Pseudogenes

Pseudogenes are ubiquitous and abundant in genomes. Pseudogenes were once called “genomic fossils” and treated as “junk DNA” several years. Nevertheless, it has been recognized that some pseudogenes play essential roles in gene regulation of their parent genes, and many pseudogenes are transcribed into RNA. Pseudogene transcripts may also form small interfering RNA or decrease cellular miRNA concentration. Thus, pseudogenes regulate tumor suppressors and oncogenes. Their essential functions draw the attention of our research group in my current work on heat shock protein 90: a chaperone of oncogenes. The paper reviews our current knowledge on pseudogenes and evaluates preliminary results of the chaperone data. Current efforts to understand pseudogenes interactions help to understand the functions of a genome. 1. History of Pseudogenes Sequencing human genome brought several debates about noncoding sequences. So what is the role of the noncoding parts since protein coding exons compromise only around two percent of the whole genome sequence? The noncoding regions are transposable elements, structural variants, segmental duplications, simple and tandem repeats, conserved noncoding elements, functional noncoding RNAs, regulatory elements, and pseudogenes [1]. Annotation of these noncoding regions through functional genomics and sequence analysis helps our understanding of genomics. Noncoding regions of human genome in general were thought to be nonfunctional and “junk,” or of no purpose DNA. Nowadays, scientists are conceding that junk DNA terminology is far from true since recent studies indicate that they have some regulatory roles. This work focuses on pseudogenes of junk DNA. Pseudogenes are gene copies that have coding-sequence deficiencies like frameshifts and premature stop codons but resemble functional genes. The first pseudogene was reported for 5S DNA of Xenopus laevis, coding for oocyte-type 5S RNA, in 1977, and several pseudogenes have been reported and described for a variety of species including plants, insects, and bacteria [2, 3]. Currently, approximately twenty thousand pseudogenes are estimated which is comparable to the number of protein-coding genes (around 27000) in human [4]. Current knowledge of these genes remains poorly understood, and many sequences once believed defunct are in fact functional RNA genes and play roles in gene silencing either by forming siRNAs or by changing mRNA levels of functional protein-coding gene [5]. Several studies focused on the pseudogene population and their regulatory roles as the function of more