Nucleosome-positioning sequence repeats impact chromatin silencing in yeast minichromosomes

The Accidental Ally: Nucleosome Barriers Can Accelerate Cohesin-Mediated Loop Formation in Chromatin

An important question in the context of the three-dimensional organization of chromosomes is the mechanism of formation of large loops between distant basepairs. Recent experiments suggest that the formation of loops might be mediated by loop extrusion factor proteins such as cohesin. Experiments on cohesin have shown that cohesins walk diffusively on the DNA and that nucleosomes act as obstacles to the diffusion, lowering the permeability and hence reducing the effective diffusion constant. An estimation of the times required to form the loops of typical sizes seen in Hi-C experiments using these low-effective-diffusion constants leads to times that are unphysically large. The puzzle then is the following: how does a cohesin molecule diffusing on the DNA backbone achieve speeds necessary to form the large loops seen in experiments? We propose a simple answer to this puzzle and show that although at low densities, nucleosomes act as barriers to cohesin diffusion, beyond a certain concentration they can reduce loop formation times because of a subtle interplay between the nucleosome size and the mean linker length. This effect is further enhanced on considering stochastic binding kinetics of nucleosomes on the DNA backbone and leads to predictions of lower loop formation times than might be expected from a naive obstacle picture of nucleosomes.

Nucleosome Positioning Regulates the Establishment, Stability, and Inheritance of Heterochromatin in Saccharomyces cerevisiae

Heterochromatic domains are complex structures composed of nucleosome arrays that are bound by silencing factors. This composition raises the possibility that certain configurations of nucleosome arrays facilitate heterochromatic silencing. We tested this possibility in Saccharomyces cerevisiae by systematically altering the distance between heterochromatic nucleosome-depleted regions (NDRs), which is predicted to affect local nucleosome positioning by limiting how nucleosomes can be packed between NDRs. Consistent with this prediction, serial deletions that altered the distance between heterochromatic NDRs revealed a striking oscillatory relationship between inter-NDR distance and defects in nucleosome positioning. Furthermore, conditions that caused poor nucleosome positioning also led to defects in both heterochromatin stability and the ability of cells to generate and inherit epigenetic transcriptional states. These findings strongly suggest that nucleosome positioning can contribute to formation and maintenance of functional heterochromatin and point to previously unappreciated roles of NDR positioning within heterochromatic domains.

Pistachios and cardiometabolic risk factors: A systematic review and meta-analysis of randomized controlled clinical trials

BACKGROUND

Previous experimental studies have reported that pistachios can elicit positive effects on lipid profile, blood pressure, and inflammation; however, a meta-analysis of the available evidence has yet to be performed.

OBJECTIVE

the aim of this study was to conduct systematic review and meta-analysis of the effect of pistachio enriched diets on cardiometabolic risk factors, such as weight, BMI, blood pressure, serum lipids, blood glucose, and inflammatory biomarkers.

DESIGN

A literature search was carried out for RCTs in medical databases, including PubMed/MEDLINE, Scopus, and Cochrane databases, with no time limitation up to August 2019, and conducted in accordance with the Preferred Reporting Items of Systematic Reviews and Meta-Analysis guidelines.

RESULTS

11 RCTs, with 506 participants, that reported the effect of pistachios consumption on cardiometabolic risk factors were included in this systematic review and meta-analysis. Our findings indicated that pistachios consumption significantly reduced FBS (WMD: -3.73, 95 % CI: -6.99, -0.46, I² = 99 %), TC/HDL (WMD: -0.46, 95 % CI: -0.76, -0.15, I² = 95 %), LDL/HDL (WMD: -0.24, 95 % CI: -0.38, -0.11, I² = 96 %), HbA1C (WMD: -0.14, 95 % CI: -0.26, -0.02, I² = 60 %), Insulin (WMD: -2.43, 95 % CI: -4.85, -0.001, I² = 58 %), SBP (WMD: -3.10, 95 % CI: -5.35, -0.85, I² = 63 %), and MDA (WMD: -0.36, 95 % CI: -0.49, -0.23, I² = 0%). Importantly, we did not observe adverse effects of pistachios consumption on BMI or blood pressure.

CONCLUSION

This systematic review and meta-analysis demonstrates that pistachios consumption can elicit a beneficial effect on some cardiometabolic risk factors. All previous clinical studies are well designed but some points have still remained unclear including the effects of different pistachios dosages on cardio metabolic risk factors and efficacy of pistachios consumption in preventing endothelial dysfunction. Further examination is required to determine the effect of pistachios consumption on further endothelial function risk factors.

High precision FRET studies reveal reversible transitions in nucleosomes between microseconds and minutes

Nucleosomes play a dual role in compacting the genome and regulating the access to DNA. To unravel the underlying mechanism, we study fluorescently labeled mononucleosomes by multi-parameter FRET measurements and characterize their structural and dynamic heterogeneity upon NaCl-induced destabilization. Species-selective fluorescence lifetime analysis and dynamic photon distribution analysis reveal intermediates during nucleosome opening and lead to a coherent structural and kinetic model. In dynamic octasomes and hexasomes the interface between the H2A-H2B dimers and the (H3-H4)₂ tetramer opens asymmetrically by an angle of ≈20° on a 50 and 15 µs time scale, respectively. This is followed by a slower stepwise release of the dimers coupled with DNA unwrapping. A mutation (H2A-R81A) at the interface between H2A and H3 facilitates initial opening, confirming the central role of the dimer:tetramer interface for nucleosome stability. Partially opened states such as those described here might serve as convenient nucleation sites for DNA-recognizing proteins.

Chromatin Higher-Order Folding: A Perspective with Linker DNA Angles

The mechanism by which the "beads-on-a-string" nucleosome chain folds into various higher-order chromatin structures in eukaryotic cell nuclei is still poorly understood. The various models depicting higher-order chromatin as regular helical fibers and the very opposite "polymer melt" theory imply that interactions between nucleosome "beads" make the main contribution to the chromatin compaction. Other models in which the geometry of linker DNA "strings" entering and exiting the nucleosome define the three-dimensional structure predict that small changes in the linker DNA configuration may strongly affect nucleosome chain folding and chromatin higher-order structure. Among those studies, the cross-disciplinary approach pioneered by Jörg Langowski that combines computational modeling with biophysical and biochemical experiments was most instrumental for understanding chromatin higher-order structure in vitro. Strikingly, many recent studies, including genome-wide nucleosome interaction mapping and chromatin imaging, show an excellent agreement with the results of three-dimensional computational modeling based on the primary role of linker DNA geometry in chromatin compaction. This perspective relates nucleosome array models with experimental studies of nucleosome array folding in vitro and in situ. I argue that linker DNA configuration plays a key role in determining nucleosome chain flexibility, topology, and propensity for self-association, thus providing new implications for regulation of chromatin accessibility to DNA binding factors and RNA transcription machinery as well as long-range communications between distant genomic sites.