Preference of the recombination sites involved in the formation of extrachromosomal copies of the human alphoid Sau3A repeat family

Circular DNA elements of chromosomal origin are common in healthy human somatic tissue

The human genome is generally organized into stable chromosomes, and only tumor cells are known to accumulate kilobase (kb)-sized extrachromosomal circular DNA elements (eccDNAs). However, it must be expected that kb eccDNAs exist in normal cells as a result of mutations. Here, we purify and sequence eccDNAs from muscle and blood samples from 16 healthy men, detecting ~100,000 unique eccDNA types from 16 million nuclei. Half of these structures carry genes or gene fragments and the majority are smaller than 25 kb. Transcription from eccDNAs suggests that eccDNAs reside in nuclei and recurrence of certain eccDNAs in several individuals implies DNA circularization hotspots. Gene-rich chromosomes contribute to more eccDNAs per megabase and the most transcribed protein-coding gene in muscle, TTN (titin), provides the most eccDNAs per gene. Thus, somatic genomes are rich in chromosome-derived eccDNAs that may influence phenotypes through altered gene copy numbers and transcription of full-length or truncated genes.

Somatic cells can accumulate structural variations such as deletions. Here, Møller et al. show that normal human cells generate large extrachromosomal circular DNAs (eccDNAs), most likely the products of excised DNA, that can be transcriptionally active and, thus, may have phenotypic consequences.

Survey of extrachromosomal circular DNA derived from plant satellite repeats

BACKGROUND

Satellite repeats represent one of the most dynamic components of higher plant genomes, undergoing rapid evolutionary changes of their nucleotide sequences and abundance in a genome. However, the exact molecular mechanisms driving these changes and their eventual regulation are mostly unknown. It has been proposed that amplification and homogenization of satellite DNA could be facilitated by extrachromosomal circular DNA (eccDNA) molecules originated by recombination-based excision from satellite repeat arrays. While the models including eccDNA are attractive for their potential to explain rapid turnover of satellite DNA, the existence of satellite repeat-derived eccDNA has not yet been systematically studied in a wider range of plant genomes.

RESULTS

We performed a survey of eccDNA corresponding to nine different families and three subfamilies of satellite repeats in ten species from various genera of higher plants (Arabidopsis, Oryza, Pisum, Secale, Triticum and Vicia). The repeats selected for this study differed in their monomer length, abundance, and chromosomal localization in individual species. Using two-dimensional agarose gel electrophoresis followed by Southern blotting, eccDNA molecules corresponding to all examined satellites were detected. EccDNA occurred in the form of nicked circles ranging from hundreds to over eight thousand nucleotides in size. Within this range the circular molecules occurred preferentially in discrete size intervals corresponding to multiples of monomer or higher-order repeat lengths.

CONCLUSION

This work demonstrated that satellite repeat-derived eccDNA is common in plant genomes and thus it can be seriously considered as a potential intermediate in processes driving satellite repeat evolution. The observed size distribution of circular molecules suggests that they are most likely generated by molecular mechanisms based on homologous recombination requiring long stretches of sequence similarity.

Mouse major satellite DNA is prone to eccDNA formation via DNA Ligase IV-dependent pathway

Elevated levels of extrachromosomal circular DNA (eccDNA or spcDNA) are closely associated with genomic instability and aging. Despite extensive studies, the mechanism of its generation in mammalian cells is unknown. We report here that mouse major satellite DNA (MSD) is prone to eccDNA formation and that the resulting molecules are multimeres of the basic repeat. Extrachromosomal circular major satellite (ECMS) DNA constitutes the majority of eccDNA in B16 mouse melanoma cells and is highly abundant in other mouse cells. Production of these molecules is enhanced in proliferating cells, suggesting that processes associated with DNA replication are involved in their appearance. Using siRNA technique we show that DNA Ligase IV is engaged in ECMS synthesis. Based on our findings we propose a novel two-step model for eccDNA formation in mammalian cells.

