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1.
Background
Alu elements are a family of SINE retrotransposons in primates. They are classified into subfamilies according to specific diagnostic mutations from the general Alu consensus. It is now believed that there may be several retrotranspositionally-competent source genes within an Alu subfamily. To investigate the evolution of young Alu elements it is critical to have access to complete subfamilies, which, following the release of the final human genome assembly, can now be obtained using in silico methods. 相似文献2.
A recently identified Alu element (Leeflang et al. J. Mol. Evol. 1993, 37:559–565), referred to as the putative founder of the HS (PV) subfamily, was found to be present at orthologous loci in the human, chimpanzee, gorilla, and gibbon lineages. The evolution of this Alu suggested that it is a source gene in the evolution of Alu family repeats for one of the most recent subfamilies, HS. We have determined that this putative founder of the HS subfamily was not present at the orthologous loci in older primates, including old world and new world monkeys. Thus, this particular Alu locus has only been responsible for the establishment of a very small subfamily of Alu sequences. We have further demonstrated that this putative founder Alu was not responsible for the de novo Alu insertion into the neurofibromatosis-1 gene of an individual causing neurofibromatosis. Our data demonstrate that although the putative founder of the HS subfamily found by Leeflang et al. (1993) probably gave rise to one of the most recent subfamilies of Alu sequences, it has not been very active in retroposition.
Correspondence to: T.H. Shaikh 相似文献
3.
Reconstruction and analysis of human alu genes 总被引:39,自引:0,他引:39
4.
Evolution of the master Alu gene(s) 总被引:34,自引:0,他引:34
M. Richard Shen Mark A. Batzer Prescott L. Deininger 《Journal of molecular evolution》1991,33(4):311-320
Summary A comparison of Alu sequences that comprise more recently amplified Alu subfamilies was made. There are 18 individual diagnostic mutations associated with the different subfamilies. This analysis confirmed that the formation of each subfamily can be explained by the sequential accumulation of mutations relative to the previous subfamily. Polymerase chain reaction amplification of orthologous loci in several primate species allowed us to determine the time of insertion of Alu sequences in individual loci. These data suggest that the vast majority of Alu elements amplified at any given time comprised a single Alu subfamily. We find that, although the individual divergence relative to a consensus sequence correlate reasonably well with sequence age, the diagnostic mutations are a more accurate measure of the age of any individual Alu family member. Our data are consistent with a model in which all Alu family members have been made from a single master gene or from a series of sequential master genes. This master gene(s) accumulated diagnostic base changes, resulting in the amplification of different subfamilies from the master gene at different times in primate evolution. The changes in the master gene(s) probably occurred individually, but their appearance is clearly punctuated. Ten of them have occurred within an 15-million-year time span, 40–25 million years ago, and 8 changes have occurred within the last 5 million years. Surprisingly, no changes appeared in the 20 milion years separating these periods. 相似文献
5.
A recent insertion of an alu element on the Y chromosome is a useful marker for human population studies 总被引:23,自引:2,他引:21
A member of the Alu family of repeated DNA elements has been identified on
the long arm of the human Y chromosome, Yq11. This element, referred to as
the Y Alu polymorphic (YAP) element, is present at a specific site on the Y
chromosome in some humans and is absent in others. Phylogenetic comparisons
with other Alu sequences reveal that the YAP element is a member of the
polymorphic subfamily-3 (PSF-3), a previously undefined subfamily of Alu
elements. The evolutionary relationships of PSF-3 to other Alu subfamilies
support the hypothesis that recently inserted elements result from multiple
source genes. The frequency of the YAP element is described in 340
individuals from 14 populations, and the data are combined with those from
other populations. There is both significant heterogeneity among
populations and a clear pattern in the frequencies of the insertion:
sub-Saharan Africans have the highest frequencies, followed by northern
Africans, Europeans, Oceanians, and Asians. An interesting exception is the
relatively high frequency of the YAP element in Japanese. The greatest
genetic distance is observed between the African and non-African
populations. The YAP is especially useful for studying human population
history from the perspective of male lineages.
相似文献
6.
Jerzy Jurka 《Journal of molecular evolution》1989,29(6):496-503
Summary Comparative analysis of the available 3′-portions of the human L1 (LINE-1) family of repeated sequences indicates that all
the sequences can be classified in two major subfamilies. The division is based on patterns of diagnostic bases shared within
L1 subfamilies of sequences but differing between them. The overall ratio of replacement to synonymous positions, occupied
by the diagnostic bases in the large open reading frame of the L1 sequence, is 1.15. This indicates that both subfamilies
were obtained from genes coding for functional proteins. The L1 subfamilies appear to be of different ages and may represent
a “fossil record” of the same active gene at different times in the history of primates. The younger subfamily can be split
further into at least two closely related branches of sequences. The above facts combined with the recent data for the Alu
subfamily structure show that LINE and SINE families of interspersed repeats share discontinuous patterns in their evolution.
