UTR tag assay for gene function discovery
First Claim
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1. A method of identifying a nucleotide sequence that modulates the activity of a transcriptional regulatory region, comprising:
- a) incorporating into a host cell population a generated library of plasmids wherein the generated library is a collection of plasmids, wherein the library of plasmids comprises multiple non-redundant U-tags, each plasmid having one or more non-redundant U-tags, each U-tag conferring an identifying marker on each plasmid in the library, and each plasmid in the generated library comprises a first DNA construct and a second DNA construct, wherein;
i) the first DNA construct comprises a transcriptional regulatory region, a reporter sequence, and an mRNA stabilizing sequence; and
,ii) the first DNA construct further comprises one or more U-tags inserted into one or more locations selected from the group of locations consisting of a 3′
UTR of the transcriptional regulatory region, a 5′
UTR of the transcriptional regulatory region, a coding region of the reporter sequence, and one or more intron sequences occurring within the first DNA construct; and
,iii) the second DNA construct comprises a promoter active in a host cell of the host cell population, wherein the promoter is operably linked to a nucleotide sequence of interest; and
b) screening for an alteration in the expression levels of each U-tag; and
,c) identifying the nucleotide sequence of interest based on U-tag identity.
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Abstract
The methods of the invention provide a means for rapid analysis of gene function in a variety of systems. The invention allows screening of large libraries of nucleotide sequences for involvement in physiological pathways of interest. The methods of the invention also provide an efficient means of identifying and isolating nucleotide sequences that modulate a physiological pathway of interest from a population of nucleotide sequences.
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Citations
67 Claims
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1. A method of identifying a nucleotide sequence that modulates the activity of a transcriptional regulatory region, comprising:
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a) incorporating into a host cell population a generated library of plasmids wherein the generated library is a collection of plasmids, wherein the library of plasmids comprises multiple non-redundant U-tags, each plasmid having one or more non-redundant U-tags, each U-tag conferring an identifying marker on each plasmid in the library, and each plasmid in the generated library comprises a first DNA construct and a second DNA construct, wherein; i) the first DNA construct comprises a transcriptional regulatory region, a reporter sequence, and an mRNA stabilizing sequence; and
,ii) the first DNA construct further comprises one or more U-tags inserted into one or more locations selected from the group of locations consisting of a 3′
UTR of the transcriptional regulatory region, a 5′
UTR of the transcriptional regulatory region, a coding region of the reporter sequence, and one or more intron sequences occurring within the first DNA construct; and
,iii) the second DNA construct comprises a promoter active in a host cell of the host cell population, wherein the promoter is operably linked to a nucleotide sequence of interest; and b) screening for an alteration in the expression levels of each U-tag; and
,c) identifying the nucleotide sequence of interest based on U-tag identity. - View Dependent Claims (2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32)
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33. A method for identifying a transcriptional regulatory region of interest that is modulated by an agent, comprising:
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a) incorporating into a host cell population a generated library of plasmids wherein the generated library is a collection of plasmids, wherein the library of plasmids comprises multiple non-redundant U-tags, each plasmid having one or more non-redundant U-tags, each U-tag conferring an identifying marker on each plasmid in the library, and each plasmid in the generated library comprises a first DNA construct, wherein i) the first DNA construct comprises the transcriptional regulatory region of interest, a reporter sequence, and an mRNA stabilizing sequence, and; ii) the first DNA construct further comprises one or more U-tags inserted into one or more locations selected from the group of locations consisting of a 3′
UTR of the transcriptional regulatory region, a 5′
UTR of the transcriptional regulatory region, a coding region or the reporter sequence, and one or more intron sequences occurring within the first DNA construct; andb) contacting the host cell population with an agent; and c) screening for an alteration in the expression levels of each U-tag. - View Dependent Claims (34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63)
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64. A method of identifying a nucleotide sequence of interest that modulates the activity of a transcriptional regulatory region, comprising:
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a) incorporating into a host cell population a generated library of plasmids wherein the generated library is a collection of plasmids, wherein the library of plasmids comprises multiple non-redundant U-tags, each plasmid having one or more non-redundant U-tags, each U-tag conferring an identifying marker on each plasmid in the library, and each plasmid in the generated library comprises a first DNA construct wherein i) the first DNA construct comprises a transcriptional regulatory region, a nucleotide sequence of interest, and an mRNA stabilizing sequence; and ii) the first DNA construct further comprises one or more U-tags inserted into one or more locations selected from the group of locations consisting of a 3′
UTR of the transcriptional regulatory region, a 5′
UTR of the transcriptional regulatory region, a coding region of the reporter sequence, and one or more intron sequences occurring within the first DNA construct; andb) screening for an alteration in the expression level of each U-tag and; c) identifying the sequence of interest based on U-tag identity. - View Dependent Claims (65, 66)
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67. A method for identifying a nucleotide sequence of interest that modulates cell death, comprising:
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a) incorporating into a host cell a plasmid having at least a first DNA construct and a second DNA construct, wherein; i) the first DNA construct comprises a transcriptional regulatory region, a reporter sequence, and an mRNA stabilizing sequence; and
,ii) the first DNA construct further comprises one or more U-tags inserted into one or more locations selected from the group of locations consisting of a 3′
UTR of the transcriptional regulatory region, a 5′
UTR of the transcriptional regulatory region, a coding region of the reporter sequence, and one or more intron sequences occurring within the first DNA construct; and
,b) the second DNA construct comprises a promoter active in the host cell operably linked to the nucleotide sequence of interest; and c) screening for a loss in the expression level of the U-tag; and d) identifying the sequence of interest based on U-tag identity.
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Specification