Spatial organisation of nuclear compartments is an important regulator of chromatin function, yet the molecular principles that maintain nuclear architecture remain ill-defined. We have used RNA interference to deplete key structural nuclear proteins, the nuclear lamins. In HeLa cells, we show that reduced expression of lamin B1, but not lamin A/C, severely inhibits RNA synthesis – first by RNA polymerase II and later by RNA polymerase I. Declining levels of transcription correlate with different morphological changes in major nuclear compartments, nucleoli and nuclear speckles. Ultimately, nuclear changes linked to the loss of synthetic activity result in expansion of the inter-chromatin domain and corresponding changes in the structure and spatial organisation of chromosome territories, which relocate towards the nuclear periphery. These results show that a lamin B1-containing nucleoskeleton is required to maintain RNA synthesis and that ongoing synthesis is a fundamental determinant of global nuclear architecture in mammalian cells.

Cell proliferation demands that identical genetic material is passed to daughter cells that form during mitosis. Genetic copies are produced during the preceding interphase, when DNA of the mother cell is copied exactly once. While few processes in biology are regulated with this precision, the fundamental importance cannot be understated as defects might compromise genetic integrity and ultimately lead to cancer. Replication of the human genome in diploid cells occurs during S phase of the cell cycle. Throughout this ~10h period, about 10% of replication units - replicons - are active at any time, even though all potential initiation sites - origins - are established before the onset of S phase. Crucially, the mechanisms that regulate origin selection and define a structured replication programme remain to be defined. We review recent progress in understanding the structure and regulation of S phase and develop a model that we believe best describes the S phase programme in human cells.

Nuclear lamins are intermediate filament proteins that define the shape and stability of nuclei in mammalian cells. In addition to this dominant structural role, recent studies have suggested that the lamin proteins also regulate fundamental aspects of nuclear function. In order to understand different roles played by lamin proteins, we used RNA interference to generate a series of HeLa cell lines to study loss-of-function phenotypes associated with depletion of lamin protein expression. In this study, we used genome-wide proteomic approaches to monitor global changes in protein expression in cells with <10% of normal lamin A/C expression. Of approximately 2000 protein spots analyzed by two-dimensional electrophoresis, only 38 showed significantly altered expression in lamin A/C depleted cells. Of these, 4 protein spots were up-regulated, and 34 were down-regulated. Significant changes were seen to involve the general reduction in expression of cytoskeletal proteins, consistent with altered functionality of the structural cellular networks. At the same time, alterations in expression of proteins involved in cellular metabolism correlated with altered patterns of metabolic activity. In order to link these two features, we used antibody microarrays to perform a focused analysis of expression of cell cycle regulatory proteins. This confirmed a general reduction in expression of proteins regulating cell cycle progression and alteration in signaling pathways that regulate the metabolic activity of cells. The cross-talk between signal transduction and the cytoskeleton emphasizes how structural and kinase-based networks are integrated in mammalian cells to fine-tune metabolic responses.

The Checkpoint kinase 1 (Chk1) plays a central role in the cellular response to DNA damage and also contributes to the efficacy of DNA replication in the absence of genomic stress. However, we have only limited knowledge regarding the molecular mechanisms that regulate differential Chk1 function in the absence and presence of DNA damage. To address this, we used vertebrate cells with compromised Chk1 function to analyze how altered Chk1 activity influences protein interactions in chromatin. Avian and mammalian cells with compromised Chk1 activity were used in combination with genomic stress, induced by UV, and DNA-associated proteomes were analyzed using 2-DE/MS proteomics and Western-blot analysis. Only one protein, the histone chaperone nucelophosmin, was altered consistently in line with changes in chromatin-associated Chk1 and increased in response to DNA damage. Purified Chk1 and NPM were shown to interact in vitro and strong in vivo interactions were implied from immunoprecipitation analysis of chromatin extracts. During chromatin immunoprecipitation, coassociation of the major cell cycle regulator proteins p53 and CDC25A with both Chk1 and NPM suggests that these proteins are components of complex interaction networks that operate to regulate cell proliferation and apoptosis in vertebrate cells.

No abstract