Analysis of nuclear receptor pseudogenes in vertebrates: How the silent tell their stories

Zhengdong Zhang, Philip Cayting, George Weinstock, Mark Gerstein

Research output: Contribution to journalArticle

19 Citations (Scopus)

Abstract

Transcription factor pseudogenes have not been systematically studied before. Nuclear receptors (NRs) constitute one of the largest groups of transcription factors in animals (e.g., 48 NRs in human). The availability of whole-genome sequences enables a global inventory of the NR pseudogenes in a number of vertebrate model organisms. Here we identify the NR pseudogenes in 8 vertebrate organisms and make our results available online at http://www.pseudogene.org/nr. The assignments reveal that NR pseudogenes as a group have characteristics related to generation and distribution contrary to expectations derived from previous large-scale pseudogene studies. In particular, 1) despite its large size, the NR gene family has only a very small number of pseudogenes in each of the vertebrate genomes examined; 2) despite the low transcription levels of NR genes, except for one, all other NR pseudogenes identified in this study are retropseudogenes; and 3) no duplicated NR pseudogenes are found, contrary to the fact that the NR gene family was expanded through several waves of gene duplication events. Our analyses further reveal a number of interesting aspects of NR pseudogenes. Specifically, through careful sequence analysis, we identify remnant introns in 2 mouse retropseudogenes, ψRev-erbβ and ψLRH1. Generated from partially processed pre-mRNAs, they appear to be rare examples of highly unusual "semiprocessed" pseudogenes. Second, by comparing the genomic sequences, we uncover a pseudogene that is unique to the human lineage relative to chimpanzee. Generated by a recent duplication of a segment in the human genome, this pseudogene is a "duplicated-processed" pseudogene, belonging to a new pseudogene species. Finally, FXRβ was nonfunctionalized in the human lineage and thus appears to be an example of a rare unitary pseudogene. By comparing orthologous sequences, we dated the FXR-FXRβ duplication and the nonfunctionalization of FXRβ in primates.

Original languageEnglish (US)
Pages (from-to)131-143
Number of pages13
JournalMolecular Biology and Evolution
Volume25
Issue number1
DOIs
StatePublished - Jan 2008
Externally publishedYes

Fingerprint

Pseudogenes
pseudogenes
Cytoplasmic and Nuclear Receptors
Vertebrates
vertebrate
vertebrates
receptors
genome
gene
Genes
primate
genomics
new species
analysis
Transcription Factors
animal
RNA Precursors
transcription factors
Transcription
Genome

Keywords

  • Nonfunctionalization
  • Nuclear receptor
  • Protein evolution
  • Pseudogene

ASJC Scopus subject areas

  • Genetics
  • Biochemistry
  • Genetics(clinical)
  • Biochemistry, Genetics and Molecular Biology(all)
  • Ecology, Evolution, Behavior and Systematics
  • Agricultural and Biological Sciences (miscellaneous)
  • Molecular Biology

Cite this

Analysis of nuclear receptor pseudogenes in vertebrates : How the silent tell their stories. / Zhang, Zhengdong; Cayting, Philip; Weinstock, George; Gerstein, Mark.

In: Molecular Biology and Evolution, Vol. 25, No. 1, 01.2008, p. 131-143.

Research output: Contribution to journalArticle

Zhang, Zhengdong ; Cayting, Philip ; Weinstock, George ; Gerstein, Mark. / Analysis of nuclear receptor pseudogenes in vertebrates : How the silent tell their stories. In: Molecular Biology and Evolution. 2008 ; Vol. 25, No. 1. pp. 131-143.
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