Chromatin Accessibility Is Associated with Artemisinin Biosynthesis Regulation in Artemisia annua

Glandular trichome (GT) is the dominant site for artemisinin production in Artemisia annua. Several critical genes involved in artemisinin biosynthesis are specifically expressed in GT. However, the molecular mechanism of differential gene expression between GT and other tissue types remains elusive. Chromatin accessibility, defined as the degree to which nuclear molecules are able to interact with chromatin DNA, reflects gene expression capacity to a certain extent. Here, we investigated and compared the landscape of chromatin accessibility in Artemisia annua leaf and GT using the Assay for Transposase-Accessible Chromatin using sequencing (ATAC-seq) technique. We identified 5413 GT high accessible and 4045 GT low accessible regions, and these GT high accessible regions may contribute to GT-specific biological functions. Several GT-specific artemisinin biosynthetic genes, such as DBR2 and CYP71AV1, showed higher accessible regions in GT compared to that in leaf, implying that they might be regulated by chromatin accessibility. In addition, transcription factor binding motifs for MYB, bZIP, C2H2, and AP2 were overrepresented in the highly accessible chromatin regions associated with artemisinin biosynthetic genes in glandular trichomes. Finally, we proposed a working model illustrating the chromatin accessibility dynamics in regulating artemisinin biosynthetic gene expression. This work provided new insights into epigenetic regulation of gene expression in GT.

Unfolding of the chromatin fiber driven by overexpression of bridging factors

Nuclear molecules control the functional properties of the chromatin fiber by shaping its morphological properties. The biophysical mechanisms controlling how bridging molecules compactify the chromatin are a matter of debate. On the one side, bridging molecules could cross-link faraway sites and fold the fiber through the formation of loops. Interacting bridging molecules could also mediate long-range attractions by first tagging different locations of the fiber and then undergoing microphase separation. Using a coarse-grained model and Monte Carlo simulations, we study the conditions leading to compact configurations both for interacting and non-interacting bridging molecules. In the second case, we report on an unfolding transition at high densities of the bridging molecules. We clarify how this transition, which disappears for interacting bridging molecules, is universal and controlled by entropic terms. In general, chains are more compact in the case of interacting bridging molecules since, in this case, interactions are not valence-limited. However, this result is conditional on the ability of our simulation methodology to relax the system towards its ground state. In particular, we clarify how, unless using reaction dynamics that change the length of a loop in a single step, the system is prone to remain trapped in metastable, compact configurations featuring long loops.

How to determine the shape of nuclear molecules with polarized gamma-rays

A method has been recently proposed to establish the geometry of the alpha-cluster arrangement in ^{12}12C making use of polarized gamma-rays. The ratio of intensities of scattered radiation at 90 degrees along and perpendicular to the initial direction of the electric field vector, called depolarization ratio, is a key quantity that allows to underpin the nature of totally symmetric modes of vibrations. This allows to connect with the underlying point-group structure and therefore to the geometric shape of the nuclear molecule. This method is reviewed for ^{12}12C and extended to other configurations, such as three unequal clusters and four identical clusters (e.g. ^{16}16O).

Hi-D: Nanoscale mapping of nuclear dynamics in single living cells

ABSTRACTBulk chromatin motion has not been analysed at high resolution. We present Hi-D, a method to quantitatively map dynamics of chromatin and abundant nuclear proteins for every pixel simultaneously over the entire nucleus from fluorescence image series. Hi-D combines reconstruction of chromatin motion, and classification of local diffusion processes by Bayesian inference. We show that DNA dynamics in the nuclear interior are spatially partitioned into 0.3 – 3 μm domains in a mosaic-like pattern, uncoupled from chromatin compaction. This pattern was remodelled in response to transcriptional activity. Hi-D can be applied to any dense and bulk structures opening new perspectives towards understanding motion of nuclear molecules.

Cluster structures, ellipsoidal shapes and nuclear molecules in light A = 12-50 nuclei

The transition from cluster structures to extremely elongated ellipsoidal shapes and nuclear molecules in light A=12-50 (N~Z) nuclei has been studied within the framework of covariant density functional theory. Nodal structure of the occupied single-particle states plays a critical role in microscopic understanding of this transition. This is illustrated by the analysis of dominant types of single-particle density distributions and their evolution (from the bottom of nucleonic potential) with deformation and particle number. The microscopic mechanism of the transition from clustered structures to ellipsoidal shapes and nuclear molecules and between them is discussed.