The Ultimate Guide to Tajima DG ML by Pulse 14 18: Everything You Need to Know

Some researchers have suggested that differences in these hemodynamic responses might be used to differentiate between CTEPH, characterized by a proximal macroscopic obstruction and pulmonary arterial hypertension (PAH), in which obstruction is limited to the distal pulmonary vessels with a diameter of less than 1 mm. This point remains controversial. Results from previous studies revealed that an early pulse wave reflection in CTEPH was the result of increased stiffness of the proximal PA [14]. This anticipated wave reflection, which normally reaches the pulmonary valve during diastole, crosses the forward pulse wave at systole; this results in an overall increase in pulse pressure due to the summation of both backward and forward waves. The overall impact of this summation would be decreased blood flow and a net increase in RV workload [14,15,16,17]. However, these results were not entirely confirmed by results from another study, in which a high-fidelity transducer catheter was used to generate pressure measurements in both CTEPH and PAH patients with the same levels of mPAP [18]. While different abnormal pressure-wave reflections were detected when comparing both groups of patients, with results indicating increases in anticipated wave reflection specifically in CTEPH patients, these differences were not sufficient to discriminate between these two diseases. Similarly, results from large animal model studies revealed that pulse pressures and the pulsatile component of RV hydraulic load increased in response to proximal obstruction accompanied by decreases in PVC [19]. However, this model focuses on acute obstruction and thus does not take into account the structural alterations encountered in response to distended proximal circulation that typically results in PH associated with distal obstruction.

Histone H3 DEVELOPMENTAL BIOLOGY Distribution of methylated H3 on polytene chromosomesIf the H3 methylation activity associated with E(z) serves as a chromatin mark for PcG silencing, correspondingly methylated H3 should be found at PcG sites on polytene chromosomes. When chromosome spreads were double stained with an antibody directed against dimethylated H3 lysine 9 (anti-me2K9) together with anti-Psc to label PcG sites, no correspondence between the two was found. The anti-me2K9 antibody stains the chromocenter very strongly, as well as a very few euchromatic sites and telomeres. Telomeres are in fact the only places where Psc and me2K9 H3 are found together, consistent with reports that heterochromatin protein Hp1 and Psc coexist at subtelomeric sites. In contrast, when anti-me3K9 was used to stain polytene chromosomes, almost perfect colocalization was obtained of me3K9 and Psc at euchromatic sites. The relative intensity of the two signals varies from site to site, but with very few exceptions the two signals colocalize. In particular, both the BX-C locus and ANT-C locus, prime sites of action of PcG proteins, stain strongly with both antibodies. Clear exceptions are the chromocenter and most of chromosome 4, where the anti-me3K9 antibody stains powerfully while Psc is not found; a few rare euchromatic sites and some telomeres, where the Psc signal is not always present. Conversely, a few sites give a strong Psc signal but only a weak me3K9 signal. Two such sites are 2D, near the tip of the X chromosome, and 49F, on chromosome 2R. The first is the locus of polyhomeotic (ph); the second contains the divergently transcribed Psc and Su(z)2 genes. All three genes are components of PcG complexes, and ph and Psc have been shown to be themselves targets of PcG regulation (Czermin, 2002).Since the me2K9 and me3K9 antibodies have nonoverlapping specificities at least in vitro for the me2K9 and me3K9 peptides, respectively, it is concluded that the cytological sites typically considered heterochromatin-like (chromocenter, chromosome 4, and telomeric regions) contain both me2K9 and me3K9 H3. While the me3K9 antibody may recognize weakly the methylated K27 peptide, the contribution of this interaction to the polytene staining cannot be evaluated. To test whether the methylation detected by the anti-me3K9 antibody is dependent on E(z) function, polytene chromosomes were prepared from larvae homozygous for the E(z)S2 temperature-sensitive mutation and raised at 29C after hatching of the larvae. Inactivation of the E(z)S2 product causes loss of binding of PcG proteins from most but not all sites, compared to wild-type chromosomes. Inactivation appears to occur to different extents in different larvae or even in different nuclei from the same gland, judging from the distribution of anti-me3K9 or anti-Psc antibody staining. In general, the euchromatic bands of anti-me3K9 staining are lost well before the Psc staining. A few Psc sites remain strong in the