Pseudogene: lessons from PCR bias, identification and resurrection

Abstract

Pseudogenes are fragments of non-functional genomic DNA with high sequences similarity to normal functional genes. They are a kind of non-coding DNA produced by gene duplications or retrotranspositions. Pseudogenes exist in human genome at a large quantity which is nearly as much as that of normal functional genes. They could cause PCR bias in molecular biology experiments and confuse related analysis. On the other hand, pesudogenes are important elements in genomics study for getting an integral picture of genome annotation. They give diverse information of evolutionary history and are regarded as genome fossils. Worldwide research project "encyclopedia of DNA elements"(ENCODE) founded in recent years have enhanced our understanding of pseudogenes. Approaches established to identify pseudogenes include PseudoPipe, HAVANA method, PseudoFinder, RetroFinder, GIS-PET method and consensus method. This paper discuss pseudogenes with respect to the formation mechanisms, distribution, and problems for PCR, importance and identification of pseudogenes. Furthermore, potential resurrection of pseudogenes and their potential function are discussed.

Using the SSU, ITS, and Ribosomal DNA Operon Arrangement to Characterize Two Microsporidia Infecting Bruce Spanworm, Operophtera bruceata (Lepidoptera: Geometridae)

“…We hypothesize that our success may be the result of PCR bias (Chen et al. ; Kurata et al. ; Ogino and Wilson ; Read and Pietersen ).…”

“…In the presence of a coinfection, we would not expect to have sequenced such high quality SSU sequences due to the presence of two competing template strands. We hypothesize that our success may be the result of PCR bias (Chen et al 2011;Kurata et al 2004;Ogino and Wilson 2002;Read and Pietersen 2016 Figure 2 Phylogenetic relationships of the two microsporidian isolates presented in this publication (bolded) against other True Nosema and Nosema/Vairimorpha species based on concatenated SSU and ITS alignments and separated by clade. The relationsips are estimated using a Neighbor Joining model.…”

Characterization of POU5F1 (OCT4) gene and its promoter in buffalo ESC-like cells identifies multiple transcription start sites and expression of four pseudogenes

“…c o m / l o c a t e / g e n e expression in different cell types. The failure to distinguish between OCT4 isoforms and pseudogenes may lead to the misinterpretation of its expression in ES cells as well as somatic cells (Chen et al, 2010;Wang and Dai, 2010). The expression of many isoforms and pseudogenes also raise the questions of their function in maintaining self-renewal of ES cells.…”

Pseudogenes

“…Identification of pseudogenes is an ongoing effort, and there are several groups continuously working on identification of pseudogenes. There are different methods developed by independent groups to identify pseudogenes such as REGEXP, PseudoPipe, PseudoFinder, RetroFinder, and GIS-PET [10, 11]. …”