The human elk-1 gene family: the functional gene and two processed pseudogenes embedded in the IgH locus

The functional gene and three intronless pseudogenes for human triosephosphate isomerase were isolated from a recombinant DNA library and characterized in detail. The functional gene spans 3.5 kilobase pairs and is split into seven exons. Its promoter contains putative TATA and CCAAT boxes and is extremely rich in G and C residues (76%). The pseudogenes share a high degree of homology with the functional gene but contain mutations that preclude the synthesis of an active triosephosphate isomerase enzyme. Sequence divergence calculations indicate that these pseudogenes arose approximately 18 million years ago. We present evidence that there is a single functional gene in the human triosephosphate isomerase gene family.

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Characterization of the functional gene and several processed pseudogenes in the human triosephosphate isomerase gene family

Molecular and Cellular Biology ◽

10.1128/mcb.5.7.1694-1706.1985 ◽

1985 ◽

Vol 5 (7) ◽

pp. 1694-1706

Author(s):

J R Brown ◽

I O Daar ◽

J R Krug ◽

L E Maquat

Keyword(s):

Gene Family ◽

Triosephosphate Isomerase ◽

Recombinant Dna ◽

Sequence Divergence ◽

Functional Gene ◽

Dna Library ◽

Enzyme Sequence ◽

Processed Pseudogenes ◽

High Degree

The functional gene and three intronless pseudogenes for human triosephosphate isomerase were isolated from a recombinant DNA library and characterized in detail. The functional gene spans 3.5 kilobase pairs and is split into seven exons. Its promoter contains putative TATA and CCAAT boxes and is extremely rich in G and C residues (76%). The pseudogenes share a high degree of homology with the functional gene but contain mutations that preclude the synthesis of an active triosephosphate isomerase enzyme. Sequence divergence calculations indicate that these pseudogenes arose approximately 18 million years ago. We present evidence that there is a single functional gene in the human triosephosphate isomerase gene family.

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The Protein Kinase ERK3 Is Encoded by a Single Functional Gene: Genomic Analysis of the ERK3 Gene Family

Genomics ◽

10.1006/geno.2002.7013 ◽

2002 ◽

Vol 80 (6) ◽

pp. 673-680 ◽

Cited By ~ 15

Author(s):

Benjamin Turgeon ◽

B.Franz Lang ◽

Sylvain Meloche

Keyword(s):

Protein Kinase ◽

Gene Family ◽

Genomic Analysis ◽

Functional Gene

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Evolution of the functional human beta-actin gene and its multi-pseudogene family: conservation of noncoding regions and chromosomal dispersion of pseudogenes.

Molecular and Cellular Biology ◽

10.1128/mcb.5.10.2720 ◽

1985 ◽

Vol 5 (10) ◽

pp. 2720-2732 ◽

Cited By ~ 222

Author(s):

S Y Ng ◽

P Gunning ◽

R Eddy ◽

P Ponte ◽

J Leavitt ◽

...

Keyword(s):

Untranslated Region ◽

Single Copy ◽

Functional Gene ◽

The Other ◽

Cdna Clones ◽

Actin Gene ◽

Noncoding Regions ◽

Beta Actin ◽

Evolutionarily Conserved ◽

Processed Pseudogenes

We have assigned six members of the human beta-actin multigene family to specific human chromosomes. The functional gene, ACTB, is located on human chromosome 7, and the other assigned beta-actin-related sequences are dispersed over at least four different chromosomes including one locus assigned to the X chromosome. Using intervening sequence probes, we showed that the functional gene is single copy and that all of the other beta-actin related sequences are recently generated in evolution and are probably processed pseudogenes. The entire nucleotide sequence of the functional gene has been determined and is identical to cDNA clones in the coding and 5' untranslated regions. We have previously reported that the 3' untranslated region is well conserved between humans and rats (Ponte et al., Nucleic Acids Res. 12:1687-1696, 1984). Now we report that four additional noncoding regions are evolutionarily conserved, including segments of the 5' flanking region, 5' untranslated region, and, surprisingly, intervening sequences I and III. These conserved sequences, especially those found in the introns, suggest a role for internal sequences in the regulation of beta-actin gene expression.

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Processed pseudogenes for rat cytochrome c are preferentially derived from one of three alternate mRNAs.

Molecular and Cellular Biology ◽

10.1128/mcb.4.11.2279 ◽

1984 ◽

Vol 4 (11) ◽

pp. 2279-2288 ◽

Cited By ~ 43

Author(s):

R C Scarpulla

Keyword(s):

Cytochrome C ◽

Gene Family ◽

Multigene Family ◽

Rat Tissues ◽

Loop Structure ◽

Base Pairs ◽

Equimolar Ratio ◽

Processed Pseudogenes ◽

Delta G ◽

Rat Genome

Three cytochrome c mRNAs (1,400, 1,100 and 700 nucleotides) are colinear with RC4, a gene that has introns and correctly encodes cytochrome c. A comparison of RC4 to six nonallelic clones isolated from the rat cytochrome c multigene family demonstrates that all three mRNAs are represented in the genome as processed pseudogenes. Four of the six pseudogenes are derived from the 1,100-nucleotide mRNA, and genomic hybridizations further establish that nearly all of the 30 or so gene family members are also genomic copies of this mRNA despite the equimolar ratio of the three messages in rat tissues. Thus, the surprising multiplicity of cytochrome c sequences in the rat genome is mainly accounted for by the selective use of the 1,100-nucleotide mRNA for the formation of processed pseudogenes. In contrast to 700- and 1,400-nucleotide species which are polyadenylated downstream from AAGUAAA and AAUUAAA, respectively, the 1,100-nucleotide mRNA uses the ubiquitous AAUAAA and also displays a unique stem and loop structure (delta G = -59.4 kJ) centered 37 base pairs upstream from this sequence.