absence of detectable me3K9 staining. Methylation at a few euchromatic sites persists; one in particular is region 31 of chromosome 2L, containing multiple bands that bind the heterochromatin protein Hp1. Staining of the chromocenter and of chromosome 4 also persists, but it is difficult to conclude unambiguously whether it is affected by the E(z)S2 mutation since the loss of function is often incomplete. Heterochromatic staining is lost in some nuclei but whether it is artifactual in these dying larvae is uncertain. Interestingly, staining at telomeres is also lost, often well before the corresponding staining with anti-Psc antibody. These results confirm the conclusion that most of the euchromatic methylation detected by the anti-me3K9 antibody is in fact dependent on E(z) (Czermin, 2002).To distinguish the histone H3 methylation due to Su(var)3-9 and that due to E(z), chromosomes from larvae homozygous for the Su(var)3-906 mutation were stained. Larvae and flies homozygous for this mutation are viable and lack most but not all of the anti-me3K9 staining at the chromocenter while staining of chromosome 4, of the base of chromosome 2R, and of telomeres, as well as euchromatic sites, persists unaffected. Staining with anti-Psc is also normal in these chromosomes (Czermin, 2002).The histone variant H3.3marks active chromatin by replication-independent nucleosome assemblyTwo very similar H3 histones -- differing at only four amino acid positions -- areproduced in Drosophila cells. A mechanism of chromatin regulation is describedwhereby the variant H3.3 histone is deposited at particular loci, including active rDNAarrays. While the major H3 is incorporated strictly during DNA replication,amino acid changes toward H3.3 allow replication-independent (RI) deposition. Incontrast to replication-coupled (RC) deposition, RI deposition does not requirethe N-terminal tail. H3.3 is the exclusive substrate for RI deposition, and itscounterpart is the only substrate retained in yeast. RI substitution of H3.3provides a mechanism for the immediate activation of genes that are silenced byhistone modification. Inheritance of newly deposited nucleosomes may then marksites as active loci (Ahmad, 2002).To monitor histone dynamics in vivo, fusion genes encodingvarious histones and the green fluorescent protein (GFP) were constructed under the control ofheat shock-inducible promoters. These constructs were transfected intoexponentially growing Kc cells and induce. The deposition ofhistone H3-GFP in the nucleus parallels that of nucleotide analog incorporationinto DNA. Localization of histone H3-GFP iscompletely blocked by pretreatment of cells with the DNA replication inhibitoraphidicolin, demonstrating that the deposition of histone H3 is strictlyreplication dependent. Detection of a component of the DNA replicationmachinery, PCNA, also confirms thatdeposition of histone H3-GFP is coupled to DNA replication: PCNA, BrdU, andH3-GFP give similar labeling patterns both in early S phase (when euchromaticDNA is replicating) and in late S phase (when heterochromatic DNA isreplicating). BrdU and H3-GFP closely overlap because both arepresent for the entire 2 hr labeling period. PCNA labeling does not preciselyoverlap, since it provides a 'snapshot' of replication only at the time of fixation. In subsequent labeling experiments, PCNA as used toindicate the cell cycle stage (Ahmad, 2002).Since histone H3 deposition is strictly replication dependent, it was reasoned thatreplication-independent deposition of histone H4 might be accompanied by the deposition of H3variants to form variant nucleosomes. Centromeric histones are thought to beincluded in nucleosomes at centromeres, and it has been demonstrated thatthe Drosophila centromeric H3 variant Cid localizes to centromeres by a replication-independentpathway. Thus, it was expected that some sites showing H4replication-independent deposition would be centromeres. Detection of centromeres inH4GFP-transfected cells demonstrates that four to six of the H4 replication-independent foci wereindeed centromeres, consistent with the assembly of nucleosomescontaining Cid and H4 at these sites. It was reasoned that the remaining H4 sitesmust be incorporating the final histone H3 variant, H3.3. Indeed, expression ofH3.3-GFP in cells demonstrated that this variant does undergo bothreplication-coupled and replication-independent deposition. None of theH3.3-GFP foci coincided with centromeres, showing that centromeres use the Cid histone exclusively (Ahmad, 2002).It was confirmed the H3.3-GFP is tightly bound to chromatin by extracting cellswith 1.5 M salt before fixation. After this treatment, nuclei retain 48% of theH3.3-GFP but only 22% of the H2B-GFP. Such differential extractionis expected from the biochemical properties of these histones,and the proper behavior of GFP-tagged histones has been extensively documented (Ahmad, 2002).To map the locations of the sites in the nucleus where replication-independent deposition of histoneH3.3 and H4 occurs, mitotic figures were examined from cells transfected withhistone-GFP constructs. The G2 phase in Kc cells is 4-6 hr long; thus, mitotic figures with H3-GFP labeling first appear 4-6 hr afterheat-shock induction and show patterns consistent with histone-GFPproduction in late S phase, when heterochromatin is replicating. In contrast, labeled mitotic figures with H3.3-GFP and H4-GFPappear within 2 hr of induction. H4-GFP showed prominentlabeling at a single extended site near the middle of an X chromosome. The pattern of H3.3-GFP is very similar to that of H4-GFP, showing thegreatest labeling over an extended site on the X chromosome and at low levelsspecifically in euchromatin. These cells must have been inthe G2 phase of the cell cycle when histone-GFP was produced. This was confirmedby the presence of H3.3 labeling on mitotic chromosomes that showed noincorporation of pulse-labeled nucleotides and by observing mitoticfigures from aphidicolin-treated cultures that nevertheless displayed H3.3-GFPlabeling. Thus, these mitotic labeling patterns with H3.3-GFP andH4-GFP must have resulted from replication-independent deposition (Ahmad, 2002).The extended appearance and proximal location of the prominent H3.3 and H4 siteon the labeled X chromosome suggested that it coincides with the large rDNA generepeat array on this chromosome. In situ hybridization with probes to the 28SrDNA gene confirmed that this is so. Quantitative measurements ofGFP signal over the rDNA array and over all of the chromosomes indicate that40% of all histone H3.3 in the cell is deposited at the rDNA locus. In Tetrahymena, a histone H3 replacement variant is enriched in thetranscriptionally active macronucleus, suggesting that this Tetrahymena variantpotentiates active chromatin (Allis, 1984). It is presumed that the highintensity of histone H3.3-GFP staining at the rDNA locus in Drosophila is due tothe combination of its densely repeated genes with high transcriptionalactivity (Ahmad, 2002).Notably, labeling with H3.3-GFP and H4-GFP was often observed of only one Xchromosome. This is not due to absence of rDNA from other X chromosomes in thesecells because the detection of 28S rDNA by in situ hybridization confirmed that rDNAarrays are present on each of the three X chromosomes. Other studieshave pointed out that many Drosophila cell lines (including Kc) carry twodistinguishable kinds of X chromosomes: a short one (XS) that resembles thenormal X of flies, and a longer X (XL). Theorigin of XL has been attributed to an expansion of the rDNA locus on thischromosome, presumably as these cells adapted to culture conditions. It was observedthat the rDNA array on XL is always labeled by H3.3-GFP, consistentwith this locus being active in all cells. However, in some experiments,variable numbers of cells had additional labeling on XS chromosomes.To test whether some of this variability between experiments was due todifferences in growth conditions, cells were transfected with the histone H3.3-GFPconstruct and then expression was induced in samples of this culture 16 or 24 hrlater. It was found that many cells from exponentially growing cultures show replication-independentlabeling on both XL and XS chromosomes, while metaphase spreads from the later timepoint, when culture growth had slowed, showed labeling on only the one XL. This change in frequency suggests that the smaller rDNAarrays on XS chromosomes are maintained in a transcriptionally silent state but can be activated (Ahmad, 2002).The silencing of XS rDNA arrays might be due toheterochromatin-mediated silencing. Indeed, staining of metaphase spreads fromcells expressing histone H3.3-GFP for the heterochromatin marker H3di-MethylK9(H3Me) revealed that rDNA arrays labeled by replication-independent deposition of H3.3-GFP aredepleted for H3Me, in spite of being flanked on both sides by heterochromatin. In every XS chromosome where the proximal region waslabeled with H3.3-GFP, a corresponding gap in the H3Me pattern was found. That sites heavily labeled with H3.3-GFP are largely unlabeled withH3Me was confirmed in interphase nuclei. It is concluded that thechromatin state of rDNA arrays can be reversed in response to changes in growthconditions, and H3.3 accumulates de novo at activated genes (Ahmad, 2002).Alternate interpretations of the phylogenetic history of the histone H3 familyhave been proposed. One analysis suggested that a replacement histone H3 variantwas the common ancestor, but other interpretations haveproposed that replacement histones have multiple independent origins. The presence ofparalogous histone H3 genes in many organisms may preclude delineation of whichsequence is ancestral. However, the findings of this study suggest that areplication-independent nucleosome