Chromosomes with high gene density are preferentially repaired in human cells

Abstract

It is known that DNA repair is heterogeneous in human cells since open chromatin, active genes and their transcribed strands are preferentially repaired. It is thus expected that DNA repair is clustered in chromosomes with high gene density. We have employed a DNA repair inhibitor, cytosine arabinoside (Ara-C), to convert ethyl methane sulfonate (EMS)-induced excision repairable lesions to chromosomal breaks, to check for the existence of heterogeneity of repair at the chromosome level. Chromosome staining by fluorescence in situ hybridization (FISH) was used to analyze breakage in chromosomes with diverse gene densities. These chromosomes were identified by means of the CpG island distribution after FISH with a CpG island-rich probe isolated from total human genomic DNA. Thus, three chromosomes with very high gene density (numbers 1, 19 and 20) were compared with two chromosomes with very low gene density (numbers 4 and 18) for clastogenicity and sensitivity to co-treatment with Ara-C and EMS. Our data indicate that those chromosome with higher gene density are more sensitive to a combination treatment with Ara-C and EMS, indicating that the level of excision repair synthesis is higher in those chromosome. It is therefore concluded that DNA excision repair is preferentially directed to chromosomes with high gene density. The implications of this finding in human biomonitoring using FISH techniques are discussed.

Fluorescence in situ hybridization is necessary to detect an association between chromosome aberrations and polycyclic aromatic hydrocarbon exposure in utero and reveals nonrandom chromosome involvement

“…Breakpoints following in vitro treatment with etoposide were over-represented in euchromatic regions [Maraschin et al, 1990]. Genedense chromosomes are more sensitive to clastogens during transcription, as their DNA is more open [Surralles et al, 1997;Palitti, 1998]. However, in our study population, there was no association between gene density and aberrations.…”

“…Each of these theories has support under the specific conditions in which the underlying observations were made [Maraschin et al, 1990;Sozzi et al, 1997;Surralles, 1997;Wu et al, 1998;Puerto et al, 1999a;Zhang et al, 1998aZhang et al, ,b, 2002Stillman et al, 2000;Eastmond et al, 2001;Stein et al, 2002;Zhu et al, 2002;Beskid et al, 2006]. Regardless of the mechanism driving the differential susceptibility to damage, the assumption that chromosome aberrations are being induced randomly, and the subsequent use of the whole genome correction factor, may not be appropriate for all exposures and/or populations.…”

Clusters of transcription-coupled repair in the human genome

“…FISH with digoxigenin-labeled DNA and antidigoxigenin detection with tetramethylrhodamine ␤-isothiocyanate-conjugated antibodies were performed as described in detail in ref. 27, and BrdUrd was simultaneously detected with mouse anti-BrdUrd and FITC-labeled goat anti-mouse antibodies as explained elsewhere (26). FISH with biotin-labeled DNA was performed as described above, and the immunodetection was done in green fluorescence with Alexa 488-conjugated streptavidin.…”

“…BrdUrd detection in FISH experiments using DOP-PCR-labeled biotin probes was performed with a mouse antiBrdUrd antibody, a digoxigenin-conjugated sheep anti-mouse antibody, and a rhodamine-conjugated antidigoxigenin sheep antibody as described in ref. 27.…”

Equal induction and persistence of chromosome aberrations involving chromosomes with heterogeneous lengths and gene densities

“…Some authors have found that the frequency of radiation-induced CAs was proportional to the DNA content or size of the target chromosomes (Tucker et al, 1993;Matsuoka et al, 1994;Johnson et al, 1998), while other studies have shown that the involvement of individual chromosomes in radiation-induced CAs was not always relative to their size or DNA content (Natarajan et al, 1992;Pandita et al, 1994;Knehr et al, 1996;Boei et al, 1997;Barquinero et al, 1998;Cigarrá n et al, 1998). Different factors have been suggested to explain the heterogeneous breakage, including differences in gene density, chromatin organization, and DNA repair among chromosomes (Pandita et al, 1992(Pandita et al, , 1994Natarajan et al, 1996;Surrallés et al, 1997Surrallés et al, , 1998Puerto et al, 1998;Surrallés, 1998).…”