Applications of fluorescence in situ hybridization (FISH) in genome research

Abstract

Fluorescence in situ hybridization (FISH) technique enables the direct detection of DNA sequences in
intact cellular materials (e.g. individual chromosomes in metaphase spreads). This review article focuses on the
applications of FISH in genome research, including validation and correction of the genome assembly from the
next-generation sequencing (NGS) projects. DNA probes for specific DNA fragments of the assembly can be
obtained from PCR amplicon or cloned products using different vector systems. Localization of these probes
on their respective chromosomal regions can be visualized by FISH, providing useful information to crosscheck
the assembly data. Furthermore, the recent refinements in the FISH technology including using smart
pooling scheme of differently colored DNA probes, together with consecutive FISH experiments (stripping and
reprobing of the same slide) are described. These advances in multicolor FISH can provide crucial linkage
information on association of linkage groups and assembly scaffolds, resulting in so-called cytogenetic maps.
Integration of the cytogenetic maps and assembly sequences assists to resolve the chromosome-level genome
assembly and to reveal new insights in genome architecture and genome evolution. Especially, comparative
chromosome painting with pooled DNA probes from one reference species can be used to investigate ancestral
relationships (chromosome homeology and rearrangements) among other not-yet-sequenced species. In
addition, FISH using DNA probes for certain specific classes of repetitive DNA elements as well as for basic
chromosome structures (e.g. centromere or telomere DNA repeats, ribosomal DNA loci) can be used to study
the genome organization and karyotype differentiation. We also discussed about limitations and future
perspectives of the FISH technology.