Search PubMed⌕ Search

Biomedical subjects

C Biémont

Publications and source records attributed to C Biémont.

At least 19 recordsLinked to original sources
PubMed2007

Insertion polymorphism of transposable elements and population structure of Anopheles gambiae M and S molecular forms in Cameroon.

The insertion polymorphism of five transposable element (TE) families was studied by Southern blots in several populations of the M and S molecular forms of the mosquito Anopheles gambiae sensu stricto from southern Cameroon. We showed that the mean TE insertion site number and the within-population insertion site polymorphism globally differed between the M and S molecular forms. The comparison of the TE insertion profiles of the populations revealed a significant differentiation between these two molecular forms (0.163 < Phi(ST) < 0.371). We cloned several insertions of a non-LTR retrotransposon (Aara8) that were fixed in one form and absent in the other one. The only insertion that could be clearly located on a chromosome arm mapped to cytological division 6 of chromosome X, confirming the importance of this region in the ongoing speciation between the M and S molecular forms.

Animals↗
PubMed2005

Is genome size influenced by colonization of new environments in dipteran species?

Genome size differences are usually attributed to the amplification and deletion of various repeated DNA sequences, including transposable elements (TEs). Because environmental changes may promote modifications in the amount of these repeated sequences, it has been postulated that when a species colonizes new environments this could be followed by an increase in its genome size. We tested this hypothesis by estimating the genome size of geographically distinct populations of Drosophila ananassae, Drosophila malerkotliana, Drosophila melanogaster, Drosophila simulans, Drosophila subobscura, and Zaprionus indianus, all of which have known colonization capacities. There was no strong statistical differences between continents for most species. However, we found that populations of D. melanogaster from east Africa have smaller genomes than more recent populations. For species in which colonization is a recent event, the differences between genome sizes do not thus seem to be related to colonization history. These findings suggest either that genome size is seldom modified in a significant way during colonization or that it takes time for genome size of invading species to change significantly.

Analysis of Variance↗
PubMed2005

What transposable elements tell us about genome organization and evolution: the case of Drosophila.

Transposable elements (TEs) have been identified in every organism in which they have been looked for. The sequencing of large genomes, such as the human genome and those of Drosophila, Arabidopsis, Caenorhabditis, has also shown that they are a major constituent of these genomes, accounting for 15% of the genome of Drosophila, 45% of the human genome, and more than 70% in some plants and amphibians. Compared with the 1% of genomic DNA dedicated to protein-coding sequences in the human genome, this has prompted various researchers to suggest that the TEs and the other repetitive sequences that constitute the so-called "noncoding DNA", are where the most stimulating discoveries will be made in the future (Bromham, 2002). We are therefore getting further and further from the original idea that this DNA was simply "junk DNA", that owed its presence in the genome entirely to its capacity for selfish transposition. Our understanding of the structures of TEs, their distribution along the genomes, their sequence and insertion polymorphisms within genomes, and within and between populations and species, their impact on genes and on the regulatory mechanisms of genetic expression, their effects on exon shuffling and other phenomena that reshape the genome, and their impact on genome size has increased dramatically in recent years. This leads to a more general picture of the impact of TEs on genomes, though many copies are still mainly selfish or junk DNA. In this review we focus mainly on discoveries made in Drosophila, but we also use information about other genomes when this helps to elucidate the general processes involved in the organization, plasticity, and evolution of genomes.

Animals↗
PubMed2005

Transposable elements in mosquitoes.

We describe the current state of knowledge about transposable elements (TEs) in different mosquito species. DNA-based elements (class II elements), non-LTR retrotransposons (class I elements), and MITEs (Miniature Inverted Repeat Transposable Elements) are found in the three genera, Anopheles, Aedes and Culex, whereas LTR retrotransposons (class I elements) are found only in Anopheles and Aedes. Mosquitoes were the first insects in which MITEs were reported; they have several LTR retrotransposons belonging to the Pao family, which is distinct from the Gypsy-Ty3 and Copia-Ty1 families. The number of TE copies shows huge variations between classes of TEs within a given species (from 1 to 1000), in sharp contrast to Drosophila, which shows only relatively minor differences in copy number between elements (from 1 to 100). The genomes of these insects therefore display major differences in the amount of TEs and therefore in their structure and global composition. We emphasize the need for more population genetic data about the activity of TEs, their distribution over chromosomes and their frequencies in natural populations of mosquitoes, to further the current attempts to develop a transgenic mosquito unable to transmit malaria that is intended to replace the natural populations.

Animals↗
PubMed2002

Tissue-specificity of 412 retrotransposon expression in Drosophila simulans and D. melanogaster.

We analyse the expression of the retrotransposon 412 in the soma, testes, and ovaries in populations of Drosophila simulans and D. melanogaster, using RT-PCR and in situ hybridization. We find that expression of 412 is highly variable in the soma, confirming previous findings based on Northern blots. No 412RNA is detected in the ovaries by either in situ hybridization or RT-PCR, in any population of either species. Transcripts are, however, detected in the male germline, which show a very characteristic spatial pattern of 412 expression in primary spermatocytes. There is no relationship between expression of the 412 element in the soma and in the testes in the populations. These findings show that the expression of 412 is independently regulated in the soma and the testes, and this raises the question of the real influence of the somatic transcripts on the organism and on the transposition rate.

