Immunological Methods for Mapping Protein Distributions on Polytene Chromosomes

This chapter focuses on immunological methods for mapping protein distributions on polytene chromosomes. The reproducible banding pattern of the polytene chromosomes has been used to map genes relative to chromosomal rearrangements, to map cloned DNAs to specific bands, to probe chromatin structure, and to map sites of protein accumulation. Polytene chromosomes are created through a process known as endoreduplication, in which multiple rounds of DNA replication occur without the concomitant strand separation and subsequent nuclear and cell division characteristic of normal mitoses. The characteristic polytene-binding pattern has been useful for mapping DNA and chromatin structure. Antibodies have been used to map regions of heterochromatization and atypical DNA structure such as non-B and Z-DNA. Antibody staining of polytene chromosomes has provided evidence for the in vivo association of transcription factors with the genes they regulate and the in vivo association of proteins with other proteins of related function.