scholarly journals Tandem repeat variation in human and great ape populations and its impact on gene expression divergence

2015 ◽  
Author(s):  
Tugce Bilgin Sonay ◽  
Tiago Carvalho ◽  
Mark Robinson ◽  
Maja Greminger ◽  
Michael Krützen ◽  
...  
Keyword(s):  
Gene Expression ◽  
Conservation Genetics ◽  
Repeat Unit ◽  
Unit Length ◽  
Potential Contribution ◽  
Great Ape ◽  
Expression Divergence ◽  
Base Pairs ◽  
Genome Wide ◽  
Repeat Unit Length

Tandem repeats (TR) are stretches of DNA that are highly variable in length and mutate rapidly, and thus an important source of genetic variation. This variation is highly informative for population and conservation genetics, and has also been associated with several pathological conditions and with gene expression regulation. However, genome-wide surveys of TR variation have been scarce due to the technical difficulties derived from short-read technology. Here, we explored the genome-wide diversity of TRs in a panel of 83 human and nonhuman great ape genomes, and their impact on gene expression evolution. We found that populations and species diversity patterns can be efficiently captured with short TRs (repeat unit length 1-5 base pairs) with potential applications in conservation genetics. We also examined the potential evolutionary role of TRs in gene expression differences between humans and primates by using 30,275 larger TRs (repeat unit length 2-50 base pairs). About one third of the 13,035 one-to-one orthologous genes contained TRs within 5 kilobase pairs of their transcription start site, and had higher expression divergence than genes without such TRs. The same observation held for genes with repeats in their 3′ untranslated region, in introns, and in exons. Using our polymorphism data for the shortest TRs, we found that genes with polymorphic repeats in their promoters showed higher expression divergence in humans and chimpanzees compared to genes with fixed or no TRs in the promoters. Our findings highlight the potential contribution of TRs to recent human evolution through gene regulation.

Comparison of protein repeat classifications based on structure and sequence families

2015 ◽  
Vol 43 (5) ◽  
pp. 832-837 ◽  
Author(s):  
Lisanna Paladin ◽  
Silvio C.E. Tosatto
Keyword(s):  
Tandem Repeats ◽  
Repeat Unit ◽  
Unit Length ◽  
Detailed Comparison ◽  
Structural Classification ◽  
Evolutionarily Conserved ◽  
Repeat Unit Length ◽  
One To One ◽  
Leucine Rich Repeats ◽  
Structural Classes

Tandem repeats (TR) in proteins are common in nature and have several unique functions. They come in various forms that are frequently difficult to recognize from a sequence. A previously proposed structural classification has been recently implemented in the RepeatsDB database. This defines five main classes, mainly based on repeat unit length, with subclasses representing specific folds. Sequence-based classifications, such as Pfam, provide an alternative classification based on evolutionarily conserved repeat families. Here, we discuss a detailed comparison between the structural classes in RepeatsDB and the corresponding Pfam repeat families and clans. Most instances are found to map one-to-one between structure and sequence. Some notable exceptions such as leucine-rich repeats (LRRs) and α-solenoids are discussed.

scholarly journals RAD1 Controls the Meiotic Expansion of the Human HRAS1 Minisatellite in Saccharomyces cerevisiae

2002 ◽  
Vol 22 (3) ◽  
pp. 953-964 ◽  
Author(s):  
Peter A. Jauert ◽  
Sharon N. Edmiston ◽  
Kathleen Conway ◽  
David T. Kirkpatrick
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Repetitive Dna ◽  
Hot Spot ◽  
Repeat Unit ◽  
Unit Length ◽  
Wild Type ◽  
Strand Breaks ◽  
Tract Length ◽  
Sequence Composition ◽  
Repeat Unit Length

ABSTRACT Minisatellite DNA is repetitive DNA with a repeat unit length from 15 to 100 bp. While stable during mitosis, it destabilizes during meiosis, altering both in length and in sequence composition. The basis for this instability is unknown. To investigate the factors controlling minisatellite stability, a minisatellite sequence 3′ of the human HRAS1 gene was introduced into the Saccharomyces cerevisiae genome, replacing the wild-type HIS4 promoter. The minisatellite tract exhibited the same phenotypes in yeast that it exhibited in mammalian systems. The insertion stimulated transcription of the HIS4 gene; mRNA production was detected at levels above those seen with the wild-type promoter. The insertion stimulated meiotic recombination and created a hot spot for initiation of double-strand breaks during meiosis in the regions immediately flanking the repetitive DNA. The tract length altered at a high frequency during meiosis, and both expansions and contractions in length were detected. Tract expansion, but not contraction, was controlled by the product of the RAD1 gene. RAD1 is the first gene identified that controls specifically the expansion of minisatellite tracts. A model for tract length alteration based on these results is presented.

