A survey of the genomic distribution of alpha satellite DNA on all the human chromosomes, and derivation of a new consensus sequence

Choo, K. H. Andy; Vissel, Bryce; Nagy, Alexander; Earle, Elizabeth D.; Kalitsis, Paul

doi:10.1093/nar/19.6.1179

Cited by 229 publications

(133 citation statements)

References 29 publications

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“…Alphoid DNA flanking an L1 could be transduced to a new location during the L1 retrotransposition event, and would produce small stretches of alphoid DNA sites outside of their normal centromeric locations. However, the synthesized 18-mer PNA probe, designed on the basis of the consensus sequence of alphoid DNA (Choo et al 1991), did not show any such hybridization signals outside the centromeric regions of chromosomes under the present experimental conditions. The relative fluorescence intensities of centromeric signals were as follows: chromosomes 9, 14, 18, 20, and 22 exhibited strong signals; chromosomes 1, 3, 8, 12 and 16 showed weak signals; other chromosomes (chromosomes 2, 4, 5, 6, 7, 10, 11, 13, 15, 17, 19, 21 and X) exhibited signals with intermediate intensity.…”

Section: Distribution Of the Hybridization Signals Of Pna Probe For Tcontrasting

confidence: 63%

Sensitive and Rapid Detection of Centromeric Alphoid DNA in Human Metaphase Chromosomes by PNA Fluorescence <i>In Situ</i> Hybridization and Its Application to Biological Radiation Dosimetry

Suto¹,

Hirai²,

Akiyama³

et al. 2012

CYTOLOGIA

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Summary Centromeres of human chromosomes contain highly repeated sequences of DNA including alphoid DNA. Because of the complicated genomic organization of the centromere, the distribution of alphoid DNA in chromosomes has not been fully investigated. We conducted fluorescence in situ hybridization using a synthetic peptide nucleic acid as a sensitive probe (PNA-FISH) to detect chromosomal sites of alphoid DNA. As a result, the size variation of centromeric alphoid DNA among chromosomes was visualized with hybridization times as short as 1-2 h. In addition to the inter-chromosomal variation, we detected possible inter-individual variation in the size of alphoid DNA sites, which had been difficult to precisely analyze by conventional molecular and cytogenetic methods. We then applied this sensitive and rapid detection method to evaluate the yield of multicentric chromosomes induced in cultured human peripheral blood lymphocytes by high-dose gamma-irradiation. This PNA-FISH allows us to unequivocally determine centromeres in complexly rearranged chromosomes, confirming its usefulness in biological radiation dosimetry.

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Section: Distribution Of the Hybridization Signals Of Pna Probe For Tcontrasting

confidence: 63%

Sensitive and Rapid Detection of Centromeric Alphoid DNA in Human Metaphase Chromosomes by PNA Fluorescence <i>In Situ</i> Hybridization and Its Application to Biological Radiation Dosimetry

Suto¹,

Hirai²,

Akiyama³

et al. 2012

CYTOLOGIA

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“…(A) Schematic drawings of the alphoid tetO DNA array and tetR fusion constructs expressed in HeLa 1C7 cells. The synthetic monomer was based on a published consensus sequence for alphoid DNA (Choo et al, 1991). (B) Real-time RT-PCR analysis of non-transfected 1C7 cells stably carrying the alphoid tetO HAC and 2 days after transfecting constructs expressing tetR-EYFP (tetR), tetR-EYFP-p65 (p65) or tetR-EYFP-VP16 (VP16).…”

Section: Resultsmentioning

confidence: 99%

“…In humans, endogenous centromeres typically form on chromosome-specific higher-order 'alphoid' DNA arrays, which are composed of 171 bp alpha-satellite monomer units that are tandemly arranged in a directional head-to-tail fashion (Choo et al, 1991;Mitchell et al, 1985;Schueler and Sullivan, 2006;Willard and Waye, 1987). Independent of this sequence preference, specific deposition of the centromeric histone H3 variant CENP-A (Earnshaw and Rothfield, 1985) is thought to form the basis for an 'epigenetic' maintenance of centromere identity (Allshire and Karpen, 2008;Okamoto et al, 2007;Vafa and Sullivan, 1997;Warburton et al, 1997).…”

