Unique Features of Satellite DNA Transcription in Different Tissues of .

A large part of the genome is known to be transcribed as non-coding DNA including some tandem repeats (satellites) such as telomeric/centromeric satellites in different species. However, there has been no detailed study on the eventual transcription of the interspersed satellites found in many species. In the present paper, we studied the transcription of the abundant DNA satellites in the nematode using available RNA-Seq results.

DNA Satellites Are Transcribed as Part of the Non-Coding Genome in Eukaryotes and Bacteria.

It has been shown in recent years that many repeated sequences in the genome are expressed as RNA transcripts, although the role of such RNAs is poorly understood. Some isolated and tandem repeats (satellites) have been found to be transcribed, such as mammalian Alu sequences and telomeric/centromeric satellites in different species. However, there is no detailed study on the eventual transcription of the interspersed satellites found in many species.

Tandem Repeats in : Unique Features and Taxonomic Distribution.

Little is known about DNA tandem repeats across prokaryotes. We have recently described an enigmatic group of tandem repeats in bacterial genomes with a constant repeat size but variable sequence. These findings strongly suggest that tandem repeat size in some bacteria is under strong selective constraints.

The influence of Ni and other ions on the trigonal structure of DNA.

We present a new structure of a DNA dodecamer obtained in the presence of Ni ions. The DNA forms Ni-guanine cross-links between neighboring molecules. Our results show that an adequate dosage of Ni may help to form well-defined DNA nanostructures.

Unique Features of Tandem Repeats in Bacteria.

DNA tandem repeats, or satellites, are well described in eukaryotic species, but little is known about their prevalence across prokaryotes. Here, we performed the most complete characterization to date of satellites in bacteria. We identified 121,638 satellites from 12,233 fully sequenced and assembled bacterial genomes with a very uneven distribution.

Satellites in the prokaryote world.

Background: Satellites or tandem repeats are very abundant in many eukaryotic genomes. Occasionally they have been reported to be present in some prokaryotes, but to our knowledge there is no general comparative study on their occurrence. For this reason we present here an overview of the distribution and properties of satellites in a set of representative species.

How Long Are Long Tandem Repeats? A Challenge for Current Methods of Whole-Genome Sequence Assembly: The Case of Satellites in .

Repetitive genome regions have been difficult to sequence, mainly because of the comparatively small size of the fragments used in assembly. Satellites or tandem repeats are very abundant in nematodes and offer an excellent playground to evaluate different assembly methods. Here, we compare the structure of satellites found in three different assemblies of the genome: the original sequence obtained by Sanger sequencing, an assembly based on PacBio technology, and an assembly using Nanopore sequencing reads.

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.

Structure of the DNA duplex d(ATTAAT)2 with Hoogsteen hydrogen bonds.

The traditional Watson-Crick base pairs in DNA may occasionally adopt a Hoogsteen conformation, with a different organization of hydrogen bonds. Previous crystal structures have shown that the Hoogsteen conformation is favored in alternating AT sequences of DNA. Here we present new data for a different sequence, d(ATTAAT)2, which is also found in the Hoogsteen conformation.

Polymorphic crystal structures of an all-AT DNA dodecamer.

In this work, we explore the influence of different solvents and ions on the crystallization behavior of an all-AT dodecamer d(AATAAATTTATT)2 In all cases, the oligonucleotides are found as continuous columns of stacked duplexes. The spatial organization of such columns is variable; consequently we have obtained seven different crystal forms. The duplexes can be made to crystallize in either parallel or crossed columns.

Long non-coding RNAs as a source of new peptides.

Deep transcriptome sequencing has revealed the existence of many transcripts that lack long or conserved open reading frames (ORFs) and which have been termed long non-coding RNAs (lncRNAs). The vast majority of lncRNAs are lineage-specific and do not yet have a known function. In this study, we test the hypothesis that they may act as a repository for the synthesis of new peptides.

In and out of the minor groove: interaction of an AT-rich DNA with the drug CD27.

The DNA of several pathogens is very rich in AT base pairs. Typical examples include the malaria parasite Plasmodium falciparum and the causative agents of trichomoniasis and trypanosomiases. This fact has prompted studies of drugs which interact with the minor groove of DNA, some of which are used in medical practice.

A satellite explosion in the genome of holocentric nematodes.

Centromere sequences in the genome are associated with the formation of kinetochores, where spindle microtubules grow in mitosis. Centromere sequences usually have long tandem repeats (satellites). In holocentric nematodes it is not clear how kinetochores are formed during mitosis; they are distributed throughout the chromosomes.

Crystal structure of a complex of DNA with one AT-hook of HMGA1.

We present here for the first time the crystal structure of an AT-hook domain. We show the structure of an AT-hook of the ubiquitous nuclear protein HMGA1, combined with the oligonucleotide d(CGAATTAATTCG)(2), which has two potential AATT interacting groups. Interaction with only one of them is found.

The distribution of alternating AT sequences in eukaryotic genomes suggests a role in homologous chromosome recognition in meiosis.

There are general features of chromosome dynamics, such as homologue recognition in early meiosis, which are expected to involve related sequence motifs in non-coding DNA, with a similar distribution in different species. A search for such motifs is presented here. It has been carried out with the CONREPP programme.

Visualization of sequence and structural features of genomes and chromosome fragments. Application to CpG islands, Alu sequences and whole genomes.

A very simple new program is presented (G-SQUARES). It is useful in order to visualize the composition and basic structural features of whole genomes and selected chromosome regions. The frequency of all dimer and tetramer sequences is reported.

Structure of a stacked anthraquinone-DNA complex.

The crystal structure of the telomeric sequence d(UBrAGG) interacting with an anthraquinone derivative has been solved by MAD. In all previously studied complexes of intercalating drugs, the drug is usually sandwiched between two DNA base pairs. Instead, the present structure looks like a crystal of stacked anthraquinone molecules in which isolated base pairs are intercalated.

Coiled-coil conformation of a pentamidine-DNA complex.

The coiled-coil structure formed by the complex of the DNA duplex d(ATATATATAT)(2) with pentamidine is presented. The duplex was found to have a mixed structure containing Watson-Crick and Hoogsteen base pairs. The drug stabilizes the coiled coil through the formation of cross-links between neighbouring duplexes.

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.

The interaction of manganese ions with DNA.

We present the structure of the duplex formed by a fragment of auto-complementary DNA with the sequence d(CGTTAATTAACG). The structure was determined by X-ray crystallography. Up to date it is the first structure presenting the interaction between a DNA oligonucleotide and manganese ions.

Stabilization by extra-helical thymines of a DNA duplex with Hoogsteen base pairs.

We present the crystal structure of the DNA duplex formed by d(ATATATCT). The crystals contain seven stacked antiparallel duplexes in the asymmetric unit with A.T Hoogsteen base pairs.

Macroscopic DNA helices.

Presently there is great interest in the construction of nanostructures from DNA fragments. Here we report the preparation of much larger helical textures with different shapes from pure DNA fragments. We have observed them while preparing crystals of the dodecamer d(AAAAAATTTTTT), which only contains adenine and thymine.

Structural families of genomic microsatellites.

We present an analysis of tandem repeats of short sequence motifs (microsatellites) in twelve eukaryotes for which a large part of the genome has been sequenced and assembled. The pattern of motif abundance varies significantly in different species, but it is very similar in different chromosomes of the same species. The most abundant repeats can be classified in two main families.