assembly pathway is essential in all cells.This implies that, functionally, a replacement histone H3 has always beenextant. In organisms that encode only one kind of canonical histone H3 proteinthat is used throughout chromatin, it is expected that this H3 variant must undergoboth replication-coupled and replication-independent deposition. Fungal lineages are particularly intriguing in thisregard because all ascomycetes, including laboratory yeasts and molds, carryonly one canonical histone H3. Each of these is identical to animal H3.3 atpositions 89 and 90, and often identical at position 31. Thus, by this criterion, it is proposed thatthe solitary histone H3 proteins in ascomycetes are equivalent to histone H3.3.Indeed, nucleosome assembly activity in the cell cycle gap phases has beendetected in Saccharomyces. These fungi appear tohave lost their ancestral H3, since genomes from the Basidiomycotasister clade have both H3 and H3.3. Histone H2A inSaccharomyces may have an analogous evolutionary history, since it now performsthe functions of the H2A and the H2A.X variants in other organisms. Thus, both histone H3 and H2A in Saccharomyces appear to beevolutionary derivatives of replacement genes (Ahmad, 2002).The lack of an H3 counterpart in yeasts and molds may provide insight intodifferences between simple fungi and complex multicellular eukaryotes inmaintaining silent chromatin. Much of the Saccharomyces genome is continually ina transcriptionally competent state similar to H3.3-containingregions in complex genomes. Perhaps this relative lack of silent chromatinallowed the loss of the strictly replication-coupled histone substrate. Heterochromatic silencingin yeast may be needed only at special sites, such as silent mating type lociand telomeres, where SIR-based silencing has evolved. In multicellulareukaryotes, the need for maintaining most of the genome in a continuously silentstate in differentiated cells may favor maintaining two distinct H3 histones (Ahmad, 2002).Functional anatomy of polycomb and trithorax chromatin landscapes in Drosophila embryosPolycomb group (PcG) and trithorax group (trxG) proteins are conserved chromatin factors that regulate key developmental genes throughout development. In Drosophila, PcG and trxG factors bind to regulatory DNA elements called PcG and trxG response elements (PREs and TREs). Several DNA binding proteins have been suggested to recruit PcG proteins to PREs, but the DNA sequences necessary and sufficient to define PREs are largely unknown. This study used chromatin immunoprecipitation (ChIP) on chip assays to map the chromosomal distribution of Drosophila PcG proteins, the N- and C-terminal fragments of the Trithorax (TRX) protein and four candidate DNA-binding factors for PcG recruitment. In addition, histone modifications associated with PcG-dependent silencing and TRX-mediated activation were mapped. PcG proteins colocalize in large regions that may be defined as polycomb domains and colocalize with recruiters to form several hundreds of putative PREs. Strikingly, the majority of PcG recruiter binding sites are associated with H3K4me3 and not with PcG binding, suggesting that recruiter proteins have a dual function in activation as well as silencing. One major discriminant between activation and silencing is the strong binding of Pleiohomeotic (PHO) to silenced regions, whereas its homolog Pleiohomeotic-like (PHOL) binds preferentially to active promoters. In addition, the C-terminal fragment of TRX (TRX-C) showed high affinity to PcG binding sites, whereas the N-terminal fragment (TRX-N) bound mainly to active promoter regions trimethylated on H3K4. The results indicate that DNA binding proteins serve as platforms to assist PcG and trxG binding. Furthermore, several DNA sequence features discriminate between PcG- and TRX-N-bound regions, indicating that underlying DNA sequence contains critical information to drive PREs and TREs towards silencing or activation (Schuettengruber, 2008; tull text of article).The genome-wide mapping of PcG factors, TRX, their associated histone marks, and potential PcG recruiter proteins in Drosophila embryos revealed several important features. First, similar to the PcG distribution in Drosophila cell lines, PcG proteins strongly colocalize and form large domains containing multiple binding sites. Second, the N-terminal and C-terminal fragments of TRX show different binding affinities to repressed and active chromatin. The N-terminal fragment of TRX has low affinity to PcG binding sites but is strongly bound to thousands of active promoter regions that are trimethylated on H3K4, whereas the C-terminal fragment of TRX only showed high binding affinity to PcG binding sites. Third, the majority of PcG recruiter binding sites are associated with H3K4me3 and TRX-N foci and not with PH binding. The binding ratio between the PHO protein and its homolog