Method for analyzing quantitative expression of genes
First Claim
1. A method of identifying gene transcription patterns in an mRNA population, comprising the steps of:
- (a) preparing double-stranded cDNAs from an mRNA population using a primer, wherein said primer contains a recognition sequence of six bases or greater for a priming restriction endonuclease;
(b) cleaving said double-stranded cDNAs with;
a first restriction endonuclease which cleaves within said cDNA sequence and not within said primer, andthe priming restriction endonuclease which cleaves within said primer to obtain a population of cDNA inserts;
(c) inserting said cDNA inserts into insertion sites of cloning vectors to obtain a population of DNA constructs, wherein said cloning vectors comprisea second restriction endonuclease recognition sequence located 5'"'"' to said insertion sites, anda third restriction endonuclease recognition sequence located 5'"'"' to or overlapping with said second restriction endonuclease recognition sequence,and wherein said cDNA inserts are inserted into said cloning vectors in an orientation in which an end cleaved by the first restriction endonuclease is proximal to the second restriction enzyme recognition site and an end cleaved by the primer restriction endonuclease is distal to the second restriction enzyme recognition site;
(d) replicating said DNA constructs;
(e) isolating said DNA constructs;
(f) digesting said DNA constructs with a second restriction endonuclease that is a Type IIs restriction endonuclease, thereby cleaving within the cDNA inserts;
(g) digesting said DNA constructs with a third restriction endonuclease, thereby cleaving the DNA constructs 5'"'"' to cleavage sites of the second restriction endonuclease to obtain tags comprising cDNA sequences;
(h) causing said tags to have blunt 5'"'"' and 3'"'"' ends, if one or more ends has an overhang resulting from restriction endonuclease digestion;
(i) ligating said tags to obtain ligated tandem arrays of tags comprising at least 10 tags;
(j) inserting said ligated tandem arrays of tags into a sequencing vector; and
(k) determining the nucleotide residue sequence of said tags to identify gene transcription patterns in said mRNA population.
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Abstract
The present invention provides novel methods for identifying gene expression patterns in mRNA populations. The methods are useful for determining differential gene expression among various cells or tissues, including cells or tissues of a target organism. The invention also provides methods of determining the frequency of gene expression in mRNA populations, thus providing a method of comparing gene expression frequency among various cells or tissues. The present invention also provides methods for isolating genes corresponding to tag sequences identified according to the methods of the present invention. Furthermore, sequences that are identified according to the present invention may be used to diagnose the presence of disease.
67 Citations
47 Claims
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1. A method of identifying gene transcription patterns in an mRNA population, comprising the steps of:
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(a) preparing double-stranded cDNAs from an mRNA population using a primer, wherein said primer contains a recognition sequence of six bases or greater for a priming restriction endonuclease; (b) cleaving said double-stranded cDNAs with; a first restriction endonuclease which cleaves within said cDNA sequence and not within said primer, and the priming restriction endonuclease which cleaves within said primer to obtain a population of cDNA inserts; (c) inserting said cDNA inserts into insertion sites of cloning vectors to obtain a population of DNA constructs, wherein said cloning vectors comprise a second restriction endonuclease recognition sequence located 5'"'"' to said insertion sites, and a third restriction endonuclease recognition sequence located 5'"'"' to or overlapping with said second restriction endonuclease recognition sequence, and wherein said cDNA inserts are inserted into said cloning vectors in an orientation in which an end cleaved by the first restriction endonuclease is proximal to the second restriction enzyme recognition site and an end cleaved by the primer restriction endonuclease is distal to the second restriction enzyme recognition site; (d) replicating said DNA constructs; (e) isolating said DNA constructs; (f) digesting said DNA constructs with a second restriction endonuclease that is a Type IIs restriction endonuclease, thereby cleaving within the cDNA inserts; (g) digesting said DNA constructs with a third restriction endonuclease, thereby cleaving the DNA constructs 5'"'"' to cleavage sites of the second restriction endonuclease to obtain tags comprising cDNA sequences; (h) causing said tags to have blunt 5'"'"' and 3'"'"' ends, if one or more ends has an overhang resulting from restriction endonuclease digestion; (i) ligating said tags to obtain ligated tandem arrays of tags comprising at least 10 tags; (j) inserting said ligated tandem arrays of tags into a sequencing vector; and (k) determining the nucleotide residue sequence of said tags to identify gene transcription patterns in said mRNA population. - 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, 33, 34, 35, 36, 37, 38)
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39. A kit for use in identifying gene transcription patterns in an mRNA population, comprising:
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(a) a DNA vector comprising an insertion site that includes a NotI recognition sequence, a first restriction endonuclease recognition sequence, Sequence A, located 5'"'"' to said insertion site, wherein said first recognition sequence is specific for a first restriction endonuclease that cleaves at a site, Sequence B, located 3'"'"' to said first recognition sequence, and a second restriction endonuclease recognition sequence, Sequence C, located 5'"'"' to or overlapping Sequence A; (b) a primer comprising an oligo dT sequence of 7 to 40 T residues; (c) a first restriction endonuclease that recognizes said Sequence A and cleaves DNA at a said Sequence B; and (d) a second restriction endonuclease that recognizes said Sequence C. - View Dependent Claims (40, 41, 42, 43, 44, 45)
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46. A method of identifying gene transcription patterns in an mRNA population, comprising the steps of:
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(a) preparing double-stranded cDNAs from a mRNA population using a primer, wherein said primer comprises an oligo dT sequence linked at its 5'"'"' end to a NotI cleavage site; (b) cleaving said double-stranded cDNAs with NotI and with MboI to obtain cDNA inserts; (c) inserting said cDNA inserts into insertion sites of cloning vectors to obtain DNA constructs, wherein said cloning vectors comprise a BsgI recognition sequence 5'"'"' to the insertion sites such that digestion of said DNA constructs with BsgI is capable of cleaving said DNA constructs at sites within the cDNA inserts, and a FokI recognition sequence which is 5'"'"' to said BsgI recognition sequence, and wherein said cDNA inserts are inserted into said cloning vectors such that an MboI-cleaved end is proximal to the BsgI recognition sequence and a NotI-cleaved end is distal to the BsgI recognition sequence; (d) replicating said DNA constructs; (e) isolating said DNA constructs; (f) digesting said DNA constructs with BsgI; (g) digesting said DNA constructs with FokI to obtain tags, wherein said tags comprise a portion of said cDNAs; (h) treating said tags with T4 DNA polymerase to obtain blunt-ended tags; (i) ligating said blunt-ended tags using DNA ligase to obtain ligated tandem arrays of tags comprising 30 to 60 tags; (j) inserting said ligated tandem arrays of tags into a sequencing vector; (k) sequencing said ligated tandem arrays of tags to determine the nucleotide residue sequence of individual tags; and (h) comparing the sequences of individual tags to known gene sequences to identify gene transcription patterns in said mRNA population. - View Dependent Claims (47)
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Specification