Characterization of a conserved extrachromosomal element isolated from the avian malarial parasite Plasmodium gallinaceum

1989 ◽  
Vol 9 (9) ◽  
pp. 3621-3629
Author(s):  
J T Joseph ◽  
S M Aldritt ◽  
T Unnasch ◽  
O Puijalon ◽  
D F Wirth
Keyword(s):  
Repeat Unit ◽  
Unit Length ◽  
Malarial Parasite ◽  
Pulse Field ◽  
Plasmodium Gallinaceum ◽  
Multiple Transcripts ◽  
Parasite Plasmodium ◽  
Extrachromosomal Element ◽  
Repeat Unit Length

We have identified a conserved, repeated, and highly transcribed DNA element from the avian malarial parasite Plasmodium gallinaceum. The element produced multiple transcripts in both zygotes and asexual blood stages of this parasite. It was found to be highly conserved in all of five malarial species tested and hybridized at reduced stringency to other members of the phylum Apicomplexa, including the genera Babesia, Eimeria, Toxoplasma, and Theileria. The copy number of the element was about 15, and it had a circularly permuted restriction map with a repeat unit length of about 6.2 kilobases. It could be separated from the main genomic DNA by using sucrose gradients and agarose gels, and it migrated separately from the recognized Plasmodium chromosomes on pulse-field gels. In the accompanying paper (S. M. Aldritt, J. T. Joseph, and D. F. Wirth, Mol. Cell. Biol. 9:3614-3620, 1989), evidence is presented that element contains the mitochondrial genes for the protein cytochrome b and a fragment of the large rRNA. We postulate that this element is an episome in the mitochondria of the obligate parasites belonging to the phylum Apicomplexa.

scholarly journals Characterization of a conserved extrachromosomal element isolated from the avian malarial parasite Plasmodium gallinaceum.

1989 ◽  
Vol 9 (9) ◽  
pp. 3621-3629 ◽  
Author(s):  
J T Joseph ◽  
S M Aldritt ◽  
T Unnasch ◽  
O Puijalon ◽  
D F Wirth
Keyword(s):  
Repeat Unit ◽  
Unit Length ◽  
Malarial Parasite ◽  
Pulse Field ◽  
Plasmodium Gallinaceum ◽  
Multiple Transcripts ◽  
Parasite Plasmodium ◽  
Extrachromosomal Element ◽  
Repeat Unit Length

We have identified a conserved, repeated, and highly transcribed DNA element from the avian malarial parasite Plasmodium gallinaceum. The element produced multiple transcripts in both zygotes and asexual blood stages of this parasite. It was found to be highly conserved in all of five malarial species tested and hybridized at reduced stringency to other members of the phylum Apicomplexa, including the genera Babesia, Eimeria, Toxoplasma, and Theileria. The copy number of the element was about 15, and it had a circularly permuted restriction map with a repeat unit length of about 6.2 kilobases. It could be separated from the main genomic DNA by using sucrose gradients and agarose gels, and it migrated separately from the recognized Plasmodium chromosomes on pulse-field gels. In the accompanying paper (S. M. Aldritt, J. T. Joseph, and D. F. Wirth, Mol. Cell. Biol. 9:3614-3620, 1989), evidence is presented that element contains the mitochondrial genes for the protein cytochrome b and a fragment of the large rRNA. We postulate that this element is an episome in the mitochondria of the obligate parasites belonging to the phylum Apicomplexa.

scholarly journals Tandem repeat variation in human and great ape populations and its impact on gene expression divergence

