Telomeres form the ends of linear chromosomes and protect these ends from being recognized as DNA doublestrand breaks. Telomeric sequences are maintained in most cells by telomerase, a reverse transcriptase that adds TG-rich repeats to chromosome ends. In budding yeast, telomeres are organized in clusters at the nuclear periphery by interactions that depend on components of silent chromatin and the telomerase-binding factor yeast Ku (yKu). In this study, we examined whether the subnuclear localization of telomeres affects end maintenance. A telomere anchoring pathway involving the catalytic yeast telomerase subunits Est2, Est1, and Tlc1 is shown to be necessary for the perinuclear anchoring activity of Yku80 during S phase. Additionally, we identify the conserved Sad1-UNC-84 (SUN) domain protein Mps3 as the principal membrane anchor for this pathway. Impaired interference with Mps3 anchoring through overexpression of the Mps3 N terminus in a tel1 deletion background led to a senescence phenotype and to deleterious levels of subtelomeric Y9 recombination. This suggests that telomere binding to the nuclear envelope helps protect telomeric repeats from recombination. Our results provide an example of a specialized structure that requires proper spatiotemporal localization to fulfill its biological role, and identifies a novel pathway of telomere protection.[Keywords: Telomere protection; telomerase; nuclear envelope; Sad1/UNC-84 (SUN) homology domain; Mps3; nuclear organization; ATM homolog Tel1] Supplemental material is available at http://www.genesdev.org.

ISWI proteins form the catalytic core of a subset of ATP-dependent chromatin remodeling activities in eukaryotes from yeast to man. Many of these complexes have been found to reposition nucleosomes but with different directionalities. We find that the yeast Isw1a, Isw2, and Chd1 enzymes preferentially move nucleosomes toward more central locations on short DNA fragments whereas Isw1b does not. Importantly, the inherent positioning properties of the DNA play an important role in determining where nucleosomes are relocated to by all of these enzymes. However, a key difference is that the Isw1a, Isw2, and Chd1 enzymes are unable to move nucleosomes to positions closer than 15 bp from a DNA end, whereas Isw1b can. We also find that there is a correlation between the inability of enzymes to move nucleosomes close to DNA ends and the preferential binding to nucleosomes bearing linker DNA. These observations suggest that the accessibility of linker DNA together with the positioning properties of the underlying DNA play important roles in determining the outcome of remodeling by these enzymes.Nucleosomes are the fundamental subunits of eukaryotic chromatin. The assembly of DNA into chromatin fulfils important functions in both packaging DNA into nuclei and regulating access to genetic information. Crystallographic structures of nucleosomes provide a detailed picture of how DNA is bound to the surface of the histone octamer (1). However, in solution nucleosomes exhibit dynamic properties that include the ability to spontaneously relocate to different positions on DNA fragments (2-4). The positioning of nucleosomes has the potential to positively or negatively regulate access to DNA and consequently all genetic processes.In addition to undergoing spontaneous thermal movements, nucleosomes can be repositioned by ATP-dependent chromatin remodeling enzymes. These enzymes consist of a catalytic subunit with a region of homology to the yeast Snf2 protein and a variable number of accessory subunits. Snf2 family proteins fall into distinct subfamilies. For example the ISWI subfamily is named after its founding member, the Drosophila ISWI protein (5). The ISWI protein was subsequently found to be a component of several distinct protein complexes that have the ability to alter chromatin structure in an ATP-dependent reaction (6). Related ISWI complexes have since been identified in a broad spectrum of eukaryotes from yeast to humans (7). These complexes have been found to function in a range of processes ranging from the regulation of transcription and DNA replication to the maintenance of chromatin structure (7

The Snf2 family represents a functionally diverse class of ATPase sharing the ability to modify DNA structure. Here, we use a magnetic trap and an atomic force microscope to monitor the activity of a member of this class: the RSC complex. This enzyme caused transient shortenings in DNA length involving translocation of typically 400 bp within 2 s, resulting in the formation of a loop whose size depended on both the force applied to the DNA and the ATP concentration. The majority of loops then decrease in size within a time similar to that with which they are formed, suggesting that the motor has the ability to reverse its direction. Loop formation was also associated with the generation of negative DNA supercoils. These observations support the idea that the ATPase motors of the Snf2 family of proteins act as DNA translocases specialized to generate transient distortions in DNA structure.

