Organization Of Repetitive DNA Research Articles

Drosophila Histone Demethylase KDM4A Has Enzymatic and Non-enzymatic Roles in Controlling Heterochromatin Integrity

Eukaryotic genomes are broadly divided between gene-rich euchromatin and the highly repetitive heterochromatin domain, which is enriched for proteins critical for genome stability and transcriptional silencing. This study shows that Drosophila KDM4A (dKDM4A), previously characterized as a euchromatic histone H3 K36 demethylase and transcriptional regulator, predominantly localizes to heterochromatin and regulates heterochromatin position-effect variegation (PEV), organization of repetitive DNAs, and DNA repair. We demonstrate that dKDM4A demethylase activity is dispensable for PEV. In contrast, dKDM4A enzymatic activity is required to relocate heterochromatic double-strand breaks outside the domain, as well as for organismal survival when DNA repair is compromised. Finally, DNA damage triggers dKDM4A-dependent changes in the levels of H3K56me3, suggesting that dKDM4A demethylates this heterochromatic mark to facilitate repair. We conclude that dKDM4A, in addition to its previously characterized role in euchromatin, utilizes both enzymatic and structural mechanisms to regulate heterochromatin organization and functions.

Karyotypes and Repetitive DNA Evolution in Six Species of the Genus Mahanarva (Auchenorrhyncha: Cercopidae)

Insects of the Cercopidae family are widely distributed and comprise 59 genera and 431 species in the New World. They are xylemophagous, causing losses in agricultural and pasture grasses, and are considered as emerging pests. Chromosomally, these insects have been studied by standard techniques, revealing variable diploid numbers and primarily X0 sex chromosome systems (males). We performed chromosome studies in 6 Mahanarva (Cercopidae) species using standard and differential chromosome staining as well as mapping of repetitive DNAs. Moreover, the relationship between the repetitive DNAs was analyzed at the interspecific level. A diploid chromosome number of 2n = 19,X0 was documented, with chromosomes gradually decreasing in size. Neutral or GC-rich regions were detected which varied depending on the species. Fluorescence in situ hybridization with a (TTAGG)_n telomeric motif probe revealed terminal signals, matching those of the Cot DNAs obtained from each species, that were also restricted to the terminal regions of all chromosomes. Dot blot analysis with the Cot fraction from M. quadripunctata showed that at least part of the repetitive genome is shared among the 6 species. Our data highlight the conservation of chromosomal features and organization of repetitive DNAs in the genus Mahanarva, suggesting a low differentiation for chromosomes and repetitive DNAs in most of the 6 species studied.

The Organization of Repetitive DNA in the Genomes of Amazonian Lizard Species in the Family Teiidae

Repetitive DNA is the largest fraction of the eukaryote genome and comprises tandem and dispersed sequences. It presents variations in relation to its composition, number of copies, distribution, dynamics, and genome organization, and participates in the evolutionary diversification of different vertebrate species. Repetitive sequences are usually located in the heterochromatin of centromeric and telomeric regions of chromosomes, contributing to chromosomal structures. Therefore, the aim of this study was to physically map repetitive DNA sequences (5S rDNA, telomeric sequences, tropomyosin gene 1, and retroelements Rex1 and SINE) of mitotic chromosomes of Amazonian species of teiids (Ameiva ameiva, Cnemidophorus sp. 1, Kentropyx calcarata, Kentropyx pelviceps, and Tupinambis teguixin) to understand their genome organization and karyotype evolution. The mapping of repetitive sequences revealed a distinct pattern in Cnemidophorus sp. 1, whereas the other species showed all sequences interspersed in the heterochromatic region. Physical mapping of the tropomyosin 1 gene was performed for the first time in lizards and showed that in addition to being functional, this gene has a structural function similar to the mapped repetitive elements as it is located preferentially in centromeric regions and termini of chromosomes.

Genomic organization of repetitive DNAs and its implications for male karyotype and the neo-Y chromosome differentiation in Erythrinus erythrinus (Characiformes, Erythrinidae).

Studies have demonstrated the effective participation of repetitive DNA sequences in the origin and differentiation of the sex chromosomes in some biological groups. In this study several microsatellites and retrotranposable sequences were cytogenetically mapped in the Erythrinus erythrinus (Bloch & Schneider, 1801) male genome (karyomorph C), focusing on the distribution of these sequences in the sex chromosomes and in the evolutionary processes related to their differentiation. Males of E. erythrinus – karyomorph C – present 2n = 51 chromosomes (7m + 2sm + 6st + 36a), including the X1X2Y sex chromosomes. The C-positive heterochromatin has a predominant localization on the centromeric region of most chromosome pairs, but also in some telomeric regions. The 5S rDNA sites are located in the centromeric region of 27 chromosomes, including 26 acrocentric ones and the metacentric Y chromosome. The retrotransposons Rex 1 and Rex 6 show a dispersed pattern in the karyotype, contrasting with the Rex 3 distribution which is clearly co-localized with all the 27 5S rDNA sites. The microsatellite sequences show a differential distribution, some of them restricted to telomeric and/or interstitial regions and others with a scattered distribution on the chromosomes. However, no preferential accumulation of these elements were observed in the neo-Y chromosome, in contrast to what usually occurs in simple sex chromosome systems.

