Chromosome Research

, Volume 20, Issue 6, pp 735–752 | Cite as

The radial nuclear positioning of genes correlates with features of megabase-sized chromatin domains

  • Alexandra C. Kölbl
  • Daniela Weigl
  • Medhanie Mulaw
  • Tobias Thormeyer
  • Stefan K. Bohlander
  • Thomas Cremer
  • Steffen Dietzel
Article

Abstract

A nonrandom radial nuclear organization of genes has been well documented. This study provides further evidence that radial positioning depends on features of corresponding ∼1 Mbp chromatin domains (CDs), which represent the basic units of higher-order chromatin organization. We performed a quantitative three-dimensional analysis of the radial nuclear organization of three genes located on chromosome 1 in a DG75 Burkitt lymphoma-derived cell line. Quantitative real-time polymerase chain reaction revealed similar transcription levels for the three selected genes, whereas the total expression strength (TES) calculated as the sum of transcription of all genes annotated within a surrounding window of about 1 Mbp DNA differed for each region. Radial nuclear position of the studied CDs correlated with TES, i.e., the domain with the highest TES occupied the most interior position. Positions of CDs with stable TES values were stably maintained even under experimental conditions, resulting in genome-wide changes of the expression levels of many other genes. Our results strongly support the hypothesis that knowledge of the local chromatin environment is essential to predict the radial nuclear position of a gene.

Keywords

nuclear architecture chromatin organization gene positioning 

Abbreviations

CD

chromatin domain

CT

chromosome territory

Ct

cycle threshold

ΔCt

delta (difference) in Ct value compared to the control

FISH

fluorescence in situ hybridization

IC

interchromatin compartment

ICD

interchromosomal domain

Mbp

Mega base pairs

qPCR

quantitative real-time polymerase chain reaction

RT-PCR

reverse transcription polymerase chain reaction

SCD

spherical 1 Mbp chromatin domain (model)

TES

total expression strength

Supplementary material

10577_2012_9309_MOESM1_ESM.xls (400 kb)
ESM 1Microarray data of differentially regulated probe sets after 24 h of CALM-AF10 induction. Induced cell populations were compared to non-induced CALM/AF10+ cells, as well as induced and non-induced empty vector control cells (24 h after induction).Only differentially regulated probe sets that are associated with annotated genes are shown, as indicated in the table header. The fold differential regulation is indicated in the last column. Probe.Set.ID = affymetrix probe set identifier; Representative.Public.ID = Representative Public domain ID; UniGene.ID = Unigene id of the gene being interrogated; Gene.Symbol = Symbol of the gene; Chromosomal.Location = chromosomal location of the gene in the human genome; Ensembl = Ensembl id; Entrez.Gene = Entrez gene id; SwissProt = SwissProt id of the protein product of the gene; RefSeq.Protein.ID = RefSeq id of the protein; RefSeq.Transcript.ID = RefSeq id of the transcript; fold change = change between induced and control samples, described as a ratio of expression of a given probe set (XLS 400 kb)

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Copyright information

© Springer Science+Business Media B.V. 2012

Authors and Affiliations

  • Alexandra C. Kölbl
    • 1
  • Daniela Weigl
    • 1
  • Medhanie Mulaw
    • 2
    • 3
  • Tobias Thormeyer
    • 1
  • Stefan K. Bohlander
    • 2
    • 3
  • Thomas Cremer
    • 1
  • Steffen Dietzel
    • 1
    • 4
  1. 1.Department Biologie IILudwig-Maximilians-Universität MünchenPlaneggGermany
  2. 2.Medizinische Klinik und Poliklinik IIILudwig-Maximilians-Universität MünchenMunichGermany
  3. 3.Clinical Cooperative Group LeukemiaHelmholtz Zentrum MünchenMunichGermany
  4. 4.Walter-Brendel-Zentrum für Experimentelle MedizinLudwig-Maximilians-Universität MünchenMunichGermany

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