Method for gene identification signature (GIS) analysis

Abstract

An isolated oligonucleotide comprising at least one ditag, wherein the ditag comprises two joined first and second sequence tags, wherein the first tag comprises the 5′-terminus sequence and the second tag comprises the 3′-terminus sequence of a nucleic acid molecule or a fragment thereof. The ditag analysis is useful for gene discovery and genome mapping.

Description

[0001] This application is a divisional of U.S. Ser. No. 10 / 664,234, filed Sep. 17, 2003.FIELD OF THE INVENTION [0002] The present invention relates generally to the field of gene and transcript expression and specifically to a method for the serial analysis of a large number of transcripts by identification of a gene signature (GIS) corresponding to defined regions within a transcript. BACKGROUND OF THE INVENTION [0003] One of the most important goals of the human genome project is to provide complete lists of genes for the genomes of human and model organisms. Complete genome annotation of genes relies on comprehensive transcriptome analysis by experimental and computational approaches. Ab initio predictions of genes must be validated by experimental data. An ideal solution is to clone all full-length transcripts and completely sequence them. This approach has gained recognition recently (Strausberg, R. L., et al., 1999, Science, 286: 455-457) and progress has been made (Jongeneel...

AI Technical Summary

Benefits of technology

[0012] The present invention solves the problems mentioned above by providing two tags (a ditag) per nucleic acid molecule, therefore increasing the specificity of the tags to represent a nucleic acid molecule (for example a gene). The two tags are extracted from the 5′ and 3′ ends of the same nucleic acid molecule, and therefore ditags are more informative to reflect the structure of the nucleic acid molecules. Critically, the invention provides a method to link the 5′ and 3′ tags of the same nucleic acid molecule into a single ditag unit. Therefore, the pairs of 5′ and 3′ tags that represent the nucleic acid molecule can be easily recognized by simple sequencing analysis. The invention can be used for the identification of new genes, for the measure of transcript abundance in transcriptomes, for the annotation of genome sequences and at the same time enhancing sequencing efficiency.

[0051] Such ditags can directly guide the process of recovering the full-length nucleic acid molecule corresponding to the newly identified genes.

Problems solved by technology

However, due to the complexity and immense volume of transcripts expressed in the various developmental stages of an organism's life cycle, complete sequencing analysis of all different transcriptomes still remains unrealistic.

Though EST is effective in identifying genes, it is prohibitively expensive to tag every transcript in a transcriptome.

Limited by the availability of type II restriction enzymes that can cut longer than 21 bp, the SAGE method currently can not generate any longer tags to improve specificity.

Further, SAGE and MPSS methods only produce a single signature per transcript in the middle of the gene.

In view of the “internal” nature of the tag in a transcript, these methods provide only limited tag information.

Therefore, despite their usefulness in sequencing efficiency, the utility of methods such as SAGE or MPSS is severely undermined by their lack of specificity and consequent inconclusiveness.

Images