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Double-strand breaks activate the ataxia telangiectasia mutated (ATM) kinase, which promotes the accumulation of DNA damage factors in the chromatin surrounding the break. The functional significance of the resulting DNA [...]

To link to full-text access for this article, visit this link: http://dx.doi.org/10.1016/j.cell.2008.03.004 Byline: R. Ileng Kumaran (1), Rajika Thakar (1), David L. Spector (1) Abstract: The mammalian cell nucleus provides a landscape where genes are regulated through their organization and association with freely diffusing proteins and nuclear domains. In many cases, specific genes are highly dynamic, and the principles governing their movements and interchromosomal interactions are currently under intensive study. Recent investigations have implicated actin and myosin in chromatin dynamics and gene expression. Here, we discuss our current understanding of the dynamics of the interphase genome and how it impacts nuclear organization and gene activity. Author Affiliation: (1) Cold Spring Harbor Laboratory, One Bungtown Road, Cold Spring Harbor, NY 11724, USA

A report reveals that PIAS1 confers DNA-binding specificity on the Msx1homeoprotein by regulating its subnuclear localization and proximity to target genes. It is shown that PIAS1 is required for the appropriate localization and retention of Msx1 at the nuclear periphery in myoblast cells.

CTN-RNA, a mouse tissue-specific ~8 kb nuclear-retained poly(A)(super +) RNA that regulated the level of its protein-coding partner was identified. Findings revealed a role of the cell nucleus in harboring RNA molecules that were not immediately needed to produce proteins but whose cytoplasmic presence was required upon physiologic stress, thus highlighting an important paradigm for the role of a nuclear-retained stable RNA transcript in regulating gene expression.

Research has been conducted on the histone H3 Lys-9 methylation. The ability of this methylation to initiate and propagate X inactivation has been investigated and the results are reported.

Pre-mRNA splicing involves several essential splicing factors, and most splicing factors within the mammalian cell nucleus, accumulate in distinct domains known as speckles. A study of the dynamic aspects of nuclear organization, aimed to visualize pre-mRNA splicing factors in living cells, through the fusion of green fluorescent protein (GFP) to the amino terminus of the SF2/ASF splicing factor. Speckles were shown to specifically response to activated genes close by. This was dependent on RNA polymerase II transcription.

Salt and detergent extraction, suppression of RNA polymerase II transcription and DNase I digestion result in stable poly(A)+ RNA elements in the nucleus of mammalian cells. The stable RNA elements regroup into small and large chromatin granule clusters containing pre-mRNA splicing factors. The poly(A)+RNA transportation to the nuclear pore complexes occurs through a controlled pathway.

A study analyzes the distribution of viral RNA within a nucleus and the response of the host cell RNA processing apparatus to the introduction of new active transcription sites. Meanwhile, Ad2 infection is utilized as a model system to prove that the spatial-temporal relationship between transcripts and pre-mRNA splicing in infected cell nuclei is very close. This is due to a presence of localization and the shuttling of splicing factors to new sites of active transcription. Thus, there is the possible existence of a recruiting mechanism which enables the cell to coordinate these events.

Temporal and spatial patterns of DNA replication in mammalian cells were investigated using fluorescence microscopy, confocal laser scanning microscopy and immunoelectron microscopy. Results indicate that there are five patterns of replication occuring at specific sites in the nucleus and at specific periods in the S-phase of the cell cycle. Further, it was shown that alpha-satellite DNA sequences replicate at the middle of the S-phase. The replication of specific DNA sequences were likewise shown to follow specific temporal and spatial patterns.

An in situ hybridization technique using oligonucleotide probes analyzed the localization of U1 and U2 small nuclear proteins (ssRNAs). These ssRNAs were in a speckled distribution in three to four foci in HeLa cell nuclei but were concentrated in nuclear speckles without foci in cells of defined passage. The localization of thesse ribonucleoprotein particles in nuclear regions indicated the involvement of these sites in pre-mRNA splicing.

A large portion of the eukaryotic genome is transcribed as noncoding RNAs (ncRNAs), which play a central role in regulating gene expression at multiple levels. An overview of recent advances in the identification and function of eukaryotic ncRNAs in chromatin organization, gene expression, and disease etiology is presented.

To link to full-text access for this article, visit this link: http://dx.doi.org/10.1016/j.cell.2006.11.026 Byline: David L. Spector

An inducible system to visualize gene expression at the levels of DNA, RNA and protein in living cells is developed. Using this system, changes are correlated in chromatin structure with the progression of transcriptional activation that allows obtaining a real-time integrative view of gene expression.

Research demonstrates that the stability of the senescent state occurs through the tumor suppressor Rb-directed process involving heterochromatin alterations and silencing of E2F target genes. Data indicate distinct heterochromatic structure accumulating in senescent human fibroblasts forming the senescence-associated heterochromatic foci.

The current state of knowledge with regard to the organization of chromosomes within the nucleus and the positioning of active versus inactive genes are described. The current understanding of the distribution and the dynamics of RNA polymerase II transcription factors are also discussed.