Establishment of expression-state boundaries by Rif1 and Taz1 in fission yeast

The Shelterin component Rif1 has emerged as a global regulator of the replication-timing program in all eukaryotes examined to date, possibly by modulating the 3D-organization of the genome. In fission yeast a second Shelterin component, Taz1, might share similar functions. Here, we identified unexpected properties for Rif1 and Taz1 by conducting high-throughput genetic screens designed to identify cis- and trans-acting factors capable of creating heterochromatin–euchromatin boundaries in fission yeast. The preponderance of cis-acting elements identified in the screens originated from genomic loci bound by Taz1 and associated with origins of replication whose firing is repressed by Taz1 and Rif1. Boundary formation and gene silencing by these elements required Taz1 and Rif1 and coincided with altered replication timing in the region. Thus, small chromosomal elements sensitive to Taz1 and Rif1 (STAR) could simultaneously regulate gene expression and DNA replication over a large domain, at the edge of which they established a heterochromatin–euchromatin boundary. Taz1, Rif1, and Rif1-associated protein phosphatases Sds21 and Dis2 were each sufficient to establish a boundary when tethered to DNA. Moreover, efficient boundary formation required the amino-terminal domain of the Mcm4 replicative helicase onto which the antagonistic activities of the replication-promoting Dbf4-dependent kinase and Rif1-recruited phosphatases are believed to converge to control replication origin firing. Altogether these observations provide an insight into a coordinated control of DNA replication and organization of the genome into expression domains

Evaluation of complex physical therapy for lymphedema of the unilateral lower limbs

We evaluated the effectiveness of the complex physical therapy (CPT) for lymphedema of the unilateral lower limbs of eleven patients who had been admitted to Tokushima Rehabilitation Hospital. Ten patients were of secondary lymphedema, nine of which were after treatment of uterine cancer and one was of primary lymphedema. Our CPT consited of skin care, manual lymph drainage (MLD), compression therapy with elastic bandages or elastic stockings, and exercise therapy under compression. MLD functionally operates to enhance the lymph drainage more proximally in both contralateral and ipsilateral truncal quadrants of the torso, then in the proximal limb, and only thereafter from the distal to proximal portion of the edematous extremity. Swelling ratio of all patients on admission was 26.9± 11.8% and that at discharge was 16.8±9.4%. Edema reduction ratio (ERR) of the entire patients was 41.5± 16.5%, and 81.8% of cases were recognized as effective, in which ERR showed more than 30% at discharge. In a consensus document about the diagnosis and treatment of peripheral lymphedema in 1995, the International Society of Lymphology Executive Committee reported that most operations designed to alleviate peripheral lymphedema have not as yet been perfected or usually are still inferior to combined physiotherapy. At present lymphedema should be accurately diagnosed in the early stage and be treated with CPT correctly by clinicians who understand lymphedema thoroughly and are well trained

Regulation of DNA Replication Timing on Human Chromosome by a Cell-Type Specific DNA Binding Protein SATB1

Background: Replication timing of metazoan DNA during S-phase may be determined by many factors including chromosome structures, nuclear positioning, patterns of histone modifications, and transcriptional activity. It may be determined by Mb-domain structures, termed as ‘‘replication domains’’, and recent findings indicate that replication timing is under developmental and cell type-specific regulation. Methodology/Principal Findings: We examined replication timing on the human 5q23/31 3.5-Mb segment in T cells and non-T cells. We used two independent methods to determine replication timing. One is quantification of nascent replicating DNA in cell cycle-fractionated stage-specific S phase populations. The other is FISH analyses of replication foci. Although the locations of early- and late-replicating domains were common between the two cell lines, the timing transition region (TTR) between early and late domains were offset by 200-kb. We show that Special AT-rich sequence Binding protein 1 (SATB1), specifically expressed in T-cells, binds to the early domain immediately adjacent to TTR and delays the replication timing of the TTR. Measurement of the chromosome copy number along the TTR during synchronized S phase suggests that the fork movement may be slowed down by SATB1. Conclusions: Our results reveal a novel role of SATB1 in cell type-specific regulation of replication timing along the chromosome

Development of Amylose- and β-Cyclodextrin-Based Chiral Fluorescent Sensors Bearing Terthienyl Pendants

Phenylcarbamate derivatives of amylose and β-cyclodextrin show excellent chiral recognition when used as chiral stationary phases (CSPs) for high-performance liquid chromatography. To open up new possibilities of carbohydrate-based materials, we developed chiral fluorescent sensors based on amylose and β-cyclodextrin (Am-1b and CyD-1b, respectively) by attaching fluorescent π-conjugated units on their side chains. Their recognition abilities toward chiral analytes containing a nitrophenyl unit were evaluated by measuring the enantioselective fluorescence quenching behavior. Both sensors showed the same degree of enantioselective fluorescence response for various aromatic nitro compounds. However, in some cases, their enantioselectivities were different depending on the analytes. The difference in the chiral recognition abilities between Am-1b and CyD-1b seems to be based on the structural difference of their inherent backbones, that is, the one-handed helical structure and cyclic structure, respectively. The study on the resolution ability of the Am-1b-based CSP revealed that the terthienyl-based pendant of Am-1b provides not only a fluorescent functionality but also a different chiral recognition site from that of amylose tris(phenylcarbamate)

Chromatin immunoprecipitation (ChIP) assays of SATB1 binding.