An unusual satellite DNA from Zamia paucijuga (Cycadales) characterised by two different organisations of the repetitive unit in the plant genome

We have cloned and characterised a highly repetitive DNA family that represents about 5% of the nuclear genome of Zamia paucijuga, a member of Cycadales, an ancient and rare group of seed plants. The unit repeat, cloned from EcoRV digested genomic DNA, has a length of about 323 bp, an high GC content (65-70%) and a subtelomeric localisation. The DNA of Z. paucijuga was digested with various restriction enzymes and analysed by Southern blot using the cloned unit repeat as a probe. These experiments indicated that the repeat is present in the plant genome in an unusual organisation, as tandem arrays typical of satellite DNA and as dispersed elements. The characterisation of these unusual "dispersed satellite DNA" elements required a complex series of experiments using combined Southern blot analyses, PCR, cloning and sequencing. Our results indicate that most of these dispersed elements are formed by few units of the GC-rich satellite DNA repeats arranged in tandem and flanked at both sites by one copy of a 0.6 kb AT-rich direct repeat. This unusual satellite DNA organisation of GC-rich repeats is present in many species of genus Zamia, and, thus, likely represent an ancient rearrangement of the satellite DNA repeats that spread in the genome as dispersed elements.

Structural rearrangements and insertions of dispersed elements in pericentromeric alpha satellites occur preferably at kinkable DNA sites

Centromeric region of human chromosome 21 comprises two long alphoid DNA arrays: the well homogenized and CENP-B box-rich alpha21-I and the alpha21-II, containing a set of less homogenized and CENP-B box-poor subfamilies located closer to the short arm of the chromosome. Continuous alphoid fragment of 100 monomers bordering the non-satellite sequences in human chromosome 21 was mapped to the pericentromeric short arm region by fluorescence in situ hybridization (alpha21-II locus). The alphoid sequence contained several rearrangements including five large deletions within monomers and insertions of three truncated L1 elements. No binding sites for centromeric protein CENP-B were found. We analyzed sequences with alphoid/non-alphoid junctions selectively screened from current databases and revealed various rearrangements disrupting the regular tandem alphoid structure, namely, deletions, duplications, inversions, expansions of short oligonucleotide motifs and insertions of different dispersed elements. The detailed analysis of more than 1100 alphoid monomers from junction regions showed that the vast majority of structural alterations and joinings with non-alphoid DNAs occur in alpha satellite families lacking CENP-B boxes. Most analyzed events were found in sequences located toward the edges of the centromeric alphoid arrays. Different dispersed elements were inserted into alphoid DNA at kinkable dinucleotides (TG, CA or TA) situated between pyrimidine/purine tracks. DNA rearrangements resulting from different processes such as recombination and replication occur at kinkable DNA sites alike insertions but irrespectively of the occurrence of pyrimidine/purine tracks. It seems that kinkable dinucleotides TG, CA and TA are part of recognition signals for many proteins involved in recombination, replication, and insertional events. Alphoid DNA is a good model for studying these processes.

Molecular characterization of a mouse genomic element mobilized by advanced glycation endproduct modified-DNA (AGE-DNA)

BACKGROUND

DNA modified by advanced glycation endproducts (AGEs) undergoes a high frequency of insertional mutagenesis. In mouse lymphoid cells, these mutations are due in part to the transposition of host genomic elements that contain a DNA region homologous to the Alu family of repetitive elements. One particular 853 bp insertion, designated INS-1, was identified previously as a DNA element common to plasmids recovered from multiple, independent lymphoid cell transfections.

MATERIALS AND METHODS

To characterize the genomic origin of this element, we used a 281-bp region of non-Alu-containing INS-1 sequence, designated. CORE, as a probe in Southern hybridization and for screening a bacteriophage mouse genomic DNA library. The resultant clones were sequenced and localized within the mouse genome.

RESULTS

Two distinct genomic clones of 15 kB and 17 kB in size were isolated. A 522-bp unique region common to INS-1 and corresponding to the CORE sequence was identified in each clone. In both cases, CORE was found to be surrounded by repetitive DNA sequences: a 339-bp MT repeat at the 5' end, and a 150-bp B1 repeat at the 3' end. The CORE sequence was localized to mouse chromosome 1.

CONCLUSIONS

These studies revealed that the CORE region of INS is present in low copy number but is associated with known repetitive DNA elements. The presence of these repetitive elements may facilitate the transposition of CORE by recombination or other, more complex rearrangement events, and explain in part the origin of AGE-induced insertional mutations.