Molecular and genomic organization of clusters of repetitive DNA sequences in Caenorhabditis elegans

Evolution of satDNAs on holocentric chromosomes: insights from hemipteran insects of the genus Mahanarva

Satellite DNAs (satDNAs) constitute one of the main components of eukaryote genomes and are involved in chromosomal organization and diversification. Although largely studied, little information was gathered about their evolution on holocentric species, i.e., diffuse centromeres, which, due to differences in repeat organization, could result in different evolutionary patterns. Here, we combined bioinformatics and cytogenetic approaches to evaluate the evolution of the satellitomes in Mahanarva holocentric insects. In two species, de novo identification revealed a high number of satDNAs, 110 and 113, with an extreme monomer length range of 18-4228 bp. The overall abundance of satDNAs was observed to be 6.67% in M. quadripunctata and 1.98% in M. spectabilis, with different abundances for the shared satDNAs. Chromosomal mapping of the most abundant repeats of M. quadripunctata and M. spectabilis on other Mahanarva reinforced the dynamic nature of satDNAs. Variable patterns of chromosomal distribution for the satDNAs were noticed, with the occurrence of clusters on distinct numbers of chromosomes and at different positions and the occurrence of scattered signals or nonclustered satDNAs. Altogether, our data demonstrated the high dynamism of satDNAs in Mahanarva with the involvement of this genomic fraction in chromosome diversification of the genus. The general characteristics and patterns of evolution of satDNAs are similar to those observed on monocentric chromosomes, suggesting that the differential organization of genome compartments observed on holocentric chromosomes compared with monocentric chromosomes does not have a large impact on the evolution of satDNAs. Analysis of the satellitomes of other holocentric species in a comparative manner will shed light on this issue.

High evolutionary turnover of satellite families in Caenorhabditis

Background

The high density of tandem repeat sequences (satellites) in nematode genomes and the availability of genome sequences from several species in the group offer a unique opportunity to better understand the evolutionary dynamics and the functional role of these sequences. We take advantage of the previously developed SATFIND program to study the satellites in four Caenorhabditis species and investigate these questions.

Methods

The identification and comparison of satellites is carried out in three steps. First we find all the satellites present in each species with the SATFIND program. Each satellite is defined by its length, number of repeats, and repeat sequence. Only satellites with at least ten repeats are considered. In the second step we build satellite families with a newly developed alignment program. Satellite families are defined by a consensus sequence and the number of satellites in the family. Finally we compare the consensus sequence of satellite families in different species.

Results

We give a catalog of individual satellites in each species. We have also identified satellite families with a related sequence and compare them in different species. We analyze the turnover of satellites: they increased in size through duplications of fragments of 100-300 bases. It appears that in many cases they have undergone an explosive expansion. In C. elegans we have identified a subset of large satellites that have strong affinity for the centromere protein CENP-A. We have also compared our results with those obtained from other species, including one nematode and three mammals.

Conclusions

Most satellite families found in Caenorhabditis are species-specific; in particular those with long repeats. A subset of these satellites may facilitate the formation of kinetochores in mitosis. Other satellite families in C. elegans are either related to Helitron transposons or to meiotic pairing centers.

Electronic supplementary material

The online version of this article (doi:10.1186/s12862-015-0495-x) contains supplementary material, which is available to authorized users.

The multiplicity of alternative splicing decisions in Caenorhabditis elegans is linked to specific intronic regulatory motifs and minisatellites

Background

Alternative splicing diversifies the pool of messenger RNA molecules encoded by individual genes. This diversity is particularly high when multiple splicing decisions cause a combinatorial arrangement of several alternate exons. We know very little on how the multiple decisions occurring during the maturation of single transcripts are coordinated and whether specific sequence elements might be involved.

Results

Here, the Caenorhabditis elegans genome was surveyed in order to identify sequence elements that might play a specific role in the regulation of multiple splicing decisions. The introns flanking alternate exons in transcripts whose maturation involves multiple alternative splicing decisions were compared to those whose maturation involves a single decision. Fifty-eight penta-, hexa-, and hepta-meric elements, clustered in 17 groups, were significantly over-represented in genes subject to multiple alternative splicing decisions. Most of these motifs relate to known splicing regulatory elements and appear to be well conserved in the related species Caenorhabditis briggsae. The usage of specific motifs is not linked to the gene product function, but rather depends on the gene structure, since it is influenced by the distance separating the multiple splicing decision sites. Two of these motifs are part of the CeRep25B minisatellite, which is also over-represented at the vicinity of alternative splicing regions. Most of the remaining motifs are not part of repeated sequence elements, but tend to occur in specific heterologous pairs in genes subject to multiple alternative splicing decisions.