<p><b>A.</b> Locations of primers (a–e) used for ChIP assays. <b>B.</b> ChIP analyses were carried out by using anti-mouse SATB1 antibody (left panel) or purified mouse IgG1 control antibody (central panel) jn HeLaS3 cells stably expressing SATB1. Chromain-immunoprecipitated DNA was purified by MinElute (QIAGEN) and used for quantitative PCR. Error bars represent the mean and standard deviations based on four independent experiments. Relative ratio (SATB1/control) is shown as SATB1-specific binding (right panel).</p

Effect of SATB1 expression on replication timing at TTR: suppression of SATB1 expression in Jurkat cells.

<p><b>A.</b> The procedure for repression of SATB1 expression in Jurkat. <b>B.</b> Whole cell extracts were examined by western blotting using anti-SATB1 antibody. Lane 1, untransfected Jurkat; lane 2, Jurkat transfected with pRS vector; lane 3 and 4, Jurkat transfected with pRS-SATB1-shRNA1 and with pRS-SATB1-shRNA1+ pRS-SATB1-shRNA2, respectively. Cells were harvested at 72 hr after transfection. <b>C.</b> Replication timing was determined by FISH across the TTR. Only the data at the Probe 4 are shown. Replication timing in the transition region changed from late (Jurkat) to early (SATB1-depleted Jurkat) (indicated by the arrows). At least 200 BrdU-positive nuclei (S-phase) were counted.</p

Analyses of replication timing by FISH.

<p><b>A.</b> Hybridization signals of replicating cells. SS, singlet-singlet: SD, singlet-doublet; DD, doublet-doublet. <b>B.</b> Replication timing analyzed by FISH at 5q23/31. Locations of DNA probes derived from 5q23/31used in this study are shown at the top. Human BAC clones were purchased from Invitrogen. A cosmid clone on the chromosome 12, cCl12–140, was kindly provided by Dr. Okumura (Nogami et al, 2000), and was used as a control for early replication. At least 200 BrdU-positive nuclei (S-phase) were counted for each probe. The signal patterns were classified into SS, SD, or DD. On the haploid segment of HL-60 (probes 2∼6), two signal patterns, singlet (S) and doublet (D), were observed. Replication timing of the human 5q23/31, estimated from the FISH analyses, is consistent with that of the cell cycle fractionation studies (see text for details). E, E/M M/L and L stand for early-, early/mid-, mid/late- or late-replicating, respectively.</p

Replication timing of the human 5q23/31.

<p><b>A.</b> Experimental strategy for determination of replication timing. Asynchronously replicating cells were labeled with BrdU and sorted by FACS into six fractions (G1, S1–4, G2/M) on the basis of DNA content. Genomic DNA from cells in each fraction was extracted, and newly replicated DNA was immunoprecipitated with anti-BrdU antibody. Semi-quantitative PCR was carried out using the newly replicated DNA as template. Relative band intensity was quantified. The values in each fraction were normalized by the levels of BrdU-labeled mitochondrial DNA (mtDNA; replicated equally throughout the cell cycle) used as an internal control for the recovery of DNA in each sample. <b>B.</b> 40,000 cells (Jurkat and HL-60) sorted (upper) and collected on the basis of DNA content (G1, S1–4, G2/M) were stained with PI, and analyzed by FACS (lower). <b>C.</b> Validation of cell cycle fractionation. The known early (PGK1) or late (F9) replicating region is enriched in appropriate fractions in comparison with the level of mtDNA in HL-60. <b>D.</b> DNA replication timing on the human chromosome 5q23/31 region (3.5 Mb) containing the cytokine cluster region in Jurkat (T cell) and HL-60 (non T cell). The 2.2 Mb segment containing the cytokine cluster (130.3–132.5) replicates in G1 or early in the S-phase (S1 and S2), whereas the 0.9 Mb segment distal to the cluster and proximal to the centromere replicates late in the S phase (S3, S4 and G2). The mean locations of the timing transition region (TTR) are located at around 130.15–130.25 (yellow box) in Jurkat (TTR-J) and at around 129.95–130.05 (green box) in HL-60 (TTR-H), and are offset by 180 kb in the two cell types. The left boundary of early replicating region coincided with the transition of chromosomal synteny (see <b><a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0042375#pone.0042375.s002" target="_blank">Fig. S2A</a></b>). <b>E.</b> The results of replication timing assays with fractionated cells are shown for each location along the 3.5 Mb human chromosome. The locations of the 9 primers used are indicated along the 5q23/31 region shown to the right of the panels. Small red solid boxes show the peak timing fraction for each probe, and large red dotted boxes show the maximum timing transition segments for Jurkat (129.98–130.22) and HL-60 (129.52–130.16).</p