Evolutionary dynamics of heterochromatin in the genome of Dichotomius beetles based on chromosomal analysis

We comparatively analyzed six Dichotomius species (Coleoptera: Scarabainae) through cytogenetic methods and mitochondrial genes sequencing in the aim to identify patterns of chromosomal evolution and heterochromatin differentiation in the group. The chromosomal data were accessed through the classical analysis of heterochromatin and mapping of high and moderately repeated DNAs (C (0) t-1 DNA fraction). Mitochondrial data were obtained from nucleotide sequences of the cytochrome oxidase I (COI) and 16S rRNA genes. The heterochromatin distribution was conserved but revealed variability in the base pair richness and repetitive DNA content, and an intense turnover of heterochromatic associated sequences seems to have occurred during Dichotomius speciation. Specifically for D. bos, an interesting pattern was observed, indicating apparently the presence of heterochromatic sequences composed of low copy-number sequences. Moreover, highly conserved terminal/sub-terminal sequences that could act as a telomeric or telomere-associated DNA were observed. The heterochromatin diversification patterns observed in Dichotomius were not accomplished by the diversification of the species studied, which may be a consequence of the intense dynamics that drive the evolution of repeated DNA clusters in the genome. Finally our findings also suggest that the use of C (0) t-1 DNA fraction represents a powerful, inexpensive and not time consuming tool to be applied in understanding heterochromatin and repetitive DNA organization.

Genome size and organization in the blacklegged tick, Ixodes scapularis and the Southern cattle tick, Boophilus microplus

Genome sizes and the organization of repetitive DNA were determined in the hard ticks Ixodes scapularis and Boophilus microplus using reassociation kinetics. The I. scapularis genome contains approximately 2.15 pg (2.1x10(3) Mbp) of DNA and consists of no foldback (FB), 27% highly repetitive (HR), 39% moderately repetitive (MR), and 34% unique DNA. The B. microplus genome contains 7.5 pg (7.1x10(3) Mbp) DNA, and consists of 0.82% FB, 31% HR, 38% MR, and 30% unique DNA. In both species, repetitive sequences occur in a mixture of long and short period interspersion but most (65-80%) of the DNA follows a pattern of short period interspersion. Genome size and organization in the three tick species so far examined are distinct from other arthropods in having a greater proportion of MR, a lower proportion of unique and HR DNA of very low sequence complexity.

Polymorphisms and Genomic Organization of Repetitive DNA from Centromeric Regions of Arabidopsis Chromosomes

A highly abundant repetitive DNA sequence family of Arabidopsis, AtCon, is composed of 178-bp tandemly repeated units and is located at the centromeres of all five chromosome pairs. Analysis of multiple copies of AtCon showed 95% conservation of nucleotides, with some alternative bases, and revealed two boxes, 30 and 24 bp long, that are 99% conserved. Sequences at the 3' end of these boxes showed similarity to yeast CDEI and human CENP-B DNA-protein binding motifs. When oligonucleotides from less conserved regions of AtCon were hybridized in situ and visualized by using primer extension, they were detected on specific chromosomes. When used for polymerase chain reaction with genomic DNA, single primers or primer pairs oriented in the same direction showed negligible amplification, indicating a head-to-tail repeat unit organization. Most primer pairs facing in opposite directions gave several strong bands corresponding to their positions within AtCon. However, consistent with the primer extension results, some primer pairs showed no amplification, indicating that there are chromosome-specific variants of AtCon. The results are significant because they elucidate the organization, mode of amplification, dispersion, and evolution of one of the major repeated sequence families of Arabidopsis. The evidence presented here suggests that AtCon, like human alpha satellites, plays a role in Arabidopsis centromere organization and function.

Organization of repetitive DNAs in the guinea pig genome

Investigation of restriction enzyme families observed in Bam HI and Eco RI digest of guinea pig DNA has led to the demonstration of a 4.0 kb cryptic satellite called MR1Cp which has 6300 copies and comprises 1% of the total genome. MR1Cp has been shown to encompass the Eco RI 4.0 kb family, the Bam HI 3.4 kb family and the Bam HI 3.7 kb family. The 1.5 kb Eco RI family is part of an L1 LINE that is present in the guinea pig and in other rodentia. It is part of a larger LINE, probably 6.5 to 7 kb in size, and some copies are embedded in satellite I DNA sequences.