Method for simultaneous identification of differentially expressed mRNAs and measurement of relative concentrations

A method for simultaneous comparison of sequences and level of expression of mRNA's in an mRNA population to data stored on a computer readable medium comprising the steps of:

• (a) preparing a double-stranded cDNA population from an mRNA population using a mixture of anchor primers, the anchor primers each including:
• (i) a tract of from 7 to 40 T residues;
• (ii) a site for cleavage by a first restriction endonuclease that recognizes more than six bases, the site for cleavage being located to the 5′-side of the tract of T residues;
• (iii) a first stuffer segment of from 4 to 40 nucleotides, the first stuffer segment being located to the 5′-side of the site for cleavage by the first restriction endonuclease;
• and (iv) phasing residues located at the 3′ end of each of the anchor primers having the sequence -V-N-N, wherein V is a deoxyribonucleotide selected from the group consisting of A, C, and G;
• and N is a deoxyribonucleotide selected from the group consisting of A, C, G, and T, the mixture including anchor primers containing all possibilities for V and N;
• (b) cleaving the double-stranded cDNA population with the first restriction endonuclease and with a second restriction endonuclease, the second restriction endonuclease recognizing a four-nucleotide sequence, to form a population of double-stranded cDNA molecules having first and second termini, respectively;
• (c) inserting the double-stranded cDNA molecules from step (b) each into a vector in an orientation that is antisense with respect to a bacteriophage-specific promoter within the vector to form a population of vectors containing the inserted cDNA molecules, said insertion defining 3′ and 5′ flanking vector sequences such that 5′ is upstream from the sense strand of the inserted cDNA and 3′ is downstream of the sense strand, and said vector having a 3′ flanking nucleotide sequence of from at least 15 nucleotides in length between said first restriction endonuclease site and a site defining transcription initiation in said promoter;
• (d) transforming a suitable host cell with a vector from step (c), producing a population of cloned inserts;
• (e) generating linearized fragments containing the inserted cDNA molecules by digestion of the vectors produced in step (c) with at least one restriction endonuclease that does not recognize sequences in the inserted cDNA molecules or in the bacterophage-specific promoter, but does recognize sequences in the vector such that the resulting linearized fragments have a 5′ flanking vector sequence of at least about 15 nucleotides 5′ to the site of insertion of the cDNA molecules into the vector at the cDNA's second terminus;
• (f) generating a cRNA preparation of antisense cRNA transcripts by incubation of the linearized fragments with a bacteriophage-specific RNA polymerase capable of initiating transcription from the bacteriophage-specific promoter;
• (g) dividing the cRNA preparation into subpools and transcribing first-strand cDNA from each subpool, using a reverse transcriptase and a 5′-RT primer, the 5′-RT primers defined as having a 3′-terminus consisting of -Nx, wherein “N” is one of the four deoxyribonucleotides A, C, G, or T, and “x” is an integer from 1 to 5, the primer being 15 to 30 nucleotides in length and complementary to the 5′ flanking vector sequence with the primer's complementarity extending across into the insert-specific nucleotides of the cRNA in a number of nucleotides equal to “x”, wherein a different one of said primers is used in different subpools and wherein there are 4 subpools if “x”=1, 16 subpools if “x”=2, 64 subpools if “x”=3,256 subpools if “x”=4, and 1,024 subpools if “x”=5;
• (h) Using the product of first-strand cDNA produced by transcribing each of the subpools as a template for a polymerase chain reaction with a 3′-PCR primer of 15 to 30 nucleotides in length that is complementary to 3′ flanking vector sequences between said first restriction endonuclease site and the site defining transcription initiation by the bacteriophage-specific promoter and a 5′-PCR primer having a 3′-terminus consisting of -Nx-Ny, where “N” and “x” are as in step (g), -Nx is the same sequence as in the 5′-RT primer from which first-strand cDNA was made for that subpool, and “y” is a whole integer such that x+y equals an integer selected from the group consisting of 3, 4, 5 and 6, the 5′-PCR primer being 15 to 30 nucleotides in length and complementary to the 5′ flanking vector sequence with the primer's complementarity extending across into the insert-specific nucleotides of the cRNA in a number of nucleotides equal to “x+y”, to produce polymerase chain reaction amplified fragments;
• (i) resolving the polymerase chain reaction amplified fragments to generate a display of sequence-specific products representing the 3′-ends of different mRNAs present in the mRNA population;
• (j) determining the sequence of a 5′ component of a sequence identifier of each sequence-specific product, the sequence of a 3′ component of a sequence identifier of each sequence-specific product, the length of each sequence-specific product, and the intensity of labeling of each sequence-specific product;
• (k) storing data comprising the sequence of a 5′ component of a sequence identifier of each sequence-specific product, the sequence of a 3′ component of a sequence identifier of each sequence-specific product, the length of each sequence-specific product;
• and the intensity of labeling of each sequence-specific product, on a computer readable medium;
• and
• (l) comparing the data stored on the computer readable medium to indicate sequence relationship matches between sequence-specific products and compare levels of expression.