These data are consistent with the model that both Alu and L1 families, as well as other pseudogene families, contain active
genes producing discrete layers of pseudogenes throughout the history of primates. Models of evolutionary processes that could
generate these discontinuities are discussed together with the possible biological role of Alu and L1 genes. 相似文献
7.
8.
Xing J Salem AH Hedges DJ Kilroy GE Watkins WS Schienman JE Stewart CB Jurka J Jorde LB Batzer MA 《Journal of molecular evolution》2003,57(Z1):S76-S89
Alu elements have inserted in the human genome throughout primate evolution. A small number of Alu insertions have occurred after the divergence of humans from nonhuman primates and therefore should not be present in nonhuman primate genomes. Most of these recently integrated Alu elements are contained with a series of discrete Alu subfamilies that are related to each other based upon diagnostic nucleotide substitutions. We have extracted members of the Alu Yd subfamily that are derivatives of the Alu Y subfamily that share a common 12-bp deletion that defines the Yd lineage from the draft sequence of the human genome. Analysis of the Yd Alu elements resulted in the recovery of two new Alu subfamilies, Yd3 and Yd6, which contain a total of 295 members (198 Yd3 and 97 Yd6). DNA sequence analysis of each of the Alu Yd subfamilies yielded age estimates of 8.02 and 1.20 million years old for the Alu Yd3 and Yd6 subfamilies, respectively. Two hundred Alu Yd3 and Yd6 loci were screened using polymerase chain reaction (PCR) assays to determine their phylogenetic origin and associated levels of human genomic diversity. The Alu Yd3 subfamily appears to have started amplifying relatively early in primate evolution and continued propagating albeit at a low level as many of its members are found in a variety of hominoid (humans, greater and lesser ape) genomes. Only two of the elements are polymorphic in the human genome and absent from the genomes of nonhuman primates. By contrast all of the members of the Alu Yd6 subfamily are restricted to the human genome, with 12% of the elements representing insertion polymorphisms in human populations. A single Alu Yd6 locus contained an independent parallel forward insertion of a paralogous Alu Sq sequence in the owl monkey. These Alu subfamilies are a source of genomic fossil relics for the study of primate phylogenetics and human population genetics. 相似文献
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10.
Dianna M. Milewicz Peter H. Byers John Reveille Austin L. Hughes Madeleine Duvic 《Journal of molecular evolution》1996,42(2):117-123
Alu elements are a class of repetitive DNA sequences found throughout the human genome that are thought to be duplicated via an RNA intermediate in a process termed retroposition. Recently inserted Alu elements are closely related, suggesting that they are derived from a single source gene or closely related source genes. Analysis of the type III collagen gene (COL3A1) revealed a polymorphic Alu insertion in intron 8 of the gene. The Alu insertion in the COL3A1 gene had a high degree of nucleotide identity to the Sb family of Alu elements, a family of older Alu elements. The Alu sequence was less similar to the consensus sequence for the PV or Sb2 subfamilies, subfamilies of recently inserted Alu elements. These data support the observations that at least three source genes are active in the human genome, one of which is distinct from the PV and Sb2 subfamilies and predates either of these two subfamilies. Appearance of the Alu insertion in different ethnic populations suggests that the insertion may have occurred in the last 100,000 years. This Alu insert should be a useful marker for population studies and for marking COL3A1 alleles. 相似文献
11.
Esther P. Leeflang Wen-Man Liu Igor N. Chesnokov Carl W. Schmid 《Journal of molecular evolution》1993,37(6):559-565
A severe bottleneck in the size of the PV Alu subfamily in the common ancestor of human and gorilla has been used to isolate an Alu source gene. The human PV Alu subfamily consists of about one thousand members which are absent in gorilla and chimpanzee DNA. Exhaustive library screening shows that there are as few as two PV Alus in the gorilla genome. One is gorilla-specific, i.e., absent in the orthologous loci in both human and chimpanzee, suggesting the independent retrotranspositional activity of the PV subfamily in the gorilla lineage. The second of these two gorilla PV Alus is present in both human and chimpanzee DNAs and is the single PV Alu known to precede the radiation of these three species. The orthologous Alu in gibbon DNA resembles the next older Alu subfamily. Thus, this Alu locus is originally templated by a non-PV source gene and acquired characteristic PV sequence variants by mutational drift in situ, consequently becoming the first member and presumptive founder of this PV subfamily.
