Complex exon-intron marking by histone modifications is not determined solely by nucleosome distribution

It has recently been shown that nucleosome distribution, histone modifications and RNA polymerase II (Pol II) occupancy show preferential association with exons (“exon-intron marking”), linking chromatin structure and function to co-transcriptional splicing in a variety of eukaryotes. Previous ChIP-sequencing studies suggested that these marking patterns reflect the nucleosomal landscape. By analyzing ChIP-chip datasets across the human genome in three cell types, we have found that this marking system is far more complex than previously observed. We show here that a range of histone modifications and Pol II are preferentially associated with exons. However, there is noticeable cell-type specificity in the degree of exon marking by histone modifications and, surprisingly, this is also reflected in some histone modifications patterns showing biases towards introns. Exon-intron marking is laid down in the absence of transcription on silent genes, with some marking biases changing or becoming reversed for genes expressed at different levels. Furthermore, the relationship of this marking system with splicing is not simple, with only some histone modifications reflecting exon usage/inclusion, while others mirror patterns of exon exclusion. By examining nucleosomal distributions in all three cell types, we demonstrate that these histone modification patterns cannot solely be accounted for by differences in nucleosome levels between exons and introns. In addition, because of inherent differences between ChIP-chip array and ChIP-sequencing approaches, these platforms report different nucleosome distribution patterns across the human genome. Our findings confound existing views and point to active cellular mechanisms which dynamically regulate histone modification levels and account for exon-intron marking. We believe that these histone modification patterns provide links between chromatin accessibility, Pol II movement and co-transcriptional splicing

Smectic-spherulitic −- a new morphology

The phase behaviour of poly(ester imide)s (PEI) based on long aliphatic diols and aminobenzoic acid trimellitimide or aminocinnamic acid trimellitimide, respectively, was investigated by means of X-ray scattering. Whereas PEI with shorter spacers form smectic LC-phases which transform into higher ordered smectic phases upon further cooling, PEI with long spacers undergo a direct phase transition from the isotropic melt into a higher ordered solid smectic phase, which is also named smectic-crystalline owing to the lateral interactions of the mesogens. This process involves a nucleation followed by the growth of a three-dimensional spherulitic superstructure. This new morphology of spherulites with internal smectic order is named smectic-spherulitic. Moreover, the spherulites consist of stacks of crystalline and lower-ordered lamellae giving rise to a small angle X-ray reflection with a long period of 150–400 Å. The crystalline lamellae in their part consist of smectic layers. In spite of the crystallinity, the system exhibits a remarkable mobility. Upon heating and cooling the lamellac expand and shrink reversibly. This polymer system combines features of semi-crystalline polymers with the mesophase character of smectic LC-polymers

Phase Transitions in Smectic Poly(Ester Imide)s Derived from 4-Aminocinnamic Acid Trimellitimide and Long Aliphatic Spacers

The phases behavior of poly(ester imide)s (PEI) based on trimellitic anhydride, 4-aminocinnamic acid and α,ω-dihydroxydodecane (n = 12) or α,ω-dihydroxyhexadecane (n = 16), resp., have been investigated by X-ray measurements employing synchrotron radiation. Both PEIs form mono-tropic LC phases which can be quenched into the glassy state. Due to the regular sequence of rigid, polar mesogens and flexible, non-polar spacers smectic phases are formed in the melt and in the solid state, giving rise to sharp X-ray reflections. During transition from the smectic LC phase to the higher ordered smectic crystalline phase these layer reflections shift towards larger scattering angles indicating a narrowing of the layers due to tilting of the mesogens with respect to the layer plane. X-ray fiber pattern indicate that this tilting already occurs in the frozen LC phase (Sc). The chains are oriented preferably parallel to the fiber direction while the staggering of the mesogens orients the layers inclining an angle of about β = 20°. During crystallization the mesogens reptate longitudinally in order to fit the lateral lattice and the tilt angle increases up to 41° (n = 12) and 35° (n = 16) (SH). Isothermal experiments reveal that PEI (n = 12) is capable of forming two different smectic-H phases depending on the thermal treatment. Above 130° C SHI, (β = 32°, d = 27 Å) is formed preferably whereas SH2 (β = 41°, d = 24 Å) dominates below 1407°C

