Nucleotide sequence of satellite DNA contained in the eliminated genome of<i>Ascaris lumbricoides</i>

Müller, Fritz; Walker, Philippe; Aeby, Pierre; Neuhaus, Heinz; Felder, Heinz; Back, Eduard; Tobler, Heinz

doi:10.1093/nar/10.23.7493

Cited by 69 publications

(31 citation statements)

References 32 publications

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“…In Ascaris, chromatin diminution occurs during the third through fifth cleavage (four-to 16-cell stage) with the loss of ;25% of the genome (Muller and Tobler 2000). Fifty percent of the eliminated DNA (;40 Mb, >300,000 copies) is the highly repetitive satellite DNA that consists primarily of several variants of a 121-bp element (Muller et al 1982;Streeck et al 1982).…”

Section: Small Rnas and Chromatin Diminutionmentioning

confidence: 99%

Deep small RNA sequencing from the nematodeAscarisreveals conservation, functional diversification, and novel developmental profiles

Wang

Czech²,

Crunk³

et al. 2011

Genome Res.

161

189

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Eukaryotic cells express several classes of small RNAs that regulate gene expression and ensure genome maintenance. Endogenous siRNAs (endo-siRNAs) and Piwi-interacting RNAs (piRNAs) mainly control gene and transposon expression in the germline, while microRNAs (miRNAs) generally function in post-transcriptional gene silencing in both somatic and germline cells. To provide an evolutionary and developmental perspective on small RNA pathways in nematodes, we identified and characterized known and novel small RNA classes through gametogenesis and embryo development in the parasitic nematode Ascaris suum and compared them with known small RNAs of Caenorhabditis elegans. piRNAs, Piwi-clade Argonautes, and other proteins associated with the piRNA pathway have been lost in Ascaris. miRNAs are synthesized immediately after fertilization in utero, before pronuclear fusion, and before the first cleavage of the zygote. This is the earliest expression of small RNAs ever described at a developmental stage long thought to be transcriptionally quiescent. A comparison of the two classes of Ascaris endo-siRNAs, 22G-RNAs and 26G-RNAs, to those in C. elegans, suggests great diversification and plasticity in the use of small RNA pathways during spermatogenesis in different nematodes. Our data reveal conserved characteristics of nematode small RNAs as well as features unique to Ascaris that illustrate significant flexibility in the use of small RNAs pathways, some of which are likely an adaptation to Ascaris' life cycle and parasitism.

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Section: Small Rnas and Chromatin Diminutionmentioning

confidence: 99%

Deep small RNA sequencing from the nematodeAscarisreveals conservation, functional diversification, and novel developmental profiles

Wang

Czech²,

Crunk³

et al. 2011

Genome Res.

161

189

View full text Add to dashboard Cite

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“…Four-cell stage embryos were harvested after 60-72 h (A. suum) or 4 h (P. univalens) and larvae after 20-30 days (A. suum) or 4-5 days (P. univalens). The removal of the chitinous layer (peeling) and the DNA isolation was performed as described in [8,9].…”

Section: Isolation Of a Suum And P Univalens Genomic Dnamentioning

confidence: 99%

Chromatin diminution leads to rapid evolutionary changes in the organization of the germ line genomes of the parasitic nematodes A. suum and P. univalens

Bachmann-Waldmann

Jentsch

Tobler

et al. 2004

Molecular and Biochemical Parasitology

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“…[I]). The increasing proportion of looped palindromes in the somatic DNA (about 54% of all palindromes compared to 38% in the germ-line DNA) could be a consequence of the presence of about 200 times more satellite DNA sequences in the germ-line DNA [36]. It is possible that the satellite DNA contains more hairpin structures without forming visible loops than the rest of the germ-line genome.…”

Section: Discussionmentioning

confidence: 99%

“…DNA fragments shorter than the inverted repeat lengths show different reassociation characteristics : unlooped palindromes still reassociate like immediate inverted repeated sequences, in contrast to the looped palindromes, which now reassociate more slowly with second-order kinetics. If we take into account the elimination of 99.5% satellite DNA sequences from the presumptive somatic cells, which represent about 20% of the germ-line genome [36], then the proportion of the looped to the unlooped foldback sequences becomes close to that of the somatic DNA (about 1:l). We do not know whether there exists a higher order of inverted repeated sequences in the satellite DNA of A .…”

Section: Discussionmentioning

confidence: 99%

Characterization of inverted repeated sequences in Ascaris nuclear DNA

Landolt

Tobler

1986

European Journal of Biochemistry

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The inverted repeated sequences of the chromatin-eliminating nematode Ascuris lumbricnides var. suum have been examined by electron microscopy and by hydroxyapatite chromatography, both in the germ-line and in the somatic DNA. 38% of the inverted repeats of the germ-line DNA analysed in the electron microscope have a single-stranded loop, in comparison to about 50% of looped structures in the somatic DNA. The loops are on average 2.3 x lo3 base pairs (bp) long. The rest of the foldback DNA consists of simple hairpins. The average length of looped and unlooped inverted repeats is of the order of 300 -400 bp in the germ-line and in the somatic DNA. The content of S1-resistant foldback duplexes isolated by hydroxyapatite chromatography amounts to 1.3% in spermatids, with an average length of 350 bp, and to 1 .I % in intestinal or larval cell nuclei, with a lcngth of about 320 bp. We estimate by two different methods that there exist approximately 12500 inverted repeats per haploid germ-line genome and approximately 8000 in the haploid somatic genome. A statistical analysis of the data indicates that the great majority of the foldback sequences are randomly distributed in the Ascuris genome, with a spacing of about (40-80) x lo3 bp, both in the germ-line and in the somatic DNA.A portion of the eucaryotic genome is composed of inverted repeated DNA sequences, which are capable of forming intrastrand base-pairing upon denaturation and renaturation [I]. DNA containing these sequences, also called foldback or hairpin DNA, can be separated from the remaining fractions of genomic DNA because these sequences reanneal with rapid kinetics independent of the DNA concentration following denaturation and incubation in annealing conditions. This fraction of DNA can be observed in the electron microscope as single-stranded molecules containing an intramolecular duplex segment, or can be isolated by hydroxyapatite chromatography.Inverted In view of the development of the chromatin-eliminating nematode Ascaris lurnhricoidcs var. suum, it is important to determine how individual sequences are arranged in the genome before and after chromatin diminution in order to elucidate the elimination process. The purpose of the present investigation is to characterize the inverted repeated sequences in the genome of A . lumhric~~id~s using the techniques of ('orrespoIt~~,nce to 1-1. 'I'obler, Zoologisches Institul, Universilat Fribourg. I'erolles. CH-1700 Fribourg, Switzerland Ahbrcviu/ions. r,,t, producl of initial concentration of DNA and time, in molcs of nucleotides x seconds/liter; bp, base pairs; kb lo3

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Nucleotide sequence of satellite DNA contained in the eliminated genome ofAscaris lumbricoides

Abstract: ABSTRACT

Cited by 69 publications

References 32 publications

Deep small RNA sequencing from the nematodeAscarisreveals conservation, functional diversification, and novel developmental profiles

Deep small RNA sequencing from the nematodeAscarisreveals conservation, functional diversification, and novel developmental profiles

Chromatin diminution leads to rapid evolutionary changes in the organization of the germ line genomes of the parasitic nematodes A. suum and P. univalens

Characterization of inverted repeated sequences in Ascaris nuclear DNA

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