Computer methods for visualization chromosome-specific DNA sequences in FISH images

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Bogomolov A.G.1, Karamysheva T.V.2, Rubtsov N.B.3
1Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia; Novosibirsk State University Novosibirsk, Russia, mantis_anton@bionet.nsc.ru
2Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia, kary@bionet.nsc.ru
3Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia; Novosibirsk State University Novosibirsk, Russia, rubt@bionet.nsc.ru

A great number of interspersed repetitive sequences in chromosomes make it difficult to identify chromosomal material via fluorescence in situ hybridization (FISH). The traditional approach to solve this problem is chromosome in situ suppression hybridization (CISS- hybridization). Unfortunately, it is impossible to be performed or fails with chromosomes of many eukaryote species. The aim of this study was to consider the image enhance procedure [1] and the in silico method of chromosome specific signal visualization (method VISSIS) [2] as alternatives to CISS-hybridization. The effectiveness of approaches for identification of specific signals was estimated by signal-to-background ratio (SNR). The computer methods were applied to images of human chromosomes, obtained with FISH of the whole chromosome painting DNA probes. Results showed that effectiveness of image processing methods depends on ratio of short and line interspersed elements (SINEs/LINEs) in DNA probes. The closer chromosomes in ratio of SINEs/LINEs, the higher specific signal intensities and signal-to-background ratios could be achieved. This suggests that computer methods can be efficient only with application of DNA probes derived from chromosomes characterized with similar ratio of SINE and LINE contents.

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Evgeny Tiys
Evgeny Tiys
1 year ago

Why you use VISSIS method inspite RENS has better signal-noise ratio?

Anton Bogomolov
Anton Bogomolov
1 year ago
Reply to  Evgeny Tiys

Thank you for the question. Yes, Rens’s method looks better if we use the signal-to-noise ratio to estimate the effectiveness of approaches for identification of specific signals . But our method VISSIS has several advantages in contrast to the method RENS. First, VISSIS results are far less dependent on the researcher’s subjective opinion. The method does not involve an arbitrary selection of limits for the range used to identify the signals due to hybridization of interspersed repetitive sequences.
Second, in contrast to the method RENS , computer processing reduces or completely eliminates the nonspecific signal for all chromosomes, including the chromosomes or chromosome regions used to derive the DNA probes.

Irina Chadaeva
Irina Chadaeva
1 year ago

Did you apply methods to images of plants chromosomes (as example of genomes with large number of repetitive sequences)?

Anton Bogomolov
Anton Bogomolov
1 year ago
Reply to  Irina Chadaeva

Thank you for the question. No, It will be interesting to do this. But we applied our method VISSIS to analys the hybridization patterns of microdissection chromosomespecific DNA probes to chromosomes in grasshoppers (as example of genomes with large number of repetitive sequences) [Jetybayev et al., 2017 “Origin and Evolution of the Neo-Sex Chromosomes in Pamphagidae Grasshoppers through Chromosome Fusion and Following Heteromorphization”]

Irina Chadaeva
Irina Chadaeva
1 year ago

thanks for answer, very interesting!