Animals↗
PubMed2002

Insertion polymorphism of retrotransposable elements in populations of the insular, endemic species Drosophila madeirensis.

The insertion site numbers of the retrotransposable elements (TE) 412, gypsy and bilbo were determined in individuals of five distinct natural populations of the endemic species Drosophila madeirensis from the island of Madeira. The TE distributions were compared to those of the paleartic, widespread and phylogenetically closely related species, D. subobscura. In situ hybridization and Southern blots showed that in D. madeirensis the number of insertion sites ranged between 10 and 15, three and six, and 35 and 42 for elements 412, gypsy and bilbo, respectively. The corresponding values for D. subobscura were similar. Two of these elements, 412 and gypsy, had very few insertions in the heterochromatin, unlike bilbo, which displayed a high heterochromatic insertion number. The Southern band polymorphism was very high, leading to within-population variation of 97.2%, whatever the population and the TE concerned. Using the polymorphic TE insertion sites as markers to analyse population structure by AMOVA, adapted for RAPD (Randomly Amplified Polymorphic DNA) data, we found small but significant genetic differences between the populations on Madeira. This slight differentiation, coupled with similar copy numbers for each TE between populations, suggests that the D. madeirensis species consists of a single, only slightly subdivided population. These data also show that insular populations and endemic species of Drosophila can have as many copies of TEs as more widespread species.

Animals↗
PubMed2000

High copy numbers of multiple transposable element families in an Australian population of Drosophila simulans.

Sudden mobilization of transposable elements in Drosophila is a well-reported phenomenon but one that usually affects no more than a few elements (one to four). We report here the existence of a D. simulans natural population (Canberra) from Australia, which had high copy numbers for various transposable elements (transposons, LTR retrotransposons and non-LTR retrotransposons). The impact of transposable elements on the host genome and populations is discussed.

Animals↗
PubMed2000

Stress and transposable elements: co-evolution or useful parasites?

The activity of transposable elements can be induced by environmental and population factors and in particular by stresses in various organisms. A consequence of the increase in transposable element mobility is the creation of new genetic variability that can be useful in the face of stressful conditions. In this review, results supporting this hypothesis are presented and discussed. The main question is how stress induces the activity of transposable elements. We discuss hypotheses based upon the existence of promoters or fixation sites of transcription activators in the untranslated regions of transposable elements, similar to those found in regulatory regions of host defence genes.

Biological Evolution↗
PubMed2000

Transposons but not retrotransposons are located preferentially in regions of high recombination rate in Caenorhabditis elegans.

We analyzed the distribution of transposable elements (TEs: transposons, LTR retrotransposons, and non-LTR retrotransposons) in the chromosomes of the nematode Caenorhabditis elegans. The density of transposons (DNA-based elements) along the chromosomes was found to be positively correlated with recombination rate, but this relationship was not observed for LTR or non-LTR retrotransposons (RNA-based elements). Gene (coding region) density is higher in regions of low recombination rate. However, the lower TE density in these regions is not due to the counterselection of TE insertions within exons since the same positive correlation between TE density and recombination rate was found in noncoding regions (both in introns and intergenic DNA). These data are not compatible with a global model of selection acting against TE insertions, for which an accumulation of elements in regions of reduced recombination is expected. We also found no evidence for a stronger selection against TE insertions on the X chromosome compared to the autosomes. The difference in distribution of the DNA and RNA-based elements along the chromosomes in relation to recombination rate can be explained by differences in the transposition processes.

Animals↗
PubMed1999

Polymorphism in structure of the retrotransposable element 412 in Drosophila simulans and D. melanogaster populations.

The structure of the 412 retrotransposable element was investigated in various natural populations of D. melanogaster and D. simulans by a restriction enzyme analysis. We show that although the canonical structure of the 412 element was the same in both species, a high structural polymorphism existed with various rearranged elements. A 412 family was thus composed of heterogeneous copies of different sizes, with a large proportion of full-size copies. D. simulans had more rearranged copies than D. melanogaster, with some specific copies, such as a 5.6-kb BsrBI fragment, present in all populations of D. simulans. Full-size and rearranged copies were detected in both the euchromatin and the heterochromatin, with many rearranged copies in D. simulans, suggesting a recent mobilization of the 412 element in this species.

Animals↗
PubMed1999

Distribution of transposable elements in Drosophila species.

We present a global analysis of the distribution of 43 transposable elements (TEs) in 228 species of the Drosophila genus from our data and data from the literature. Data on chromosome localization come from in situ hybridization and presence/absence of the elements from southern analyses. This analysis shows great differences between TE distributions, even among closely related species. Some TEs are distributed according to the phylogeny of their host species; others do not entirely follow the phylogeny, suggesting horizontal transfers. A higher number of insertion sites for most TEs in the genome of D. melanogaster is observed when compared with that in D. simulans. This suggests either intrinsic differences in genomic characteristics between the two species, or the influence of differing effective population sizes, although biases due to the use of TE probes coming mostly from D. melanogaster and to the way TEs are initially detected in species cannot be ruled out. Data on TEs more specific to the species under consideration are necessary for a better understanding of their distribution in organisms and populations.

