Epigenetic profiling of heterochromatic satellite DNA.

Abstract:

:Sugar beet (Beta vulgaris) chromosomes consist of large heterochromatic blocks in pericentromeric, centromeric, and intercalary regions comprised of two different highly abundant DNA satellite families. To investigate DNA methylation at single base resolution at heterochromatic regions, we applied a method for strand-specific bisulfite sequencing of more than 1,000 satellite monomers followed by statistical analyses. As a result, we uncovered diversity in the distribution of different methylation patterns in both satellite families. Heavily methylated CG and CHG (H=A, T, or C) sites occur more frequently in intercalary heterochromatin, while CHH sites, with the exception of CAA, are only sparsely methylated, in both intercalary and pericentromeric/centromeric heterochromatin. We show that the difference in DNA methylation intensity is correlated to unequal distribution of heterochromatic histone H3 methylation marks. While clusters of H3K9me2 were absent from pericentromeric heterochromatin and restricted only to intercalary heterochromatic regions, H3K9me1 and H3K27me1 were observed in all types of heterochromatin. By sequencing of a small RNA library consisting of 6.76 million small RNAs, we identified small interfering RNAs (siRNAs) of 24 nucleotides in size which originated from both strands of the satellite DNAs. We hypothesize an involvement of these siRNAs in the regulation of DNA and histone methylation for maintaining heterochromatin.

journal_name

Chromosoma

journal_title

Chromosoma

authors

Zakrzewski F,Weisshaar B,Fuchs J,Bannack E,Minoche AE,Dohm JC,Himmelbauer H,Schmidt T

doi

10.1007/s00412-011-0325-x

subject

Has Abstract

pub_date

2011-08-01 00:00:00

pages

409-22

issue

4

eissn

0009-5915

issn

1432-0886

journal_volume

120

pub_type

杂志文章
  • Y chromosome aneuploidy, micronuclei, kinetochores and aging in men.

    abstract::This investigation was conducted to determine the relationship between Y chromosome loss and increased micronucleus formation with age. We also investigated the status of kinetochore proteins in the micronuclei. Umbilical cord blood samples were obtained from 18 newborn males, and peripheral blood was obtained from 35...

    journal_title:Chromosoma

    pub_type: 杂志文章

    doi:10.1007/BF00344234

    authors: Nath J,Tucker JD,Hando JC

    更新日期:1995-07-01 00:00:00

  • Mechanisms of chromosome banding. VII. Interaction of methylene blue with DNA and chromatin.

    abstract::The binding of methylene blue to DNA and chromatin treated in various ways was examined by equilibrium dialysis. The maximum r value (moles of bound dye/mole of nucleotide) was 1.0 for DNA, 0.6 for unfixed chromatin, and 0.83 for chromatin fixed in methanol-acetic acid. When fixed chromatin was treated with saline-cit...

    journal_title:Chromosoma

    pub_type: 杂志文章

    doi:10.1007/BF00326323

    authors: Comings DE,Avelino E

    更新日期:1975-08-11 00:00:00

  • Study of mitomycin C-induced chromosomal exchange.

    abstract::Mitomycin C-induced sister chromatic exchange and quadriradial formation were studied in chromosomes from Muntiacus muntjac fibroblasts and A9, a transformed mouse cell line. We present the first direct cytological evidence for the induction of true somatic recombination involving homologous chromosomes. Analysis of t...

    journal_title:Chromosoma

    pub_type: 杂志文章

    doi:10.1007/BF00293724

    authors: Huttner KM,Ruddle FH

    更新日期:1976-06-30 00:00:00

  • Direct repeats at nuclear matrix-associated DNA regions and their putative control function in the replicating eukaryotic genome.

    abstract::Short DNA regions, known to contain replication origins, were isolated from 2 M NaCl resistant nuclear structures of Physarum polycephalum after predigestion with DNase. Regions of 100 bp average length were cloned and sequenced. About 25% of the clones contained direct repeats of 12 to 16 bp and variable base sequenc...

