REGULATION OF GENE EXPRESSION

ROBERT P. PERRY, Ph.D., Senior Member, Stanley P. Reimann Endowed Chair in Research

The genomes of humans and other mammals contain about 80,000 individual genes, which serve as the blueprints for the growth and development of their respective organisms. The genes are composed of DNA tracts of varying length and base sequence, linked together on 20 to 30 extremely long linear strands that are packaged with histones and other proteins into chromatin (chromosomal) fibers. In the nucleus of a typical mammalian cell, these fibers, which collectively contain about 2 meters of DNA, are compressed into a volume of about 65 mm3. Despite this enormous compression, the expression of each gene is tightly controlled. An important level of control involves the localized modification of chromatin structure so as to alter the accessibility of particular genes to RNA polymerase and other components of the transcriptional machinery. Understanding how this is achieved is the major goal of our current research.

Several years ago we fortuitously discovered the first member of the CHD family of proteins when screening a mouse cDNA library for a sequence-specific transcription factor. Our interest in this protein, termed CHD1, was stimulated by its novel combination of sequence motifs: a chromo (C) domain that is generally associated with chromatin-compacting repressor proteins; an ATPase/helicase-like (H) domain, generally associated with chromatin-decompacting activator proteins; and, a DNA-binding domain (D), which selectively recognizes AT-rich DNA tracts, including those in the nuclear matrix/scaffold attachment regions of the genome. We subsequently observed that this protein is associated with noncompacted interphase chromatin in mammalian cells and that it is released into the cytoplasm when chromosomes condense during mitosis. We also characterized a CHD1 ortholog in Drosophila and found that it is preferentially located in the transcriptionally active, decompacted regions of polytene chromosomes. Collectively, these observations favor the idea that CHD1 helps to create and/or maintain chromatin structure that is conducive to transcription.

In more recent studies of CHD1, we learned that both the C and H domains are essential for its proper association with chromatin, and that it interacts in vivo with an high mobility group (HMG) box-containing protein termed structure-specific recognition protein 1 (SSRP1), apparently as part of a multiprotein complex. This interaction of CHD1 and SSRP1 was also indicated by the colocalization of these proteins in both mammalian interphase nuclei and Drosophila polytene chromosomes.

Recent research in other laboratories has identified additional members of the CHD family: CHD2, a relatively close relative, and two more distantly related proteins, CHD3 and CHD4. Interestingly, the CHD3/4 variants are found in a multiprotein complex that contains a histone deacetylase believed to be associated with transcriptional repression. This complex also exhibits ATP-dependent nucleosome-disruption activity. These new findings raise the possibility of an evolutionary bifurcation of the CHD family into variants with either activator or repressor functions.

Our ongoing studies are aimed at delineating the biological roles of CHD1 and other family members. At the present, it is impossible to assign a particular niche in the overall remodeling of chromatin to any of the known complexes that are believed to participate in this activity. It is not clear whether different complexes operate at different levels of chromatin structure or as components of different regulatory circuits. Our current studies may help provide insight into these issues.

KELLEY, D.E., STOKES, D.G., PERRY, R.P. CHD1 interacts with SSRP1 and depends on both its chromodomain and its ATPase/helicase-like domain for proper association with chromatin. Chromosoma 108:10-25, 1999.

Illustrations or unpublished data in these reports should not be used without permission of the author.

Fox Chase Cancer Center

Scientific Report 1998