Imaging of telomere features

Contact: M. Gunkel, H. Erfle group and I. Chung, K. Deeg, in the K. Rippe group

  • Automated targeted 3D imaging using a combined widefield and confocal laser scanning microscopy
  • Super-resolution microscopy (PALM, STORM)
  • FISH and immunostaining
  • Fluorescence microscopy based visualization of ALT-asscociated PML bodies, protocol for stainig
  • Chromosome orientation FISH (CO-FISH) , protocol for staining

more information about the imaging methodes can be found in

  • Osterwald, S. et al. A three-dimensional colocalization RNA interference screening platform to elucidate the alternative lengthening of telomeres pathway. (2012) Biotechnol J 7, 103-116 doi: 10.1002/biot.201000474
  • Wörtz, S. et al. 3D geometry-based quantification of colocalizations in multichannel 3D microscopy images of human soft tissue tumors. (2010) IEEE Transactions on Medical Imaging 29, 1474-1484 doi: 10.1109/TMI.2010.2049857
  • Gunkel M. et al. (2016). Quantification of telomere features in tumor tissue sections by an automated 3D imaging-based workflow. bioRxiv doi: 10.1101/053132 | Abstract | Preprint (4.4 MB).

Experimental methods to dissect telomere maintenance mechansims

Contact: I. Chung, K. Deeg, in the K. Rippe group & Brian Luke

  • Terminal restriction fragment (TRF) heterogeneity analysis, protocol
  • C-circle assay, protocol
  • Telomere-repeat quantitative PCR, protocol
  • Reverse transcription quantitative PCR of TERRA, protocol
  • TERRA RNA dot blot

Bioinformatical analysis and modeling

Image analysis methods

Contact: S. Wörz, K. Rohr group

  • 3D segmentation of subcellular structures (e.g., telomeres) in 3D microscopy images of cell lines and tissue microarrays (TMAs)
  • Determination of 3D colocalization (e.g., telomeres and PML bodies)
  • Quantification of cytological features (e.g.., telomere length distribution)

Modeling of telomere maintenance mechanisms

Contact: A. Poos, R. König group

  • MIPRIP: The Mixed Integer linear Programming based Regulatory Interaction Predictor (R-package, publication)

Analysis of telomere features from deep sequencing data

Contact: L. Feuerbach

Telomere maintenance genes

Contact: D. Braun, N. Kepper in the K. Rippe group

  • TelNet database of human and yeast genes that are involved in telomere maintenance, see TelNet web page.

ALT prediction in tumors

Contact: I. Chung in the K. Rippe group, and A. Poos in the R. König group

  • PAINT is a classification scheme for predicting the active telomere maintenance mechanism, see PAINT web page.

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