Abstract: This invention provides novel methods for producing a plurality of polynucleotides prepared from a polynucleotide sample and the plurality of polynucleotides so produced. The plurality of polynucleotides is either substantially enriched in high-abundance polynucleotide sequences relative to the polynucleotide sample or substantially enriched in low-abundance polynucleotide sequences relative to the polynucleotide sample. Each of the polynucleotides in the plurality of polynucleotides includes a RNA promoter sequence and a universal primer site. The invention also provides kits useful in the methods of the invention and for using the pools of polynucleotides produced thereby. The polynucleotide pools are useful in a wide variety of applications, such as cloning, expression, and hybridization studies. Pools enriched in low-abundance polynucleotides are particularly useful in studies aimed at identifying important regulatory proteins.