    journal_title:Chromosoma

    pub_type: 杂志文章

    doi:10.1007/BF00292787

    authors: Opstelten RJ,Clement JM,Wanka F

    更新日期:1989-12-01 00:00:00

  • Cell-specific variation of X chromosome replication in the Syrian hamster (Mesocricetus auratus).

    abstract::The sub-division of S-phase in Syrian hamsters, on the basis of Brd/U/Hoechst 33258/Giemsa banding, has allowed a quantitative comparison of the replication of individual chromosome bands within defined subphases of S. This analysis has shown that in hamsters, as has been reported in humans, there are distinct pattern...

    journal_title:Chromosoma

    pub_type: 杂志文章

    doi:10.1007/BF00286026

    authors: Cawood AH

    更新日期:1981-01-01 00:00:00

  • Cell cycle dependent chromosomal movement in pre-mitotic human T-lymphocyte nuclei.

    abstract::Fluorescent in situ hybridization with chromosome specific probes was used in conjunction with laser scanning confocal microscopy to assess the three-dimensional distribution of chromosomes in human T-lymphocyte nuclei. Cells in the G1-phase of the cell cycle exhibit a distinctly non-random chromosome organization:cen...

    journal_title:Chromosoma

    pub_type: 杂志文章

    doi:10.1007/BF00660315

    authors: Ferguson M,Ward DC

    更新日期:1992-08-01 00:00:00

  • A group of non-Y encoded Drosophila hydei primary spermatocyte nuclear glycoproteins exhibits epitopes depending on formation of Y chromosomal giant lampbrush loops.

    abstract::In wild-type Drosophila hydei (genotype X/Y) four different primary spermatocyte nuclear glycoproteins, classified as non-Y encoded because of their occurrence in X/O genotypes, were demonstrated to possess a few epitopes that depended on formation of the Y chromosomal giant lampbrush loops threads (th; Mr 55,000 prot...

    journal_title:Chromosoma

    pub_type: 杂志文章

    doi:10.1007/BF00291050

    authors: Tischendorf G,Liebrich W,Trapitz P,Wood G,Schwochau M

    更新日期:1989-08-01 00:00:00

  • Resolving complex chromosome structures during meiosis: versatile deployment of Smc5/6.

    abstract::The Smc5/6 complex, along with cohesin and condensin, is a member of the structural maintenance of chromosome (SMC) family, large ring-like protein complexes that are essential for chromatin structure and function. Thanks to numerous studies of the mitotic cell cycle, Smc5/6 has been implicated to have roles in homolo...

    journal_title:Chromosoma

    pub_type: 杂志文章,评审

    doi:10.1007/s00412-015-0518-9

    authors: Verver DE,Hwang GH,Jordan PW,Hamer G

    更新日期:2016-03-01 00:00:00

  • Cloning and characterisation of polymorphic heterochromatic segments of Brachycome dichromosomatica.

    abstract::After selective enrichment and differential hybridisation of Cot-1 DNA fractions of plants with and without polymorphic heterochromatic segments, a repetitive sequence (called Bds1) specific to the polymorphic chromosome segments of Brachycome dichromosomatica (Brachyscome dichromosomatica) was isolated. A single repe...

    journal_title:Chromosoma

    pub_type: 杂志文章

    doi:10.1007/s004120050430

    authors: Houben A,Wanner G,Hanson L,Verlin D,Leach CR,Timmis JN

    更新日期:2000-06-01 00:00:00

  • Ultrastructure of regions containing homologous loci in polytene chromosomes of Drosophila melanogaster and Drosophila subobscura.

    abstract::We have used a new approach involving in situ hybridisation and electron microscopy to establish ultrastructural homologies between polytene chromosome regions of Drosophila melanogaster and Drosophila subobscura. Twelve probes were chosen to cover all the chromosomal elements: the myospheroid gene, the collagen type ...

    journal_title:Chromosoma

    pub_type: 杂志文章

    doi:10.1007/s004120050287

    authors: Cuenca JB,Galindo MI,Saura AO,Sorsa V,de Frutos R

    更新日期:1998-05-01 00:00:00

  • Decrease of DNA synthesis in amniotic fluid cells during the middle part of S-phase revealed by differential chromosome staining after incorporation of BrdU.