2015 ◽  
Vol 25 (11) ◽  
pp. 1591-1599 ◽  
Author(s):  
Tugce Bilgin Sonay ◽  
Tiago Carvalho ◽  
Mark D. Robinson ◽  
Maja P. Greminger ◽  
Michael Krützen ◽  
...  
Keyword(s):  
Gene Expression ◽  
Tandem Repeat ◽  
Great Ape ◽  
Expression Divergence ◽  
Gene Expression Divergence

scholarly journals Support for the dominance theory in Drosophila transcriptomes

2018 ◽  
Author(s):  
Ana Llopart ◽  
Evgeny Brud ◽  
Nikale Pettie ◽  
Josep M. Comeron
Keyword(s):  
Gene Expression ◽  
Expression Patterns ◽  
Transcriptional Networks ◽  
Expression Divergence ◽  
Gene Expression Divergence ◽  
Genome Wide ◽  
Regulatory Mutations ◽  
Opposite Sex ◽  
High Degree

ABSTRACTInteractions among divergent elements of transcriptional networks from different species can lead to misexpression in hybrids through regulatory incompatibilities, some with the potential to generate sterility. Genes with male-biased expression tend to be overrepresented among genes misexpressed in hybrid males. While the possible contribution of faster-male evolution to this misexpression has been explored, the role of the hemizygous X chromosome (i.e., the dominance theory for transcriptomes) remains yet to be determined. Here we study genome-wide patterns of gene expression in females and males of Drosophila yakuba and D. santomea and their hybrids. We used attached-X stocks to specifically test the dominance theory, and we uncovered a significant contribution of recessive alleles on the X chromosome to hybrid misexpression. Our analysis of gene expression patterns suggests that there is a contribution of weakly deleterious regulatory mutations to gene expression divergence in the sex towards which the expression is biased. In the opposite sex (e.g., genes with female-biased expression analyzed in male transcriptomes), we detect stronger selective constraints on gene expression divergence. Although genes with high degree of male-biased expression show a clear signal of faster-X evolution for gene expression divergence, we also detected slower-X evolution of gene expression in other gene classes (e.g. female-biased genes) that is mediated by significant decreases of cis- and trans-regulatory divergence. The distinct behavior of X-linked genes with high degree of male-biased expression is consistent with these genes experiencing a higher incidence of positively selected regulatory mutations than their autosomal counterparts. We propose that both dominance theory and faster-X evolution of gene expression may be major contributors to hybrid misexpression and possibly the large X-effect in these species.

scholarly journals Characterization and application of multiple genetic markers forPlasmodium malariae

Parasitology ◽  
2006 ◽  
Vol 134 (5) ◽  
pp. 637-650 ◽  
Author(s):  
M. C. BRUCE ◽  
A. MACHESO ◽  
M. R. GALINSKI ◽  
J. W. BARNWELL
Keyword(s):  
Genetic Markers ◽  
Repeat Unit ◽  
Unit Length ◽  
Allelic Diversity ◽  
Protozoan Parasite ◽  
Epidemiological Data ◽  
Plasmodium Malariae ◽  
Multiplicity Of Infection ◽  
Single Genotype ◽  
Repeat Unit Length

SUMMARYPlasmodium malariae, a protozoan parasite that causes malaria in humans, has a global distribution in tropical and subtropical regions and is commonly found in sympatry with otherPlasmodiumspecies of humans. Little is known about the genetics or population structure ofP. malariae. In the present study, we describe polymorphic genetic markers forP. malariaeand present the first molecular epidemiological data for this parasite. Six microsatellite or minisatellite markers were validated using 76P. malariaesamples from a diverse geographical range. The repeat unit length varied from 2 to17 bp, and up to 10 different alleles per locus were detected. Multiple genotypes ofP. malariaewere detected in 33 of 70 samples from humans with naturally acquired infection. Heterozygosity was calculated to be between 0·236 and 0·811. Allelic diversity was reduced for samples from South America and, at some loci, in samples from Thailand compared with those from Malawi. The number of unique multilocus genotypes defined using the 6 markers was significantly greater in Malawi than in Thailand, even when data from single genotype infections were used. There was a significant reduction in the multiplicity of infection in symptomatic infections compared with asymptomatic ones, suggesting that clinical episodes are usually caused by the expansion of a single genotype.

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