A unified model of eukaryotic chromosomes

Abstract

A revised model of DNA packaging into chromosomes is presented. Its features are consistent with observed structural dimensions and the molecular periodicities related to transcription, replication and matrix attachment domains. Thetransitions between euchromatic, heterochromatic and metaphase states are explained simply. Molecular and physical properties of chromosomal bands, and their correlation with specific DNA sequence motifs are discussed.Key terms: Chromatin, chromosome structure, matrix, replication, Giemsa bands, repeated DNA The higher order molecular and physical structure of chromosomes is still poorly understood. The winding of the DNA double helix around histones to form 10 nm thick nucleosomes or "beads on a string," and the subsequent coiling of nucleosomes into solenoids of -30 nm x 10 nm is by now well-established. Each solenoid turn however encompasses only -1.2 kb of DNA, and is too small to embrace complex transcriptional and replication domains that may span several hundred kilobases of DNA. These larger "functional" units of DNA are likely to be arranged into hierarchical structures that can be recognized and conveniently utilized in a n orderly fashion. On a purely structural level, the delineation of metaphase chromosome bands by Giemsa staining suggests that such hierarchies exist; Giemsa bands encompass megabase (Mb) stretches of DNA and are not meaningless artifacts; for example, Giemsalight bands are preferentially digested by trypsin, indicating structural andior molecular components are specifically organized in these compartments, and overall binding patterns may be conserved in evolution (27). Furthermore, domains of similar large size, that may correspond to Giemsa bands, are involved in sister chromatid exchanges, translocations and replication. Sam Latt made many original contributions to the molecular organization of the genome, and one of his eminent contributions was the delineation of sister chromatid exchanges (32). In his honor, we present a physical model of chromosome structure that encompasses units of this size.We here build an updated model that incorporates the longer features of molecular gene organization that have become apparent in the last 10 years. Such features include units that range in size from very long linear lengths of DNA, as defined by chromosome banding techniques, pulse-field gel electrophoresis (PFGE), and high-resolution non-isotopic in-situ hybridization, through smaller DNA lengths of 30-120kb that periodically attach to matrix proteins and replication complexes. To date, no model of chromosome structure adequately addresses the folding or compaction of these longer DNA lengths in both interphase and metaphase chromosomes of known dimensions. Since these dimensional constraints are essential to any realistic model of chromosome folding, we first address the actual sizes of chromosome domains i n both interphase and metaphase chromosomes. The structure of interphase chromosomes is pivotal, since interphase cells carry out key functions such as...

Evidence for the organization of chromatin in megabase pair-sized loops arranged along a random walk path in the human G0/G1 interphase nucleus.

“…When the chromosomes reappear for the next mitosis, they have been duplicated and prepared for rapid partitioning over the daughter cells. The complexity of these processes raises many questions about the large-scale organization of chromosomes and how this organization relates to cell function (e.g., Blobel, 1985;Manuelidis and Chen, 1990;Cook, 1991;Lawrence and Singer, 1991;De Boni, 1994).Diverse models, ranging from highly random to highly organized, have been proposed for the higher-order organization of interphase chromatin. These models variously involve irregularly folded fibers (DuPraw, 1965), radial loop structures (Manuelidis and Chen, 1990), giant loops (Ostashevsky and Lange, 1994), semirigid orientation ("Rabl" configuration) (Rabl, 1885;Comings, 1968), or random polymers confined by tethering or external forces (Hahnfeldt et al, 1993).…”

The Barr body is a looped X chromosome formed by telomere association.

“…SB). However, the span (30)], the 1-,um distance between inactive X telomeres is roughly equivalent to one or two megabases of interphase DNA. This is only slightly greater than the 700-nm fiber that characterizes metaphase chromosomes and is considerably less than the >10-,um length of chromosome 1 (smaller than the smallest isodicentric chromosome analyzed) measured by electron microscopy in an acid-fixed prometaphase preparation.…”

Evolution Without Genes

“…In this phenomenon constant, fundamental elements of chromosome organization are manifested. The dense and weakly stained chromosome segments in the first place reflect different degrees of density of the DNA packaging [38,39]. It has been also established that in the G+ and Q+ bands the number of genes is much less than in the G-, Q-or R+ bands.…”