    abstract::The time sequence of DNA replication in partially synchronized human amniotic fluid cells has been analysed, employing BrdU incorporation techniques.--Regardless of the interval between removal of the methotrexate/uridine block and addition of BrdU during S-phase, the treatment results in an R-type replication pattern...

    journal_title:Chromosoma

    pub_type: 杂志文章

    doi:10.1007/BF00293176

    authors: Schempp W,Vogel W

    更新日期:1978-06-28 00:00:00

  • Re-evaluating the role of Tao1 in the spindle checkpoint.

    abstract::The spindle checkpoint restrains anaphase onset and mitotic exit until all chromosomes are stably attached to the mitotic spindle via their kinetochores. The Tao1 protein kinase was recently reported as a novel spindle checkpoint component. When an siRNA was used to repress Tao1, the essential spindle checkpoint compo...

    journal_title:Chromosoma

    pub_type: 杂志文章

    doi:10.1007/s00412-010-0261-1

    authors: Westhorpe FG,Diez MA,Gurden MD,Tighe A,Taylor SS

    更新日期:2010-08-01 00:00:00

  • Karyotypic conservation in the mammalian order monotremata (subclass Prototheria).

    abstract::The order Monotremata, comprising the platypus and two species of echidna (Australian and Nuigini) is the only extant representative of the mammalian subclass Prototheria, which diverged from subclass Theria (marsupials and placental mammals) 150-200 million years ago. The 2n = 63 male, 64 female karyotype (newly desc...

    journal_title:Chromosoma

    pub_type: 杂志文章

    doi:10.1007/BF00302363

    authors: Wrigley JM,Graves JA

    更新日期:1988-01-01 00:00:00

  • Contrasting behavior of heterochromatic and euchromatic chromosome portions and pericentric genome separation in pre-bouquet spermatocytes of hybrid mice.

    abstract::The spatial distribution of parental genomes has attracted much interest because intranuclear chromosome distribution can modulate the transcriptome of cells and influence the efficacy of meiotic homologue pairing. Pairing of parental chromosomes is imperative to sexual reproduction as it translates into homologue seg...

    journal_title:Chromosoma

    pub_type: 杂志文章

    doi:10.1007/s00412-014-0479-4

    authors: Scherthan H,Schöfisch K,Dell T,Illner D

    更新日期:2014-12-01 00:00:00

  • Fluorescent in situ hybridization (FISH) analysis of the relationship between chromosome location and nuclear morphology in human neutrophils.

    abstract::Human neutrophil nuclei typically consist of three of four large heterochromatic lobes joined by thin, DNA-containing filaments. In addition, some lobes exhibit appendages of various sizes and shapes. Classical genetic and cytological studies suggest that some appendages contain specific chromosomes. The studies repor...

    journal_title:Chromosoma

    pub_type: 杂志文章

    doi:10.1007/s004120050236

    authors: Aquiles Sanchez J,Karni RJ,Wangh LJ

    更新日期:1997-08-01 00:00:00

  • Evidence for three "classes" of microtubules in the interpolar space of the mitotic micronucleus of a ciliate and the participation of the nuclear envelope in conferring stability to microtubules.

    abstract::Exposure of Nyctotherus ovalis to low temperatures or vinblastine caused similar reactions of "classes" of microtubules (mt) present in the mitotic micronucleus of this ciliate towards both treatments. However, differences of sensitivity between certain "classes" of mt at individual mitotic stages exist. Unlike the ki...

    journal_title:Chromosoma

    pub_type: 杂志文章

    doi:10.1007/BF00330781

    authors: Eichenlaub-Ritter U,Ruthmann A

    更新日期:1982-01-01 00:00:00

  • Comparative study of the function of polytene chromosomes in laboratory stocks of Drosophila melanogaster and the l(3)tl mutant (lethal tumorous larvae). II. Changes of banding pattern and transcriptional activity in the salivary chromosome of l(3)tl.

