A + T-rich linkers define functional domains in eukaryotic DNA

Abstract

Although an increasing number of detailed DNA sequence studies are being carried out, little is known about the long-range organization of the eukaryotic genome in relation to chromosomal organization and to functional units of transcription, replication, meiotic crossing-over and nuclear architecture. Based on electron microscope (EM) observations of partially denatured DNA of duck, mouse and rat, we have recently reported a systematic punctuation of DNA by early melting zones (‘A + T-rich linkers’)¹ ∼800 base pairs (bp) long which are either clustered or at intervals of 10–40 kbp. In an attempt to correlate this feature with the organization of specific genes, we examined cloned genomic DNA from chick and Drosophila, including the globin gene family, and an isolated high-molecular-weight mRNA. We show here that the chick α-globin gene cluster is framed by a cluster of A + T-rich linkers at the 5′ end and by an isolated linker at the 3′ end which maps close to the sites of transcription termination and DNase hypersensitivity. The resulting frame of ∼15 kbp correlates well with the maximum size of globin gene transcripts found at the pre-mRNA level. The β-globin gene cluster is also framed, 5′ by a single A + T-rich linker and 3′ a cluster of four linkers. In Drosophila, the single mRNA sequence of ∼3.3 kbp for the ecdysone-inducible P1 protein is similarly delimited by A + T-rich linkers. A + T-rich linkers thus seem to define domains of the eukaryotic genome which may correlate with putative functional units. The specific organization observed in total DNA of duck, mouse, rat, man, chicken and Drosophila is confirmed in gene-specific cloned genomic DNA.