Molecular Order of the Mesogens in Smectic Poly(ester imide) Fibers

The molecular order of the mesogens in the smectic liquid-crystalline (LC) and smectic-crystalline phases of different poly(ester imide)s (PEI) with similar chemical structure is investigated by means of X-ray fiber patterns. During the fiber spinning from the melt, the smectic LC phase is frozen. Above the glass transition temperature, a transition into a higher-ordered smectic-crystalline phase occurs. The PEI which are based on aminobenzoic acid trimellitimide and long aliphatic spacers form exclusively orthogonal smectic phases (SA, SB, SE). In contrast, the PEI based on aminocinnamic acid trimellitimide and those derived from 4-hydroxyphthalic acid, aminophenol, and aliphatic dicarbon acids form tilted SC phases. The layer line broadening of the X-ray reflections indicates a poor lateral order of the smectic layers in the LC phase due to a frequent inversion of the staggering direction between adjacent mesogens. As a result of the equatorial smearing of the four-point-pattern, the splitting angle of the reflections is not identical with the tilt angle between the mesogens and the normal of the smectic layer plane. The order of the mesogens in the direction perpendicular to the fiber axis is evaluated on the basis of the paracrystallinity model. The resulting local tilt angle corresponds to an average staggering amount of the mesogens. Furthermore, the parameter ε, introduced by Porod, is interpreted as a probability for the inversion of the staggering direction

Enumerating the forest before the trees: The time courses of estimation-based and individuation-based numerical processing

Ensemble perception refers to the ability to report attributes of a group of objects, rather than focusing on only one or a few individuals. An everyday example of ensemble perception is the ability to estimate the numerosity of a large number of items. The time course of ensemble processing, including that of numerical estimation, remains a matter of debate, with some studies arguing for rapid, “preattentive” processing and other studies suggesting that ensemble perception improves with longer presentation durations. We used a forward-simultaneous masking procedure that effectively controls stimulus durations to directly measure the temporal dynamics of ensemble estimation and compared it with more precise enumeration of individual objects. Our main finding was that object individuation within the subitizing range (one to four items) took about 100–150 ms to reach its typical capacity limits, whereas estimation (six or more items) showed a temporal resolution of 50 ms or less. Estimation accuracy did not improve over time. Instead, there was an increasing tendency, with longer effective durations, to underestimate the number of targets for larger set sizes (11–35 items). Overall, the time course of enumeration for one or a few single items was dramatically different from that of estimating numerosity of six or more items. These results are consistent with the idea that the temporal resolution of ensemble processing may be as rapid as, or even faster than, individuation of individual items, and support a basic distinction between the mechanisms underlying exact enumeration of small sets (one to four items) from estimation

Layer Structures 8. Poly(benzoxazole-ester)s with a Four-Layer or a Six-Layer Repeat Unit

Two isomeric polyesters (3a and 3b) were synthesized from 2-(4-hydroxyphenyl)benzoxazolecarboxylic acid, 1,12-dodecanediol, and tetraethylene glycol, so that an alternating sequence of four subunits was obtained. Both polyesters differ in their internal orientation of the benzoxazole units with the consequence that only one of them (3a) is liquid-crystalline forming an enantiotropic smectic-C phase. Furthermore, a third polyester (4) was prepared with an alternating sequence of six subunits using 4,4‘-dimercaptobiphenyl as a third stiff building block. Both DSC and X-ray measurements confirm that all three polyesters form a crystalline solid state with a smectic type layer structure. Fiber pattern indicate that in the case of 3a and 3b the chains are tilted with an angle of about 45° relative to the layer planes, and the solid state corresponds to a smectic-H structure. In the case of 4 the chains are in upright position, although four subunits are identical with the repeat unit of 3b. Therefore, the solidification of 4 may be understood as a self-assembling process. The thermal phase transitions were also characterized by synchrotron radiation measurements up to the isotropization temperature