription factors.

Method for screening for drug candidates for modulating transcription factor activity

Methods, arrays and kits are provided for rapidly and efficiently identifying and quantifying multiple different activated transcription factors in a biological sample at the same time. In one embodiment, the method includes the step of mixing a library of transcription factor probes with a sample containing activated transcription factors. The transcription factor probes that have bound to the activated transcription factors may be isolated from the complexes formed between the probes and the activated transcription factors. The bound probes can be identified, for example, by using an array of hybridization probes.

Method, array and kit for detecting activated transcription factors by hybridization array

A method for in vivo selective targeted degradation of intracellular proteins in situ by inducing in vivo or ex vivo in cells a production of dual-function protein comprising N-terminal domain as well as a C-terminal domain or delivering the dual-function protein. The N-terminal domain of the dual-function protein destabilizes the target protein and directs its degradation when linked to it through a linker between the target protein and between the protein agent of the invention. The protein degradation directing N-terminal domain is a subregion within the first 97 amino acids corresponding to the N-terminus of protein antizyme.

Method for targeted degradation of intracellular proteins in vivo or ex vivo

Green fluorescent protein (GFP) is widely used as a reporter in determining gene expression and protein localization. The present invention provides fusion proteins with a half life of ten hours or less. Such proteins may be constructed by fusing C-terminal amino acids of the degradation domain of mouse ornithine decarboxylase (MODC), which contains a PEST sequence, to the C-terminal end of an enhanced variant of GFP (EGFP). Fluorescence intensity of the fusion protein in transfected cells is similar to that of EGFP, but the fusion protein, unlike EGFP, is unstable in the presence of cycloheximide. Specific mutations in the MODC region have resulted in mutants with varying half lives, useful for a variety of purposes.

Rapidly degrading GFP-fusion proteins

The present invention provides fusion protein comprising I.kappa.B and green fluorescent protein. Also provided is DNA encoding this protein and vector expressing such DNA and various methods of using a fusion protein comprising I.kappa.B and green fluorescent protein.

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Palo Alto, CA, United States of America

Xianqiang Li