ATP-dependent chromatin remodeling activities function to manipulate chromatin structure during gene regulation. One of the ways in which they do this is by altering the positions of nucleosomes along DNA. Here we provide support for the ability of these complexes to move nucleosomes into positions in which DNA is unraveled from one edge. This is expected to result in the loss of histone-DNA contacts that are important for retention of one H2A/H2B dimer within the nucleosome. Consistent with this we find that several chromatin remodeling complexes are capable of catalyzing the exchange of H2A/H2B dimers between chromatin fragments in an ATP-dependent reaction. This provides eukaryotes with additional means by which they may manipulate chromatin structure.

Alteration of chromatin structure by chromatin modifying and remodelling activities is a key stage in the regulation of many nuclear processes. These activities are frequently interlinked, and many chromatin remodelling enzymes contain motifs that recognise modified histones. Here we adopt a peptide ligation strategy to generate specifically modified chromatin templates and used these to study the interaction of the Chd1, Isw2 and RSC remodelling complexes with differentially acetylated nucleosomes. Specific patterns of histone acetylation are found to alter the rate of chromatin remodelling in different ways. For example, histone H3 lysine 14 acetylation acts to increase recruitment of the RSC complex to nucleosomes. However, histone H4 tetra-acetylation alters the spectrum of remodelled products generated by increasing octamer transfer in trans. In contrast, histone H4 tetra-acetylation was also found to reduce the activity of the Chd1 and Isw2 remodelling enzymes by reducing catalytic turnover without affecting recruitment. These observations illustrate a range of different means by which modifications to histones can influence the action of remodelling enzymes.

Nucleosomes fulfill the apparently conflicting roles of compacting DNA within eukaryotic genomes while permitting access to regulatory factors. Central to this is their ability to stably associate with DNA while retaining the ability to undergo rearrangements that increase access to the underlying DNA. Here, we have studied different aspects of nucleosome dynamics including nucleosome sliding, histone dimer exchange, and DNA wrapping within nucleosomes. We find that alterations to histone proteins, especially the histone tails and vicinity of the histone H3 ␣N helix, can affect these processes differently, suggesting that they are mechanistically distinct. This raises the possibility that modifications to histone proteins may provide a means of fine-tuning specific aspects of the dynamic properties of nucleosomes to the context in which they are located.The organization of DNA into chromatin creates the functional template for any process requiring access to the genetic information such as transcription, DNA replication, recombination, and repair. The basic repeating unit of chromatin is the nucleosome core particle, which consists of 147 bp of DNA wrapped almost twice around an octamer of histone H2A, H2B, H3, and H4 proteins (12, 32). Chromatin packaging tends to restrict access to the underlying DNA, meaning that regulation of chromatin structure is a key feature of many genetic processes.Eukaryotes have adopted an assortment of different strategies by which they can manipulate chromatin structure. One means involves the posttranslational modification of histone proteins by, for example, acetylation, methylation, and phosphorylation. These are often correlated with particular chromatin states, and the levels of many of these modifications are observed to change during the course of gene regulation (38). To date, the majority of the best-characterized modifications occur in the N-terminal extensions of the histone proteins. These N-terminal tails extend beyond the globular core of the nucleosome and do not take up distinct conformations in highresolution crystal structures (12, 32). Modification of residues within the tail domains has been shown to affect chromatin structure by generating epitopes for the recruitment of external chromatin binding proteins. These include the chromodomains of HP1 and PRC1, which interact specifically with histones methylated at histone H3 lysine 9 and 27, respectively (4, 14, 27), and bromodomain-containing proteins which bind acetylated histone tails (26,42).An alternative means by which histone tails can influence chromatin structure is through direct alteration of the dynamic properties of nucleosomes. Chromatin is not a static entity but can undergo an assortment of dynamic alterations. Arrays of nucleosomes spontaneously condense to form chromatin fibers (5, 9, 57), the positions of nucleosomes on DNA fragments can change as a result of thermally driven nucleosome sliding (16,37), and the outer turns of DNA are prone to transient dissociation from the histone octamer via a ...

