Characteristics of a multicopy gene family predominantly consisting of processed pseudogenes

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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Multicopy gene family evolution on primate Y chromosomes

BMC Genomics ◽

10.1186/s12864-015-2187-8 ◽

2016 ◽

Vol 17 (1) ◽

Cited By ~ 13

Author(s):

Ana-Hermina Ghenu ◽

Benjamin M. Bolker ◽

Don J. Melnick ◽

Ben J. Evans

Keyword(s):

Gene Family ◽

Gene Family Evolution ◽

Y Chromosomes ◽

Multicopy Gene

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The P5 multicopy gene family in the MHC is related in sequence to human endogenous retroviruses HERV-L and HERV-16

Immunogenetics ◽

10.1007/s002510050513 ◽

1999 ◽

Vol 49 (5) ◽

pp. 404-412 ◽

Cited By ~ 33

Author(s):

J. K. Kulski ◽

Roger L. Dawkins

Keyword(s):

Gene Family ◽

Endogenous Retroviruses ◽

Human Endogenous Retroviruses ◽

Multicopy Gene

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The human prothymosin α gene family contains several processed pseudogenes lacking deleterious lesions

Genomics ◽

10.1016/0888-7543(92)90248-q ◽

1992 ◽

Vol 13 (2) ◽

pp. 319-331 ◽

Cited By ~ 13

Author(s):

Richard E. Manrow ◽

Alvaro Leone ◽

Marc S. Krug ◽

William H. Eschenfeldt ◽

Shelby L. Berger

Keyword(s):

Gene Family ◽

Prothymosin Α ◽

Processed Pseudogenes

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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.4.11.2279-2288.1984 ◽

1984 ◽

Vol 4 (11) ◽

pp. 2279-2288

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

Gene ◽

10.1016/s0378-1119(98)00448-x ◽

1998 ◽

Vol 221 (2) ◽

pp. 215-224 ◽

Cited By ~ 12

Author(s):

Nagaradona Harindranath ◽

Frederick C Mills ◽

Mary Mitchell ◽

Alfons Meindl ◽

Edward E Max

Keyword(s):

Gene Family ◽

Functional Gene ◽

Igh Locus ◽

Processed Pseudogenes

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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 ◽

1985 ◽

Vol 5 (7) ◽

pp. 1694-1706 ◽

Cited By ~ 53

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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HOW MANY PROCESSED PSEUDOGENES ARE ACCUMULATED IN A GENE FAMILY?

Genetics ◽

10.1093/genetics/110.2.345 ◽

1985 ◽

Vol 110 (2) ◽

pp. 345-364

Author(s):

James Bruce Walsh

Keyword(s):

Transposable Elements ◽

Gene Family ◽

Gene Families ◽

Direct Selection ◽

Functional Genes ◽

Nucleotide Mutation ◽

Simple Kinetic Model ◽

Processed Pseudogenes ◽

Selective Forces ◽

Per Gene

ABSTRACT A simple kinetic model is developed that describes the accumulation of processed pseudogenes in a functional gene family. Insertion of new pseudogenes occurs at rate ν per gene and is countered by spontaneous deletion (at rate δ per DNA segment) of segments containing processed pseudogenes. If there are k functional genes in a gene family, the equilibrium number of processed pseudogenes is k(ν/δ), and the percentage of functional genes in the gene family at equilibrium is 1/[1 + (ν/δ)]. ν/δ values estimated for five gene families ranged from 1.7 to 15. This fairly narrow range suggests that the rates of formation and deletion of processed pseudogenes may be positively correlated for these families. If δ is sufficiently large relative to the per nucleotide mutation rate μ (δ > 20μ), processed pseudogenes will show high homology with each other, even in the absence of gene conversion between pseudogenes. We argue that formation of processed pseudogenes may share common pathways with transposable elements and retroviruses, creating the potential for correlated responses in the evolution of processed pseudogenes due to direct selection for control of transposable elements and/or retroviruses. Finally, we discuss the nature of the selective forces that may act directly or indirectly to influence the evolution of processed pseudogenes.

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