    abstract::The salivary chromosomes of the l(3)tl mutant of D. melanogaster are considerably thicker and shorter than those of normal larvae. In most nuclei, chromosome shortening is associated with morphological changes of two types. a) The bands lose their distinctive pattern and become loose. The chromosome appears as a granu...

    journal_title:Chromosoma

    pub_type: 杂志文章

    doi:10.1007/BF01798344

    authors: Zhimulev IF,Belyaeva ES,Lychev VA

    更新日期:1976-04-21 00:00:00

  • Relationship between incomplete synapsis and chiasma localization.

    abstract::One of the subjects within the meiotic field that has been actively investigated in the recent years is the temporal and functional relationships between meiotic recombination, cohesin loading and synaptonemal complex (SC) assembly. Although the study of meiotic mutants has shed some light, many questions remain to be...

    journal_title:Chromosoma

    pub_type: 杂志文章

    doi:10.1007/s00412-009-0204-x

    authors: Viera A,Santos JL,Rufas JS

    更新日期:2009-06-01 00:00:00

  • A specific SR protein binds preferentially to the secretory protein gene transcripts in salivary glands of Chironomus tentans.

    abstract::The members of the serine-arginine (SR) family of proteins play multiple roles in posttranscriptional gene expression. Initially considered as essential splicing factors confined to the nucleus and regulating constitutive and alternative splicing, SR proteins are now known to shuttle between the nucleus and the cytopl...

    journal_title:Chromosoma

    pub_type: 杂志文章

    doi:10.1007/s00412-006-0073-5

    authors: Singh OP,Visa N,Wieslander L,Daneholt B

    更新日期:2006-12-01 00:00:00

  • A structural analysis of Balbiani ring dna sequences in Chironomus tentans.

    abstract::The Balbiani rings in the salivary gland polytene chromosomes of Chironomus tentans include the most active structural genes in this organ. Two of them (BR1 and BR2) contain repetitive sequences and are transcribed into giant RNA molecules. On Southern blots of restriction digests, we have identified fragments of geno...

    journal_title:Chromosoma

    pub_type: 杂志文章

    doi:10.1007/BF00327354

    authors: Degelmann A,Hollenberg CP

    更新日期:1981-01-01 00:00:00

  • The histone chaperone Asf1 at the crossroads of chromatin and DNA checkpoint pathways.

    abstract::Nucleosome assembly involves deposition of a heterotetramer of histones H3/H4 onto DNA followed by two heterodimers of histones H2A/H2B. Cycles of nucleosome assembly and disassembly are essential to cellular events such as replication, transcription, and DNA repair. After synthesis in the cytoplasm, histones are shut...

    journal_title:Chromosoma

    pub_type: 杂志文章,评审

    doi:10.1007/s00412-006-0087-z

    authors: Mousson F,Ochsenbein F,Mann C

    更新日期:2007-04-01 00:00:00

  • Contrasting DNA sequence organisation patterns in sauropsidian genomes.

    abstract::The genomic DNA organisation patterns of four sauropsidian species, namely Python reticularis, Caiman crocodilus, Terrapene carolina triungius and Columba livia domestica were investigated by reassociation of short and long DNA fragments, by hyperchromicity measurements of reannealed fragments and by length estimation...

    journal_title:Chromosoma

    pub_type: 杂志文章

    doi:10.1007/BF00292208

    authors: Epplen JT,Diedrich U,Wagenmann M,Schmidtke J,Engel W

    更新日期:1979-11-01 00:00:00

  • The perichromosomal layer.

    abstract::In addition to genetic information, mitotic chromosomes transmit essential components for nuclear assembly and function in a new cell cycle. A specialized chromosome domain, called the perichromosomal layer, perichromosomal sheath, chromosomal coat, or chromosome surface domain, contains proteins required for a variet...

    journal_title:Chromosoma

    pub_type: 杂志文章,评审

    doi:10.1007/s00412-005-0021-9

    authors: Van Hooser AA,Yuh P,Heald R

    更新日期:2005-12-01 00:00:00

  • Control of gene expression and assembly of chromosomal subdomains by chromatin regulators with antagonistic functions.