Correspondence to: C.W. Schmid 相似文献
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13.
Background
The ethylene receptor family of Arabidopsis consists of five members, falling into two subfamilies. Subfamily 1 is composed of ETR1 and ERS1, and subfamily 2 is composed of ETR2, ERS2, and EIN4. Although mutations have been isolated in the genes encoding all five family members, the only previous insertion allele of ERS1 (ers1-2) is a partial loss-of-function mutation based on our analysis. The purpose of this study was to determine the extent of signaling mediated by subfamily-1 ethylene receptors through isolation and characterization of null mutations. 相似文献14.
Using Kimura's distance measure we have calculated the average age of all major Alu subfamilies based on the most recent available data. We conclude that AluJ sequences are some 26 Myr older than previously thought. Furthermore, the origin of the FLA (Free Left Arm) Alu family can be traced back to the very beginning of the mammalian radiation.One new minor subfamily is reported and discussed in the context of sequence diversity in major Alu subfamilies.
Correspondence to: J. Jurka 相似文献
15.
It is generally thought that only a few Alu elements are capable of retrotransposition and that these 'master' sources produce inactive copies. Here, we use a network phylogenetic approach to demonstrate that recently integrated human-specific Alu subfamilies typically contain 10-20% of secondary source elements that contributed 20-40% of all subfamily members. This multiplicity of source elements provides new insight into the remarkably successful amplification strategy of the Alu family. 相似文献
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17.
Background
The evolution of type II MADS box genes has been extensively studied in angiosperms. One of the best-understood subfamilies is that of the Arabidopsis gene APETALA3 (AP3). Previous work has demonstrated that the ancestral paleo AP3 lineage was duplicated at some point within the basal eudicots to give rise to the paralogous TM6 and eu AP3 lineages. This event was followed in eu AP3 orthologs by the replacement of the C-terminal paleoAP3 motif with the derived euAP3 motif. It has been suggested that the new motif was created by an eight-nucleotide insertion that produced a translational frameshift. 相似文献18.
Thomas D Niehaus Svetlana Gerdes Kelsey Hodge-Hanson Aleksey Zhukov Arthur JL Cooper Mona ElBadawi-Sidhu Oliver Fiehn Diana M Downs Andrew D Hanson 《BMC genomics》2015,16(1)
Background
It is now recognized that enzymatic or chemical side-reactions can convert normal metabolites to useless or toxic ones and that a suite of enzymes exists to mitigate such metabolite damage. Examples are the reactive imine/enamine intermediates produced by threonine dehydratase, which damage the pyridoxal 5''-phosphate cofactor of various enzymes causing inactivation. This damage is pre-empted by RidA proteins, which hydrolyze the imines before they do harm. RidA proteins belong to the YjgF/YER057c/UK114 family (here renamed the Rid family). Most other members of this diverse and ubiquitous family lack defined functions.Results
Phylogenetic analysis divided the Rid family into a widely distributed, apparently archetypal RidA subfamily and seven other subfamilies (Rid1 to Rid7) that are largely confined to bacteria and often co-occur in the same organism with RidA and each other. The Rid1 to Rid3 subfamilies, but not the Rid4 to Rid7 subfamilies, have a conserved arginine residue that, in RidA proteins, is essential for imine-hydrolyzing activity. Analysis of the chromosomal context of bacterial RidA genes revealed clustering with genes for threonine dehydratase and other pyridoxal 5''-phosphate-dependent enzymes, which fits with the known RidA imine hydrolase activity. Clustering was also evident between Rid family genes and genes specifying FAD-dependent amine oxidases or enzymes of carbamoyl phosphate metabolism. Biochemical assays showed that Salmonella enterica RidA and Rid2, but not Rid7, can hydrolyze imines generated by amino acid oxidase. Genetic tests indicated that carbamoyl phosphate overproduction is toxic to S. enterica cells lacking RidA, and metabolomic profiling of Rid knockout strains showed ten-fold accumulation of the carbamoyl phosphate-related metabolite dihydroorotate.Conclusions
Like the archetypal RidA subfamily, the Rid2, and probably the Rid1 and Rid3 subfamilies, have imine-hydrolyzing activity and can pre-empt damage from imines formed by amine oxidases as well as by pyridoxal 5''-phosphate enzymes. The RidA subfamily has an additional damage pre-emption role in carbamoyl phosphate metabolism that has yet to be biochemically defined. Finally, the Rid4 to Rid7 subfamilies appear not to hydrolyze imines and thus remain mysterious.Electronic supplementary material
The online version of this article (doi:10.1186/s12864-015-1584-3) contains supplementary material, which is available to authorized users. 相似文献19.
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