Conclusions

The existence of specific intronic sequence elements linked to multiple alternative splicing decisions is intriguing and suggests that these elements might have some specialized regulatory role during splicing.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2164-15-364) contains supplementary material, which is available to authorized users.

The cytogenetic architecture of the aphid genome

In recent years aphids, with their well-defined polyphenism, have become favoured as model organisms for the study of epigenetic processes. The availability of the pea aphid (Acyrthosiphon pisum) genome sequence has engendered much research aimed at elucidating the mechanisms by which the phenotypic plasticity of aphids is inherited and controlled. Yet so far this research effort has paid little attention to the cytogenetic processes that play a vital part in the organisation, expression and inheritance of the aphid genome. Aphids have holocentric chromosomes, which have very different properties from the chromosomes with localised centromeres that are found in most other organisms. Here we review the diverse forms of aphid chromosome behaviour that occur during sex determination and male and female meiosis, often in response to environmental changes and mediated by endocrine factors. Remarkable differences occur, even between related species, that could have significant effects on the inheritance of all or parts of the genome. In relation to this, we review the particular features of the distribution of heterochromatin, rDNA genes and other repetitive DNA in aphid chromosomes, and discuss the part that these may play in the epigenetic modification of chromatin structure and function.

The most frequent short sequences in non-coding DNA

The purpose of this work is to determine the most frequent short sequences in non-coding DNA. They may play a role in maintaining the structure and function of eukaryotic chromosomes. We present a simple method for the detection and analysis of such sequences in several genomes, including Arabidopsis thaliana, Caenorhabditis elegans, Drosophila melanogaster and Homo sapiens. We also study two chromosomes of man and mouse with a length similar to the whole genomes of the other species. We provide a list of the most common sequences of 9–14 bases in each genome. As expected, they are present in human Alu sequences. Our programs may also give a graph and a list of their position in the genome. Detection of clusters is also possible. In most cases, these sequences contain few alternating regions. Their intrinsic structure and their influence on nucleosome formation are not known. In particular, we have found new features of short sequences in C. elegans, which are distributed in heterogeneous clusters. They appear as punctuation marks in the chromosomes. Such clusters are not found in either A. thaliana or D. melanogaster. We discuss the possibility that they play a role in centromere function and homolog recognition in meiosis.

Evolution of the Caenorhabditis elegans genome

A fundamental problem in genome biology is to elucidate the evolutionary forces responsible for generating nonrandom patterns of genome organization. As the first metazoan to benefit from full-genome sequencing, Caenorhabditis elegans has been at the forefront of research in this area. Studies of genomic patterns, and their evolutionary underpinnings, continue to be augmented by the recent push to obtain additional full-genome sequences of related Caenorhabditis taxa. In the near future, we expect to see major advances with the onset of whole-genome resequencing of multiple wild individuals of the same species. In this review, we synthesize many of the important insights to date in our understanding of genome organization and function that derive from the evolutionary principles made explicit by theoretical population genetics and molecular evolution and highlight fertile areas for future research on unanswered questions in C. elegans genome evolution. We call attention to the need for C. elegans researchers to generate and critically assess nonadaptive hypotheses for genomic and developmental patterns, in addition to adaptive scenarios. We also emphasize the potential importance of evolution in the gonochoristic (female and male) ancestors of the androdioecious (hermaphrodite and male) C. elegans as the source for many of its genomic and developmental patterns.

Twelve novel C. elegans RNA candidates isolated by two-dimensional polyacrylamide gel electrophoresis

C. elegans small RNAs (<50 nt) were separated by two-dimensional gel electrophoresis (2D-PAGE). cDNAs were prepared from the RNAs extracted from randomly chosen 2D-PAGE spots. Although many cDNA sequences corresponded to parts of known RNAs, twelve novel small RNA candidates were identified: eleven from 2D-PAGE spots of the mixed-stage worm RNA preparation and one from those of the embryonic RNA preparation. These are encoded in the intergenic regions, in the introns of protein-coding genes, in the anti-sense strand of protein-coding sequences and repetitive sequence regions of the genome. None of them showed a characteristic structure of miRNAs, suggesting that they are candidates of other or new classes of RNAs.