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An unusual adenine phosphoribosyltransferase pseudogene is syntenic with its functional gene and is flanked by highly polymorphic DNAs.

Molecular and Cellular Biology ◽

10.1128/mcb.6.12.4161 ◽

1986 ◽

Vol 6 (12) ◽

pp. 4161-4167 ◽

Cited By ~ 11

Author(s):

M K Dush ◽

J A Tischfield ◽

S A Khan ◽

E Feliciano ◽

J M Sikela ◽

...

Keyword(s):

Dna Sequences ◽

Ecori Fragment ◽

Chromosome 8 ◽

Functional Gene ◽

Direct Repeats ◽

Coding Region ◽

Adenine Phosphoribosyltransferase ◽

Protein Coding ◽

Dna Library ◽

Processed Pseudogenes

A mouse adenine phosphoribosyltransferase (aprt) pseudogene that had previously been recovered from a BALB/c sperm DNA library possessed several unusual features. Its nucleotide sequence, like that of other processed pseudogenes, was colinear with its corresponding mRNA, but it was truncated at its 3' end and lacked a poly(A) tail. The pseudogene was 82% homologous with corresponding regions of the functional gene and had incurred mutations that included transitions, transversions, deletions, and a point insertion. Even though the pseudogene was truncated within the protein-coding region of the corresponding functional gene, it was flanked at both ends by 13-base-pair direct repeats. Curiously, the direct repeats exhibited homology to APRT mRNA at the site of pseudogene divergence. The pseudogene appeared to be common to BALB/c and A/J mice, but it was contained on a 3-kilobase EcoRI fragment in the former strain and a 4.5-kilobase EcoRI fragment in the latter. The BALB/c and apparently the A/J pseudogene both mapped to chromosome 8, which also contains the functional aprt gene. The DNA sequences immediately surrounding the pseudogene in the two strains appeared to be similar, suggesting that the BALB/c and A/J pseudogenes are allelic. However, DNA sequences more distal to the pseudogene in the two strains appeared to vary. Thus, the EcoRI polymorphism was not due to simple loss of an EcoRI site, but was more complex. The pattern of flanking restriction sites was different for each of several enzymes, consistent with extensive DNA rearrangement. Double digests of BALB/c and A/J genomic DNAs revealed complex polymorphisms on both sides of the pseudogene. The results were consistent with insertion, deletion, or other rearrangement of DNA sequences that flank the pseudogene and suggest that this region of mouse chromosome 8 may be a region active for mutation or recombination.

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Differential expression of VH gene families in peripheral B cell repertoires of newborn or adult immunoglobulin H chain congenic mice.

Journal of Experimental Medicine ◽

10.1084/jem.175.6.1449 ◽

1992 ◽

Vol 175 (6) ◽

pp. 1449-1456 ◽

Cited By ~ 30

Author(s):

A C Viale ◽

A Coutinho ◽

A A Freitas

Keyword(s):

Gene Family ◽

B Cell ◽

Expression Pattern ◽

Gene Families ◽

Cell Repertoire ◽

Adult Mice ◽

Igh Locus ◽

B Cell Repertoire ◽

Vh Gene ◽

Old Mice

The pattern of VH gene family expression in the primary B cell repertoire of the mouse is strain dependent. In C57Bl/6 mice, the VH J558 family is expressed by more than 45% of the cells, while the expression of VH 7183, VH Q52, and VH 36-60 families together does not exceed 20%. In BALB/c mice, relative expression of VH J558 is lower than 35%, while the sum of the other three families reaches 25%. To assess which genetic loci control strain-specific VH gene family expression, we studied VH gene family usage in splenic B cell repertoires of different congenic strains of mice. Changes in major histocompatibility complex or immunoglobulin (Ig) K light chain genes did not modify VH gene family expression in adult mice. Differences at the IgH locus, however, modified VH gene family usage. In 1-d-old mice, the strain-specific VH gene family expression pattern is determined by the IgH haplotype. In adult mice, the VH gene family expression pattern of resting B cells is independent of the IgH locus and follows the genetic background of the congenic strain, while it is determined by the IgH haplotype among Ig-secreting spleen cells. In F1(B6 x BALB/c) mice, each of the two spleen B cell populations, sorted on the basis of mu heavy chain allotype expression, shows an independent VH gene family expression pattern, determined by the IgH locus. The implications of these results in the control of VH gene family expression, and in the selection of peripheral B cell repertoires are discussed.

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