Previous studies have identified sin mutations that alleviate the requirement for the yeast SWI/SNF chromatin remodelling complex, which include point changes in the yeast genes encoding core histones. Here we characterise the biochemical properties of nucleosomes bearing these mutations. We find that sin mutant nucleosomes have a high inherent thermal mobility. As the SWI/SNF complex can alter nucleosome positioning, the higher mobility of sin mutant nucleosomes provides a means by which sin mutations may substitute for SWI/SNF function. The location of sin mutations also provides a new opportunity for insights into the mechanism for nucleosome mobilisation. We find that both mutations altering histone DNA contacts at the nucleosome dyad and mutations in the dimertetramer interface influence nucleosome mobility. Furthermore, incorporation of H2A.Z into nucleosomes, which also alters dimer-tetramer interactions, affects nucleosome mobility. Thus, variation of histone sequence or subtype provides a means by which eukaryotes may regulate access to chromatin through alterations to nucleosome mobility. The EMBO Journal (2004) IntroductionNucleosomes are the universal molecular packaging state of DNA in nuclei. They are responsible for compacting eukaryotic genomes to allow them to fit into the limited volume of the cell nucleus. The nucleosome core particle and an additional variable length of unbound linker DNA together comprise the fundamental repeating unit of chromatin (Kornberg, 1974). The nucleosome core particle consists of a core of eight polypeptides, two copies each of the four highly conserved histone proteins H2A, H2B, H3 and H4, around which 147 bp of DNA are wrapped in 1.7 superhelical turns (Luger et al, 1997). H3 and H4 associate to form histone fold dimers as do histones H2A and H2B. Each histone fold dimer associates to form an octameric spiral with dyad symmetry.The H2AÀH2B histone fold dimer units are less stably associated within the octamer than the two H3ÀH4 histone fold dimers (Eickbush and Moudrianakis, 1978). A number of extra protein elements decorate the regular spiral of histone fold dimers, including unstructured 'tails' that extend outside the DNA superhelix, the additional H3 aN helix that organises the most exterior turn of bound DNA, a structured H2A C-terminal extension that passes over the top face of the histone octamer, and an H2B aC helix lying above the histone dimer (Luger and Richmond, 1998).A consequence of the organisation of DNA into nucleosomes is that all genetic processes must contend with a chromatin substrate. In the case of gene regulation, wrapping into nucleosomes makes DNA sequences differentially accessible to transcription factors (Owen-Hughes and Workman, 1994). Accessibility of a particular site depends on the absolute 'position' of the nucleosome (Polach and Widom, 1995), and many cases have been recognised in which nucleosome positioning affects genomic accessibility (Simpson, 1990;Lomvardas and Thanos, 2002;Miller and Widom, 2003). In this way, nucleoso...

ATP-dependent chromatin remodelling proteins represent a diverse family of proteins that share ATPase domains that are adapted to regulate protein–DNA interactions. Here, we present structures of the Saccharomyces cerevisiae Chd1 protein engaged with nucleosomes in the presence of the transition state mimic ADP-beryllium fluoride. The path of DNA strands through the ATPase domains indicates the presence of contacts conserved with single strand translocases and additional contacts with both strands that are unique to Snf2 related proteins. The structure provides connectivity between rearrangement of ATPase lobes to a closed, nucleotide bound state and the sensing of linker DNA. Two turns of linker DNA are prised off the surface of the histone octamer as a result of Chd1 binding, and both the histone H3 tail and ubiquitin conjugated to lysine 120 are re-orientated towards the unravelled DNA. This indicates how changes to nucleosome structure can alter the way in which histone epitopes are presented.