High mutation rate and predominance of insertions in the Caenorhabditis elegans nuclear genome

Mutations have pivotal functions in the onset of genetic diseases and are the fundamental substrate for evolution. However, present estimates of the spontaneous mutation rate and spectrum are derived from indirect and biased measurements. For instance, mutation rate estimates for Caenorhabditis elegans are extrapolated from observations on a few genetic loci with visible phenotypes and vary over an order of magnitude. Alternative approaches in mammals, relying on phylogenetic comparisons of pseudogene loci and fourfold degenerate codon positions, suffer from uncertainties in the actual number of generations separating the compared species and the inability to exclude biases associated with natural selection. Here we provide a direct and unbiased estimate of the nuclear mutation rate and its molecular spectrum with a set of C. elegans mutation-accumulation lines that reveal a mutation rate about tenfold higher than previous indirect estimates and an excess of insertions over deletions. Because deletions dominate patterns of C. elegans pseudogene variation, our observations indicate that natural selection might be significant in promoting small genome size, and challenge the prevalent assumption that pseudogene divergence accurately reflects the spontaneous mutation spectrum.

Cytogenetic and molecular characterization of the MBSAT1 satellite DNA in holokinetic chromosomes of the cabbage moth, Mamestra brassicae (Lepidoptera)

Digestion of Mamestra brassicae DNA with DraI produced a prominent fragment of approximately 200 bp and a ladder of electrophoretic bands with molecular weights which are a multiple of 200 bp. Southern blotting revealed that this ladder is composed of DNA fragments that are multimers of the 200-bp DraI band suggesting that DraI isolated a satellite that has been called Mamestra brassicae satellite DNA1 (MBSAT1). MBSAT1 is the first satellite DNA isolated in Lepidoptera. In-situ DraI digestion of chromosome spreads, together with fluorescent in-situ hybridization, showed that MBSAT1 sequences are clustered in heterochromatin of the sex chromosomes, Z and W. MBSAT1 was 234 bp long with an AT content of 60.7%. The curvature-propensity plot suggested a curvature in the MBSAT1 structure.

Rolling-circle transposons in eukaryotes

All eukaryotic DNA transposons reported so far belong to a single category of elements transposed by the so-called "cut-and-paste" mechanism. Here, we report a previously unknown category of eukaryotic DNA transposons, Helitron, which transpose by rolling-circle replication. Autonomous Helitrons encode a 5'-to-3' DNA helicase and nuclease/ligase similar to those encoded by known rolling-circle replicons. Helitron-like transposons have conservative 5'-TC and CTRR-3' termini and do not have terminal inverted repeats. They contain 16- to 20-bp hairpins separated by 10--12 nucleotides from the 3'-end and transpose precisely between the 5'-A and T-3', with no modifications of the AT target sites. Together with their multiple diverged nonautonomous descendants, Helitrons constitute approximately 2% of both the Arabidopsis thaliana and Caenorhabditis elegans genomes and also colonize the Oriza sativa genome. Sequence conservation suggests that Helitrons continue to be transposed.

Asymmetrically distributed oligonucleotide repeats in the Caenorhabditis elegans genome sequence that map to regions important for meiotic chromosome segregation

The roundworm Caenorhabditis elegans has a haploid karyotype containing six linear chromosomes. The termini of worm chromosomes have been proposed to play an important role in meiotic prophase, either when homologs are participating in a genome-wide search for their proper partners or in the initiation of synapsis. For each chromosome one end appears to stimulate crossing-over with the correct homolog; the other end lacks this property. We have used a bioinformatics approach to identify six repetitive sequence elements in the sequenced C.elegans genome whose distribution closely parallels these putative meiotic pairing centers (MPC) or homolog recognition regions (HRR). We propose that these six DNA sequence elements, which are largely chromosome specific, may correspond to the genetically defined HRR/MPC elements.

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.

New transposable elements identified as insertions in rice transposon Tnr1

Tnr1 (235 bp long) is a transposable element in rice. Polymerase chain reactions (PCRs) done with a primer(s) that hybridizes to terminal inverted repeat sequences (TIRs) of Tnr1 detected new Tnr1 members with one or two insertions in rice genomes. Six identified insertion sequences (Tnr4, Tnr5, Tnr11, Tnr12, Tnr13 and RIRE9) did not have extensive homology to known transposable elements, rather they had structural features characteristic of transposable elements. Tnr4 (1767 bp long) had imperfect 64-bp TIRs and appeared to generate duplication of a 9-bp sequence at the target site. However, the TIR sequences were not homologous to those of known transposable elements, indicative that Tnr4 is a new transposable element. Tnr5 (209 bp long) had imperfect 46-bp TIRs and appeared to generate duplication of sequence TTA like that of some elements of the Tourist family. Tnr11 (811 bp long) had 73-bp TIRs with significant homology to those of Tnr1 and Stowaway and appeared to generate duplication of sequence TA, indicative that Tnr11 is a transposable element of the Tnr1/Stowaway family. Tnr12 (2426 bp long) carried perfect 9-bp TIRs, which began with 5'-CACTA- -3' from both ends and appeared to generate duplication of a 3-bp target sequence, indicative that Tnr12 is a transposable element of the En/Spm family. Tnr13 (347 bp long) had 31-bp TIRs and appeared to generate duplication of an 8-bp target sequence. Two sequences, one the transposon-like element Crackle, had partial homology in the Tnr13 ends. All five insertions appear to be defective elements derived from autonomous ones encoding the transposase gene. All had characteristic tandem repeat sequences which may be recognized by transposase. The sixth insertion sequence, named RIRE9 (3852 bp long), which begins with 5'-TG- -3' and ends with 5'- -CA-3', appeared to generate duplication of a 5-bp target sequence. These and other structural features indicate that this insertion is a solo LTR (long terminal repeat) of a retrotransposon. The transposable elements described above could be identified as insertions into Tnr1, which do not deleteriously affect the growth of rice cells.