PHOL is a major predictive feature of PcG versus TRX recruitment. Finally, supervised and unsupervised sequence analysis methods led to the identification of sequence motifs that discriminate between most of the PcG and TRX binding sites, but these motifs are likely to be working jointly, and none of them seems to drive recruitment by itself (Schuettengruber, 2008).To date, PREs have been only characterized in Drosophila. These elements are not defined by a conserved sequence, but include several conserved motifs, which are recognized by known DNA binding proteins like GAGA factor (GAF), Pipsqueak (PSQ), Pleiohomeotic and Pleiohomeotic-(like) (PHO and PHOL), dorsal switch protein (DSP1), Zeste, Grainyhead (GH), and SP1/KLF. The genomic profiles provide a comprehensive view on the potential role of these factors in the establishment of PcG domains (Schuettengruber, 2008).The presence of PHO at all PREs indicates that PHO is a crucial determinant of PcG-mediated silencing, consistent with earlier analysis on one particular PRE. On the other hand, PHOL and Zeste were bound at a small subset of PREs. Zeste was previously shown to be necessary for maintaining active chromatin states at the Fab-7 (Frontabdominal-7) PRE/TRE. Therefore, Zeste and PHOL may primarily assist transcription rather than PcG-mediated silencing. GAF and DSP1 resemble PHO as they bind to many (albeit less than PHO) PREs as well as to active promoters. Supervised DNA motif analysis indicated a higher density of GAF, DSP1, and PHO binding sites at PREs as compared to other bound regions at non-PH sites. This suggests that cooperative binding of these proteins may provide a platform for PcG protein binding. Moreover, GAF may act by inducing chromatin remodeling to remove nucleosomes, since the regions bound by PcG proteins show a characteristic dip in H3K27me3 signal that has been attributed to the absence of nucleosomes in those regions. These nucleosome depletion sites are the places wherein histone H3 to H3.3 replacement takes place. Indeed, several of the Zeste-bound regions and GAGA binding sequences were shown to localize to peaks of H3.3, suggesting the possibility that GAF may recruit PcG components to PHO-site-containing PREs as well as recruit TRX to promoters via nucleosome disruption (Schuettengruber, 2008).In addition to an increased density of motifs for GAF, PHO, and PHOL, unsupervised spatial cluster analysis identified specific motifs that distinguish the PH sites from the K4me3 cluster. Although the identity of the factors binding to these motifs is unknown, this suggests that the DNA sequence of PREs contains much of the information needed to recruit PcG proteins and to define silent or active chromatin states. With this distinction, it may be possible to develop an algorithm to faithfully predict the genomic location of PREs. Earlier attempts to predict PREs in the fly genome have made progress toward this goal, but they are still far from reaching the required sensitivity and specificity. The use of a sequence analysis pipeline that is not dependent on prior knowledge was demonstrated here to generate new discriminative motifs with a potential predictive power. The unique genomic organization of PcG domains may suggest that the genome is using, not only local sequence (high-affinity transcription factor binding sites located at the binding peaks) information to determine PREs, but also integration of regional sequence information (stronger affinity on 5 kb surrounding PREs). Using such regional information to predict PREs may break the current specificity and sensitivity barriers (Schuettengruber, 2008).ChIP on chip data showed that PHO binding comes in two distinct flavors. In one class of target sites, PHO binding coincides with PH sites within PC domains, whereas outside these domains, it is largely colocalized with PHOL, TRX-N, and H3K4me3 . PHOL binding was weaker at PH sites and was mainly present along with marks associated with gene activation. Quantitative ChIP assays revealed that PH, PHO, and PHOL were bound in PREs/TSS of their target genes in both ON and OFF states, but the ON state was marked by a decrease in PH binding and a corresponding increase in PHOL levels, whereas the OFF state was characterized by an increase in both PH and PHO binding levels (Schuettengruber, 2008).Chromatin at the Ubx TSS, the bx PRE, and the bxd PRE (the same primers were used in the current study) by comparing haltere/third leg imaginal discs (ON state) with wing imaginal discs (OFF state). A 50% reduction was found of PH binding levels at the bx PRE, a minor decrease at bxd, and no change in the Ubx TSS. ChIP experiments demonstrated a 50% decrease in PH levels at bx PRE and at the Ubx TSS and a minor decrease at bxd PRE when comparing haltere/third leg imaginal discs to eye imaginal discs. 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