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 language | English (US) |
|---|---|
| Pages (from-to) | 131-143 |
| Number of pages | 13 |
| Journal | Molecular Biology and Evolution |
| Volume | 25 |
| Issue number | 1 |
| DOIs | |
| State | Published - Jan 2008 |
| Externally published | Yes |
Fingerprint
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 journal › Article
}
TY - JOUR
T1 - Analysis of nuclear receptor pseudogenes in vertebrates
T2 - How the silent tell their stories
AU - Zhang, Zhengdong
AU - Cayting, Philip
AU - Weinstock, George
AU - Gerstein, Mark
PY - 2008/1
Y1 - 2008/1
N2 - 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.
AB - 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.
KW - Nonfunctionalization
KW - Nuclear receptor
KW - Protein evolution
KW - Pseudogene
UR - http://www.scopus.com/inward/record.url?scp=38349110922&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=38349110922&partnerID=8YFLogxK
U2 - 10.1093/molbev/msm251
DO - 10.1093/molbev/msm251
M3 - Article
C2 - 18065488
AN - SCOPUS:38349110922
VL - 25
SP - 131
EP - 143
JO - Molecular Biology and Evolution
JF - Molecular Biology and Evolution
SN - 0737-4038
IS - 1
ER -