The family of Caenorhabditis elegans tyrosine kinase receptors: similarities and differences with mammalian receptors

Transmembrane receptors with tyrosine kinase activity (RTK) constitute a superfamily of proteins present in all metazoans that is associated with the control and regulation of cellular processes. They have been the focus of numerous studies and are a good subject for comparative analyses of multigene families in different species aimed at understanding metazoan evolution. The sequence of the genome of the nematode worm Caenorhabditis elegans is available. This offers a good opportunity to study the superfamily of nematode RTKs in its entirety and to compare it with its mammalian counterpart. We show that the C. elegans RTKs constitute various groups with different phylogenetic relationships with mammalian RTKs. A group of four RTKs show structural similarity with the three mammalian receptors for the vascular endothelial growth factors. Another group comprises RTKs with a short extracellular region, a feature not known in mammals; the genes encoding these RTKs are clustered on chromosome II with other gene families, including genes encoding chitinase-like proteins. Most of the C. elegans RTKs have no direct orthologous relationship with any mammalian RTK, providing an illustration of the importance of the separate evolution of the different phyla.

Deep within the filarial genome: progress of the filarial genome project

Four years ago, a WHO/United Nations Development Programme/World Bank-sponsored genome project to study the filarial lymphatic nematode parasite Brugia malayi was initiated. The project took as its aims gene discovery for drug target and vaccine candidate identification, genome mapping, dissemination of genomic data to the world community and training of endemic country partners in genomic research. In this article, the principal investigators in the laboratories behind the project describe the background to the project, the data now emerging and goals for the future. Open access to filarial genome data is emphasized.

CeRep25B forms chromosome-specific minisatellite arrays in Caenorhabditis elegans

With the completion of the Genome Sequencing Project, it is now possible to rapidly and accurately determine the frequency and position of a particular repeat sequence in the Caenorhabditis elegans genome. Several repeat sequences with a variety of characteristics have been examined and with few exceptions they show a near-random distribution throughout the genome. We characterized several genes near the left end of Chromosome III in the C. elegans genome, and found a 24-bp minisatellite repeat sequence present in the introns of two unrelated genes. This prompted a search of the databank for other occurrences of this sequence. Multiple copy arrays of this repeat are all located on the same autosome and fall in two clusters: one near the left end, and one in the central region separated by approximately 10 Mb. There are >200 copies of this repeat on the chromosome. This euchromatic repeat sequence seems unrelated to gene expression, is absent from homologous sites in a related species, is unstable in Escherichia coli, and is polymorphic between different wild isolates of C. elegans. Most CeRep25B units in the array match the consensus sequence very well, suggesting that either this repeat originated quite recently or its sequence is functionally constrained. Although chromosome-specific repeat sequences have been reported previously in many organisms, such sequences are usually structural and heterochromatic (e.g., centromeric alpha-satellite) or on the mammalian sex chromosomes. This report describes the first confirmed instance from a whole genome sequencing project of an autosomal euchromatic chromosome-specific minisatellite repeat.

