The current understanding of the relationships between cell shape, intracellular forces and signaling, nuclear shape and organization, and gene expression is in its infancy. Here we introduce a method for investigating gene-specific responses in individual cells with controlled nuclear shape and projected area. The shape of the nuclei of primary osteogenic cells were controlled on microfabricated substrata with regiospecific chemistry by confining attachment and spreading of isolated cells on adhesive islands. Gene expression and protein synthesis were altered by changing nuclear shape. Collagen I synthesis correlated directly with cell shape and nuclear shape index (NSI), where intermediate values of nuclear distension (6 < NSI < 8) promoted maximum synthesis. Osteocalcin mRNA, a bone-specific differentiation marker, was observed intracellularly by using reverse transcription in situ PCR at 4 days in cells constrained by the pattern and not detected in unconstrained cells of similar projected area, but different NSI. Our data supports the concept of gene expression and protein synthesis based on optimal distortion of the nucleus, possibly altering transcription factor affinity for DNA, transport to the nucleus, or nuclear matrix organization. The combination of microfabricated surfaces, reverse transcription in situ PCR, and NSI measurement is an excellent system to study how transcription factors, the nuclear matrix, and the cytoskeleton interact to control gene expression and may be useful for studying a wide variety of other cell shape͞gene expression relationships.patterning ͉ cell size ͉ osteocalcin ͉ reverse transcription-PCR ͉ photolithography C ell morphology has a profound effect on a range of cellular events, such as proliferation (1-3), differentiation (4-7), cytoskeletal organization (8), and presumably gene expression. Changes to the cytoskeleton lead to altered stress levels imparted on the nucleus (9-11) and could affect organelle and DNA organization and distribution, ultimately altering cell function. For example, the rate of albumin secretion from hepatocytes can be altered by constraining cell size on patterned culture surfaces (3). In human epidermal kareatinocytes cell shape can modulate between terminal differentiation and proliferation (4). Furthermore, cells can be forced to enter the apoptotic cascade when the area on which the cell is allowed to spread is constrained (1). One proposed mechanism for the transduction of cell shape information into gene expression is through mechanical forces transmitted by means of the direct link of the cytoskeleton to the nucleus (9, 12), and in particular to nuclear matrix proteins (NMPs) such as NMP-1 and NMP-2 (13). These architectural transcription factors, which are components of the nuclear scaffold, induce changes in DNA supercoiling and can interact directly with gene promoter sequences (14). This interaction between the nuclear architecture and regulation of transcription or DNA topography raises the question of whether gross deformation of th...