The changes in the fundamental biological processes of nuclear RNA transcription and splicing under altered gravity conditions are still unclear. The quantitative and qualitative characteristics of the proteins involved in nuclear RNA metabolism in control and under clinorotation were investigated by two-dimensional gel electrophoresis. We revealed firstly a decrease in the isoelectric point range of nuclear soluble proteins, which are known to be actively engaged in nuclear RNA metabolism, and a shortening in the molecular weight range of them under clinorotation. Moreover, minor and major proteins in clinorotated samples had decreased optical densities in comparison with control ones. Our results are in agreement with the hypothesis that a rearrangement of the pattern of nuclear proteins involved in gene expression processes occurs in seedlings grown and developed in altered gravity.