The replication timing of CFTR and adjacent genes Andreas Englmann 1 , Luka A. Clarke 2 , Susanne Christan 1,3 , Margarida D. Amaral 2,4 , Dirk Schindelhauer 3 & Daniele Zink 1* 1 Ludwig Maximilians University Munich, Department of Biology II, Grosshaderner Str. 2, 82152 Planegg-Martinsried, Germany; Tel: þ 49 89-2180-74133; Fax: þ 49 89-2180-74112; E-mail: Dani.Zink@lrz.uni-muenchen.de; 2 Department of Chemistry and Biochemistry, Faculty of Sciences, University of Lisboa, 1749-016 Lisboa, Portugal; 3 Technical University of Munich, Life Science Center Weihenstephan, 85354 Freising, Germany; 4 Center of Human Genetics, National Institute of Health, 1649-016 Lisboa, Portugal *Correspondence Received 6 December 2004. Received in revised form and accepted for publication by Hans Lipps 5 January 2005 Key words: CFTR, chromatin, nuclear positioning, replication timing Abstract Correlations between transcriptional activity and replication timing have been observed for the human cystic fibrosis transmembrane conductance regulator (CFTR) gene, as well as for other tissue-specific genes. In addition, the patterns of histone modifications and the nuclear positioning of chromosomal loci appear to be related to their replication timing. It is not understood why and how these different features are functionally linked. To address this problem, we investigated the replication timing of the human CFTR gene and of adjacent genes. Recently, we could show that CFTR and adjacent genes associate independently from each other with different nuclear regions and chromatin fractions, in accordance with their individual transcriptional regulation. Together, the results show that not the transcriptional activity, but rather the nuclear position of CFTR and adjacent genes appears to be a major determinant of their replication timing. Furthermore, the results imply a specific functional order of nuclear changes related to switches in replication timing. Introduction Since the early 1960s it has been observed that distinct regions of a eukaryotic genome replicate at distinct times during S phase (Stambrook & Flickinger 1970, Fangman & Brewer 1992). Still, it is not known what determines these differences in replication timing, nor is it understood what their functional significance might be. The observed relationships between the transcrip- tional activity of DNA sequences and their repli- cation timing (Goldman et al. 1984, Hatton et al. 1984, Schu ¨beler et al. 2002) led to the hypothesis that replication timing plays an important role in the epigenetic regulation of transcription (Wolffe 1994, Gilbert 2002, Goren & Cedar 2003). How- ever, a variety of exceptions from the general rule that active genes replicate early, while inac- tive DNA replicates at later time points during S phase have been observed (Benard et al. 1992, Smith & Higgs 1999, Azuara et al. 2003). Fur- thermore, the replication timing of distinct geno- mic regions is not only often related to their transcriptional activity but also to their pattern Chromosome Research 13: 183–194, 2005. 183 # 2005 Springer. Printed in the Netherlands