Conserved noncoding sequences in plant genomes

Abstract

Plant genomes carry a great diversity of all sorts of sequences and many have functions. Some of these sequences specify functions important to the plant by encoding RNA sequences, some of which (genes or coding domain sequences) encode proteins. Some sequences encode binding functions important to the plant, such as the DNA sites near genes that bind regulatory proteins (motifs), while others may function to block the binding or movement of chromosomal proteins (e.g. insulators). One of the goals of molecular biology studies is to discover the exact functions specified by the genome. However, this is not a simple task. A typical plant has about 30,000 genes, and this does not include genes that function largely selfishly such as most transposons. All of these about 30,000 genes encode one or more messenger RNAs (mRNAs) and many of these genes contain different parts: introns, exons, RNA binding sites, DNA binding sites and similar. Somewhere near the transcriptional units of a gene comprised of its coding regions are the chromosomal regulatory regions that enable the gene to be a part of one or more biological pathways or networks, transcription factor binding sites, enhancer sites, insulator sites and so forth. Added up, there are “millions” of specific DNA sequences that carry specific coding, binding or blocking functions important to gene function sequences with a chromosomal start, stop and strand. We know something functional, however vague, about several thousand of these sequences and almost nothing about the meaning of their combinations.