Animals↗
PubMed1999

Wake up of transposable elements following Drosophila simulans worldwide colonization.

Transposable elements (TEs) make up around 10%-15% of the Drosophila melanogaster genome, but its sibling species Drosophila simulans carries only one third as many such repeat sequences. We do not, however, have an overall view of copy numbers of the various classes of TEs (long terminal repeat [LTR] retrotransposons, non-LTR retrotransposons, and transposons) in genomes of natural populations of both species. We analyzed 34 elements in individuals from various natural populations of these species. We show that D. melanogaster has higher average chromosomal insertion site numbers per genome than D. simulans for all TEs except five. The LTR retrotransposons gypsy, ZAM, and 1731 and the transposon bari-1 present similar low copy numbers in both species. The transposon hobo has a large number of insertion sites, with significantly more sites in D. simulans. High variation between populations in number of insertion sites of some elements of D. simulans suggests that these elements can invade the genome of the entire species starting from a local population. We propose that TEs in the D. simulans genome are being awakened and amplified as they had been a long time ago in D. melanogaster.

Animals↗
PubMed1999

Transposable elements and genome evolution: the case of Drosophila simulans.

Drosophila simulans presents a large variation in copy number among various transposable elements (TEs) and among natural populations for a given element. Some elements such as HMS beagle, blood, flea, tirant, coral, prygun, jockey, F, nomade and mariner are absent in most populations, except in one or two which have copies on their chromosome arms. This suggests that some TEs are being awakened in D. simulans and are in the process of invading the species while it is colonizing the world. The elements 412 and roo/B104 present a wide insertion polymorphism among D. simulans populations, but only the 412 copy number follows a temperature cline. One population (Canberra from Australia) has a very high copy number for the 412 element and for many other TEs as well, indicating that some populations may have lost control of some of their TEs. While the 412 transposition rate is similar in all populations, its transcription level throughout developmental stages varies with populations, depending on copy number. Populations with 412 copy number higher than 10-12 exhibit co-suppression, while the expression in populations with lower numbers depends on the insertion location. All these results suggest genomic invasions by 412 and other TEs during the worldwide spread of the D. simulans species.

Animals↗
PubMed1998

A temperature cline in copy number for 412 but not roo/B104 retrotransposons in populations of Drosophila simulans.

The copy number of the retrotransposable element 412 of Drosophila simulans from populations collected worldwide shows a negative correlation with minimum temperature. No association was detected for the roo/B104 element. The possibility that selective pressures might regulate the 412 copy number in these natural populations is supported by detection of selection against the detrimental effects of 412 insertions (estimated by the proportion of insertions on the X chromosome in comparison with the autosomes) but not roo/B104. These data reveal different spatial patterns for two element families, and strongly suggest that some factors in the environment, such as temperature, may interfere with the control of retrotransposition, thus affecting important aspects of genomic evolution.

Animals↗
PubMed1998

Distribution of the retrotransposable element 412 in Drosophila species.

Copy numbers of sequences homologous to the Drosophila melanogaster retrotransposable element 412, their distribution between the chromosome arms and the chromocenter, and whether they contain full-size copies were analyzed for 55 species of the Drosophila genus. Element 412 insertion sites were detected on the chromosome arms of D. melanogaster, Drosophila simulans, and a few species of the obscura group, but the chromocenter was labeled in almost all species. The presence of element 412 sequences in the majority of species shows that this element has a long evolutionary history in Drosophilidae, although it may have recently invaded the chromosomes in some species, such as D. simulans. Differences in copy number between species may be due to population size or specific endogenous or environmental factors and may follow the worldwide invasion of the species. Putative full-length copies were detected in the chromocenters of some species with no copies on the chromosome arms, suggesting that the chromocenter may be a shelter for such copies and not only for deleted ones.

Animals↗
PubMed1997

Chromosomal distribution of the 412 retrotransposon in natural populations of Drosophila simulans.

The insertion site localization of the 412 retrotransposable element was analysed by in situ hybridization to the polytene chromosomes of 57 individual genomes from 25 natural populations of Drosophila simulans. The 412 insertion sites along the chromosomes show a tendency to aggregate in the distal and proximal ends of the 2R arm, and in several local regions along the 3R arm. The distribution of the 412 insertion sites, weighted by DNA content, along the chromosome arms reveals an overall tendency for the site number to increase from the middle of the arm to the base and tip, with a decrease at the tips, especially pronounced for the X chromosome. Such a distribution differs slightly from that of D. melanogaster, which globally shows an increase of the 412 site number from base to tip of the chromosome arms, indicating differing behaviour of the 412 element in the two species. These results are discussed in connection with the recombination rate along the chromosome arms.

Animals↗