Chromosome Scaffolds

Chromosome Scaffolds

Majority of chains of chromosomal DNA “within the interphase nucleus” are said to be held on a backbone or a scaffold structure (“Nucleic Acids and Chromatin”).  This structure is made with a variety of proteins forming loops of approximately 20 to 200 kb that extrude from the sites of attachment (“Nucleic Acids and Chromatin”).  Thus, the chromosome scaffold is believed to be a continuous substructure of proteins, revealed only in “isolated metaphase chromosomes after harsh extraction (Sheval & Polyakov, 2005).”  

     Studies of the “radial loop model” have led developmental biologists to believe that the chromosome scaffold is essential for the configuration as well as maintenance of the structures of mitotic chromosomes (Sheval & Polyakov, 2005).  With reference to DNA, the purpose of the chromosome scaffold may be understood as being twofold: (1) The chromosome scaffold permits further compression; and (2) It helps to organize the areas where DNA must be brought together (“Nucleic Acids and Chromatin”).  Berezney & Jeon (1995) explain the chromosome scaffold further:

         The chromosome scaffold is a nonhistone core framework extending along the axis of the chromosome arms.  With structural features similar to the nuclear matrix, the scaffold is usually demonstrated by sequentially extracting mitotic chromosomes with detergent, nuclease, and salt…  After extraction, the chromosome scaffold can be resolved as a dense filamentous network that accounts for 3-4% of the total chromosome mass…  Unlike the nuclear matrix, the chromosome scaffold can be visualized in intact chromosomes by silver staining…  Recently, using the highly AT-specific fluorochrome daunomycin, a coiled or folded AT-rich core was observed in native chromosomes and thought to correspond to the chromosome scaffold where the GC-rich DNA loops protrude…  Although some morphological aspects of the chromosome scaffold, such as thickness, length, and helical intensity, appear to differ in various studies due to individual extraction protocols, the composition of scaffolds are quite similar based on electrophoresis analysis… (Berezney &

    Jeon, p. 21-22).

Although there is not enough researched evidence to comprehend the individual parts of the chromosome scaffold – scientists are aware that the structure of the nuclear matrix is comparable to the chromosome scaffold, as both are involved in structuring and organizing the genome (Berezney & Jeon).  Because the chromosome scaffold and the nuclear matrix are both revealed through similar protocols of biochemistry, it is assumed that they both originate from “similar components in the nucleus (Berezney & Jeon, p. 22).”  With the use of “embedding-free EM techniques,” the chromosome scaffold in an early phase has even been shown to be part of the nuclear matrix (Berezney & Jeon, p. 22).

     DNA topoisomerase type II happens to be the best known component of the nuclear matrix as well as the chromosome scaffold.  SCII and the proteins known as centromere, for example, CENP-B, are some of the other components that have been identified in chromosome scaffolds that were isolated (Berezney & Jeon).  By identifying and characterizing “DNA sequence elements” that are referred to as SARs (regions that are attached to scaffolds) or MARs, along with the proteins that are bound to them; scientists believe it should be relatively easy to define various interactions of DNA within the chromosome scaffold as well as the nuclear matrix (Berezney & Jeon, p. 22).  Because proteins that bind MAR have thus far appeared as the most stable and/or unchanging in terms of their purposes and structure while the cells move on from the “interphase to mitosis,” these are the regions that should prove to be the most reliable signs as developmental biologists search for chromosome scaffolds (Berezney & Jeon, p. 22).

     Enhanced understanding of DNA topoisomerases must also aid development biologists as they study chromosome scaffolds (“Nucleic Acids and Chromatin”).  Scientists are aware that DNA topoisomerases are engaged in regulating the structure of chromatin “in loops (“Nucleic Acids and Chromatin”).”  Here the act of compaction is known to be an influence of the status of modifications of the “histone tail (“Nucleic Acids and Chromatin”).”  Modification of histone and activity of topoisomerases is said to regulate gene activity in a region that appears as a loop; this process of modification and activity is said to organize genes across “stretches of DNA” that are longer (“Nucleic Acids and Chromatin”).  These areas of chromatin are called domains.  Another important reason for the arrangement referred to as the chromosome scaffold – with reference to DNA topoisomerases – is that the activity of topoisomerases and the enzymes that alter chromatin may affect the compression of single loops without modifying domains in the neighborhood (“Nucleic Acids and Chromatin”).

     For biologists new to the scaffold, it is also useful to know that even though visualization of the chromosome scaffold and structures identified as loops is impossible with the use of “light microscope[s],” it is still possible to view these arrangements in the “lamp brush chromosomes in the developing amphibian oocyte (egg cell)” with the use of such microscopes (“Nucleic Acids and Chromatin”).  DNA in these egg cells is known to be very “transcriptionally active” as the egg cell synthesizes large protein stores (“Nucleic Acids and Chromatin”).  Big loops as extensions of a structure that appears as a scaffold are clearly visible through this process of visualization (“Nucleic Acids and Chromatin”).  Indeed, this process also resolves some of the mysteries surrounding the chromosome scaffold.


Berezney, R., & Jeon, K. W. (1995). Structural and Functional Organization of the Nuclear

Matrix: Structural and Functional Organization of the Nuclear Matrix. Academic Press. Retrieved Oct 28, 2008, from Google Books.

Nucleic Acids and Chromatin. OU. Retrieved Oct 28, 2008, from

Sheval, E. V., & Polyakov, V. Y. (2005, Oct 1). Chromosome Scaffold and Structural Integrity

of Mitotic Chromosomes. Russian Journal of Developmental Biology 37(6).

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