Tc7, a Tc1-hitch hiking transposon in Caenorhabditis elegans

We have found a novel transposon in the genome of Caenorhabditis elegans. Tc7 is a 921 bp element, made up of two 345 bp inverted repeats separated by a unique, internal sequence. Tc7 does not contain an open reading frame. The outer 38 bp of the inverted repeat show 36 matches with the outer 38 bp of Tc1. This region of Tc1 contains the Tc1-transposase binding site. Furthermore, Tc7 is flanked by TA dinucleotides, just like Tc1, which presumably correspond to the target duplication generated upon integration. Since Tc7 does not encode its own transposase but contains the Tc1-transposase binding site at its extremities, we tested the ability of Tc7 to jump upon forced expression of Tc1 transposase in somatic cells. Under these conditions Tc7 jumps at a frequency similar to Tc1. The target site choice of Tc7 is identical to that of Tc1. These data suggest that Tc7 shares with Tc1 all the sequences minimally required to parasitize upon the Tc1 transposition machinery. The genomic distribution of Tc7 shows a striking clustering on the X chromosome where two thirds of the elements (20 out of 33) are located. Related transposons in C. elegans do not show this asymmetric distribution.

A dot-matrix program with dynamic threshold control suited for genomic DNA and protein sequence analysis

Graphical dot-matrix plots can provide the most complete and detailed comparison of two sequences. Presented here is DOTTER2, a dot-plot program for X-windows which can compare DNA or protein sequences, and also DNA versus protein. The main novel feature of DOTTER is that the user can vary the stringency cutoffs interactively, so that the dot-matrix only needs to be calculated once. This is possible thanks to a 'Greyramp tool' that was developed to change the displayed stringency of the matrix by dynamically changing the greyscale rendering of the dots. The Greyramp tool allows the user to interactively change the lower and upper score limit for the greyscale rendering. This allows exploration of the separation between signal and noise, and fine-grained visualisation of different score levels in the dot-matrix. Other useful features are dot-matrix compression, mouse-controlled zooming, sequence alignment display and saving/loading of dot-matrices. Since the matrix only has to be calculated once and since the algorithm is fast and linear in space, DOTTER is practical to use even for sequences as long as cosmids. DOTTER was integrated in the gene-modelling module of the genomic database system ACEDB3. This was done via the homology viewer BLIXEM in a way that also allows segments from the BLAST suite of searching programs to be superimposed on top of the full dot-matrix. This feature can also be used for very quick finding of the strongest matches. As examples, we analyse a Caenorhabditis elegans cosmid with several tandem repeat families, and illustrate how DOTTER can improve gene modelling.

The C. elegans genome sequencing project. C. elegans Genome Mapping and Sequencing Consortium

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A binary model of repetitive DNA sequence in Caenorhabditis elegans

A great amount of genomic DNA in multicellular eukaryotic organisms is regarded as junk because it has no real function in protein coding. However, there is growing evidence that noncoding DNA can play a vital role in the regulation of gene expression during development (Lee et al., 1993). This indicates that the so-called junk DNA may have essential functions that are yet to be found (Nowak, 1994). A novel binary model of noncoding repetitive DNA sequence is proposed to illustrate its possible structure and implications in genome organization and development.

A repetitive DNA family, conserved throughout the evolution of free-living nematodes

This paper concerns the molecular evolution of a tandemly repeated DNA family, RcC9, originally identified in Caenorhabditis elegans. The minimum unit of periodicity of this family is the pentanucleotide [nGAAn] and its complement [nTTCn] recurring several times in alternating tandem arrays. This consensus sequence is identical to that of the heat-shock element (HSE). Multiple HSEs are present in the regulatory regions of heat-inducible genes in a wide range of eukaryotic species; HSEs mediate transcriptional activation through the binding of the heat-shock factor (HSF). I describe some repeated DNA families sharing this same consensus and found in nematode species other than C. elegans. Although the consensus is conserved, the repeated sequence diverged between species to the point that cross-hybridization is abolished. Evolutionary implications will be discussed.

A comparative analysis of distinctive features of yeast protein sequences

The recently published sequence of yeast chromosome III (YCIII) provides the longest continuous stretch of a eukaryotic DNA molecule sequenced to date (315 kb). The sequence contains 116 distinct AUG-initiated open reading frames of at least 200 codons in length, more than 50 of which had not been described previously nor bear significant similarity to known proteins. We have analysed the YCIII known and putative protein sequences with respect to significant statistical features which might reflect on structural and functional characteristics. The YCIII proteins have striking similarities and differences in their sequence attribute distributions compared to the corresponding distributions for all available yeast sequences and other protein collections. Nine examples of YCIII proteins with distinctive sequence features are discussed in detail.

Repetitive DNA sequences located in the terminal portion of the Caenorhabditis elegans chromosomes

We describe the distribution along the chromosomes of Caenorhabditis elegans of two repetitive DNA families, RcS5 and Cerep3 and interstitial telomeric sequences. Both families show, among other interesting features, a preferential location in the terminal 30% of the chromosomes. It is known that in these regions of the genome the frequency of recombination is much higher than in the central portion, genes are rarer and sequences important for chromosome disjunction may lie.