Section: Introductionmentioning

confidence: 99%

Epigenetic engineering: histone H3K9 acetylation is compatible with kinetochore structure and function

Bergmann

Jakubsche

Martins

et al. 2012

Journal of Cell Science

103

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SummaryHuman kinetochores are transcriptionally active, producing very low levels of transcripts of the underlying alpha-satellite DNA. However, it is not known whether kinetochores can tolerate acetylated chromatin and the levels of transcription that are characteristic of housekeeping genes, or whether kinetochore-associated 'centrochromatin', despite being transcribed at a low level, is essentially a form of repressive chromatin. Here, we have engineered two types of acetylated chromatin within the centromere of a synthetic human artificial chromosome. Tethering a minimal NF-kB p65 activation domain within kinetochore-associated chromatin produced chromatin with high levels of histone H3 acetylated on lysine 9 (H3K9ac) and an ,10-fold elevation in transcript levels, but had no substantial effect on kinetochore assembly or function. By contrast, tethering the herpes virus VP16 activation domain produced similar modifications in the chromatin but resulted in an ,150-fold elevation in transcripts, approaching the level of transcription of an endogenous housekeeping gene. This rapidly inactivated kinetochores, causing a loss of assembled CENP-A and blocking further CENP-A assembly. Our data reveal that functional centromeres in vivo show a remarkable plasticity -kinetochores tolerate profound changes to their chromatin environment, but appear to be critically sensitive to the level of centromeric transcription.

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“…31,32 Even the so-called DNA alpha satellite sequences are heterogeneous and each centromere differs in DNA subtypes. [33][34][35][36][37][38][39] Moreover functional centromeres can lack alphoid DNA. [40][41][42][43] It has been shown that the heterochromatin of some chromosomes such as chromosome 1 could be uncoiled by the hypomethylating agent azacytidine.…”

Section: Discussionmentioning

confidence: 99%

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Leukemia

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Cytogenetic and fluorescence in situ hybridization (FISH) analysis of 10 patients with various hematopoietic malignancies revealed the presence of dicentric chromosomes or pericentric chromosome rearrangements. Dicentrics were only ascertained by FISH studies in six patients. Two types of pericentric chromosome rearrangements have been observed: 'classical' dicentrics with two clearly separated centromeric regions, and more unusual rearrangements with a breakpoint within the centromeric or heterochromatic area, but outside the alphoid domain. FISH analysis of partial chromosome 1 q duplications present in three Burkitt lymphoma cell lines confirmed the partial involvement of the non-alphoid centromeric domain in the duplicated chromosome segment. The incidence of centromeric and pericentromeric rearrangements in hematopoietic malignancies may be higher than hitherto admitted. The chromosomal localization of these rearrangements suggests several mechanisms possibly involved in the malignant process and deserves more systematic study.

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A survey of the genomic distribution of alpha satellite DNA on all the human chromosomes, and derivation of a new consensus sequence

Abstract: A survey of the genomic distribution of alpha satellite DNA on all the human chromosomes, and derivation of a new consensus sequence by K.

Cited by 229 publications

References 29 publications

Sensitive and Rapid Detection of Centromeric Alphoid DNA in Human Metaphase Chromosomes by PNA Fluorescence <i>In Situ</i> Hybridization and Its Application to Biological Radiation Dosimetry

Sensitive and Rapid Detection of Centromeric Alphoid DNA in Human Metaphase Chromosomes by PNA Fluorescence <i>In Situ</i> Hybridization and Its Application to Biological Radiation Dosimetry

Epigenetic engineering: histone H3K9 acetylation is compatible with kinetochore structure and function

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