Chromosomes and Expression Mechanisms

Introduction Whether one considers a single cell or a multicellular organism, a complex and precisely coordinated series of regulatory events and communications is required to ensure its proper configuration and function. One of the major goals in biology is to understand how cells differentiate into specific types to perform their roles in vivo. Genome sequencing projects have produced enormous amounts of data that are beginning to reveal the blue print of body plans for various organisms. Despite this wealth of new information, we are still far from understanding how cells differentiate. This is, in part, because we are not yet able to fully appreciate how this genetic information is being read by the transcription machineries. It is widely accepted that specific gene expression patterns are responsible for differentiation and maintenance of specific cell types, with mistakes in these regulatory steps often leading to developmental defects and the onset of cancers. Therefore, understanding the mechanisms of transcriptional control is a necessary prerequisite to achieve this major goal in biology. To this end, we need to know more about the substrate of transcription (chromatin), as well as the effectors of transcription (transcription factors). The theme of this issue of Current Opinion in Genetics & Development is the mechanism of transcriptional regulation, with an emphasis on latest topics in this rapidly moving area of research. Because chromatin structure deeply affects transcription at multiple stages, a significant portion of this issue is devoted to the mechanisms related to chromatin regulation

ISWI, a member of the SWl2/SNF2 ATPase family, encodes the 140 kDa subunit of the nucleosome remodeling factor

AbstractThe generation of an accessible heat shock promoter in chromatin in vitro requires the concerted action of the GAGA transcription factor and NURF, an ATP-dependent nucleosome remodeling factor. NURF is composed of four subunits and is biochemically distinct from the SWI2/SNF2 multiprotein complex, a transcriptional activator that also appears to alter nucleosome structure. We have obtained protein microsequence and immunological evidence identifying the 140 kDa subunit of NURF as ISWI, previously of unknown function but highly related to SWI2/SNF2 only in the ATPase domain. The ISWI protein is localized to the cell nucleus and is expressed throughout Drosophila development at levels as high as 100,000 molecules/cell. The convergence of biochemical and genetic studies on ISWI and SWI2/SNF2 underscores these ATPases and their close relatives as key components of independent systems for chromatin remodeling

Novel features of nuclear forces and shell evolution in exotic nuclei

Novel simple properties of the monopole component of the effective nucleon-nucleon interaction are presented, leading to the so-called monopole-based universal interaction. Shell structures are shown to change as functions of $N$ and $Z$ consistently with experiments. Some key cases of this shell evolution are discussed, clarifying the effects of central and tensor forces. The validity of the present tensor force is examined in terms of the low-momentum interaction V$_{low k}$ and the Q$_{box}$ formalism.Comment: 4 pages, 4 figure

Yeast Isw1p forms two separable complexes in vivo - Supplementary Materials Only

There are several classes of ATP-dependent chromatin remodeling complexes, which modulate the structure of chromatin to regulate a variety of cellular processes. The budding yeast, Saccharomyces cerevisiae, encodes two ATPases of the ISWI class, Isw1p and Isw2p. Previously Isw1p was shown to copurify with three other proteins. Here we identify these associated proteins and show that Isw1p forms two separable complexes in vivo (designated Isw1a and Isw1b). Biochemical assays revealed that while both have equivalent nucleosome-stimulated ATPase activities, Isw1a and Isw1b differ in their abilities to bind to DNA and nucleosomal substrates, which possibly accounts for differences in specific activities in nucleosomal spacing and sliding. In vivo, the two Isw1 complexes have overlapping functions in transcriptional regulation of some genes yet distinct functions at others. In addition, these complexes show different contributions to cell growth at elevated temperatures

No Origin, No Problem for Yeast DNA Replication

Eukaryotic DNA replication initiates from multiple sites on each chromosome called replication origins (origins). In the budding yeast Saccharomyces cerevisiae, origins are defined at discrete sites. Regular spacing and diverse firing characteristics of origins are thought to be required for efficient completion of replication, especially in the presence of replication stress. However, a S. cerevisiae chromosome III harboring multiple origin deletions has been reported to replicate relatively normally, and yet how an origin-deficient chromosome could accomplish successful replication remains unknown. To address this issue, we deleted seven well-characterized origins from chromosome VI, and found that these deletions do not cause gross growth defects even in the presence of replication inhibitors. We demonstrated that the origin deletions do cause a strong decrease in the binding of the origin recognition complex. Unexpectedly, replication profiling of this chromosome showed that DNA replication initiates from non-canonical loci around deleted origins in yeast. These results suggest that replication initiation can be unexpectedly flexible in this organism

ATP-dependent chromatin remodeling shapes the DNA replication landscape.

The eukaryotic DNA replication machinery must traverse every nucleosome in the genome during S phase. As nucleosomes are generally inhibitory to DNA-dependent processes, chromatin structure must undergo extensive reorganization to facilitate DNA synthesis. However, the identity of chromatin-remodeling factors involved in replication and how they affect DNA synthesis is largely unknown. Here we show that two highly conserved ATP-dependent chromatin-remodeling complexes in Saccharomyces cerevisiae, Isw2 and Ino80, function in parallel to promote replication fork progression. As a result, Isw2 and Ino80 have especially important roles for replication of late-replicating regions during periods of replication stress. Both Isw2 and Ino80 complexes are enriched at sites of replication, suggesting that these complexes act directly to promote fork progression. These findings identify ATP-dependent chromatin-remodeling complexes that promote DNA replication and define a specific stage of replication that requires remodeling for normal function

The conserved HDAC Rpd3 drives transcriptional quiescence in S. cerevisiae

Quiescence is a ubiquitous cell cycle stage conserved from microbes through humans and is essential to normal cellular function and response to changing environmental conditions. We recently reported a massive repressive event associated with quiescence in Saccharomyces cerevisiae, where Rpd3 establishes repressive chromatin structure that drives transcriptional shutoff [6]. Here, we describe in detail the experimental procedures, data collection, and data analysis related to our characterization of transcriptional quiescence in budding yeast (GEO: GSE67151). Our results provide a bona fide molecular event driven by widespread changes in chromatin structure through action of Rpd3 that distinguishes quiescence as a unique cell cycle stage in S. cerevisiae