Methods and systems for identifying naturally occurring antisense transcripts and methods, kits and arrays utilizing same

A kit for quantifying at least one mRNA transcript of interest, the kit comprising at least one oligonucleotide being designed and configured so as to be complementary to a sequence region of the mRNA transcript of interest, said sequence region not being complementary with a naturally occurring antisense transcript.

A kit for quantifying at least one mRNA transcript of interest, the kit comprising at least one pair of oligonucleotides including a first oligonucleotide capable of binding the at least one mRNA transcript of interest and a second oligonucleotide being capable of binding a naturally occurring antisense transcript complementary to the mRNA of interest.

A kit for quantifying at least one naturally occurring antisense transcript of interest, the kit comprising at least one oligonucleotide being designed and configured so as to be complementary to a sequence region of the at least one naturally occurring antisense transcript of interest, said sequence region not being complementary with a naturally occurring mRNA transcript.

A computer readable storage medium comprising a database including a plurality of sequences, wherein each sequence is of a naturally occurring antisense transcript.

A system for generating a database of a plurality of putative naturally occurring antisense transcripts, the system comprising a processing unit, said processing unit executing a software application configured for:

• (a) computationally aligning a first database including sense-oriented polynucleotide sequences with a second database including expressed polynucleotide sequences;
• and
• (b) identifying expressed polynucleotide sequences from said second database being capable of forming a duplex with at least one sense-oriented polynucleotide sequence of said first database.

A method of identifying putative naturally occurring antisense transcripts, the method comprising screening a database of expressed polynucleotides sequences according to at least one sequence criterion, said at least one sequence criterion being selected to identify putative naturally occurring antisense transcripts.

The method of claim 63, wherein said database includes sequences of a type selected from the group consisting of expressed sequence tags, contigs, complementary DNA (cDNA) sequences, pre-messenger RNA (mRNA) sequences and mRNA sequences.

A method of quantifying at least one mRNA of interest in a biological sample, the method comprising:

• (a) contacting the biological sample with at least one oligonucleotide capable of binding with the at least one mRNA of interest, wherein said at least one oligonucleotide is designed and configured so as to be complementary to a sequence region of the mRNA transcript of interest, said sequence region not being complementary with a naturally occurring antisense transcript;
• and
• (b) detecting a level of binding between the at least one mRNA of interest and said at least one oligonucleotide to thereby quantify the at least one mRNA of interest in the biological sample.

A method of quantifying the expression potential of at least one mRNA of interest in a biological sample, the method comprising:

• (a) contacting the biological sample with at least one pair of oligonucleotides including a first oligonucleotide capable of binding the at least one mRNA of interest and a second oligonucleotide being capable of binding a naturally occurring antisense transcript complementary to the mRNA of interest;
• and
• (b) detecting a level of binding between the at least one mRNA of interest and said first oligonucleotide and a level of binding between said naturally occurring antisense transcript complementary to the mRNA of interest and said second oligonucleotide to thereby quantify the expression potential of the at least one mRNA of interest in the biological sample.

A method of quantifying at least one naturally occurring antisense transcript of interest in a biological sample, the method comprising:

• (a) contacting the biological sample with at least one oligonucleotide capable of binding with the at least one naturally occurring antisense transcript of interest, wherein said at least one oligonucleotide is designed and configured so as to be complementary to a sequence region of the naturally occurring antisense transcript of interest, said sequence region not being complementary with a naturally occurring mRNA transcript;
• and
• (b) detecting a level of binding between the at least one naturally occurring antisense transcript of interest and said at least one oligonucleotide to thereby quantify the at least one naturally occurring antisense transcript of interest in the biological sample.

A method of identifying a novel drug target, the method comprising:

• (a) determining expression level of at least one naturally occurring antisense transcript of interest in cells characterized by an abnormal phenotype;
• and
• (b) comparing said expression level of said at least one naturally occurring antisense transcript of interest in said cells characterized by an abnormal phenotype to an expression level of said at least one naturally occurring antisense transcript of interest in cells characterized by a normal phenotype, to thereby identify the novel drug target.

A method of treating or preventing a disease, condition or syndrome associated with an upregulation of a naturally occurring antisense transcript complementary to a naturally occurring mRNA transcript, the method comprising administering a therapeutically effective amount of an agent for regulating expression of the naturally occurring antisense transcript.

A method of diagnosing a disease, condition or syndrome associated with a substandard expression ratio of an mRNA of interest over a naturally occurring antisense transcript complementary to the mRNA of interest, the method comprising:

• (a) quantifying expression level of the mRNA of interest and the naturally occurring antisense transcript complementary to the mRNA of interest;
• (b) calculating the expression ratio of the mRNA of interest over the naturally occurring antisense transcript complementary to the mRNA of interest, thereby diagnosing the disease, condition or syndrome.