    abstract::Epigenetic regulation of higher-order chromatin structure controls gene expression and the assembly of chromosomal domains during cell division, differentiation, and development. The proposed "histone code" integrates a complex system of histone modifications and chromosomal proteins that establish and maintain distin...

    journal_title:Chromosoma

    pub_type: 杂志文章,评审

    doi:10.1007/s00412-005-0001-0

    authors: Lam AL,Pazin DE,Sullivan BA

    更新日期:2005-09-01 00:00:00

  • Developmental variation of the SUUR protein binding correlates with gene regulation and specific chromatin types in D. melanogaster.

    abstract::Eukaryotic genomes are organized in large chromatin domains that maintain proper gene activity in the cell. These domains may be permissive or repressive to the transcription of underlying genes. Based on its protein makeup, chromatin in Drosophila cell culture has been recently categorized into five color-coded state...

    journal_title:Chromosoma

    pub_type: 杂志文章

    doi:10.1007/s00412-013-0445-6

    authors: Maksimov DA,Koryakov DE,Belyakin SN

    更新日期:2014-06-01 00:00:00

  • RNA polymerase II transcription and the functional organization of the mammalian cell nucleus.

    abstract::The study of RNA pol II-mediated transcription regulation has been dominated by molecular biological approaches. Although these methods continue to provide important insights, other approaches are required to insure against an oversimplified view of gene expression. Improvements in EM methods and the development of th...

    journal_title:Chromosoma

    pub_type: 杂志文章,评审

    doi:10.1007/BF00355315

    authors: Hendzel MJ,Bazett-Jones DP

    更新日期:1995-02-01 00:00:00

  • DNA representation of variegating heterochromatic P-element inserts in diploid and polytene tissues of Drosophila melanogaster.

    abstract::Position-effect variegation (PEV) is the mosaic expression of a euchromatic gene brought into juxtaposition with heterochromatin. Fourteen different transformed Drosophila melanogaster lines with variegating P-element inserts were used to examine the DNA levels of these transgenes. Insert sites include pericentric, te...

    journal_title:Chromosoma

    pub_type: 杂志文章

    doi:10.1007/BF00352116

    authors: Wallrath LL,Guntur VP,Rosman LE,Elgin SC

    更新日期:1996-04-01 00:00:00

  • Variation in transcriptome size: are we getting the message?

    abstract::The number of RNA molecules per cell (transcriptome size) is highly variable, differing among and within cell types depending on cell size, stage of the cell cycle, ploidy level, age, disease state, and growth condition. Such variation has been observed at the level of total RNA, ribosomal RNA, messenger RNA (mRNA), a...

    journal_title:Chromosoma

    pub_type: 杂志文章,评审

    doi:10.1007/s00412-014-0496-3

    authors: Coate JE,Doyle JJ

    更新日期:2015-03-01 00:00:00

  • On the transposition of copia-like nomadic elements in cultured Drosophila cells.

    abstract::We studied the stability of the genomic distribution of six retrotransposon families in long-term and short-term cultures of Drosophila cells. In a subclone derived from Kc cells, no significant rearrangements were detected over an 8 year period. On the contrary, extensive reshuffling and amplification of transposon f...

    journal_title:Chromosoma

    pub_type: 杂志文章

    doi:10.1007/BF00292963

    authors: Junakovic N,Di Franco C,Best-Belpomme M,Echalier G

    更新日期:1988-11-01 00:00:00

  • Distribution of 18+28S ribosomal genes in mammalian genomes.

    abstract::In situ hybridization with 3H 18S and 28S ribosomal RNA from Xenopus laevis has been used to study the distribution of DNA sequences coding for these RNAs (the nucleolus organizing regions) in the genomes of six mammals. Several patterns of distribution have been found: 1) A single major site (rat kangaroo, Seba's fru...

    journal_title:Chromosoma

    pub_type: 杂志文章

    doi:10.1007/BF00329388

    authors: Hsu TC,Spirito SE,Pardue ML

    更新日期:1975-11-20 00:00:00