Epigenetic Memory in Mammals

Epigenetic information can be passed on from one generation to another via DNA methylation, histone modifications, and changes in small RNAs, a process called epigenetic memory. During a mammal’s lifecycle epigenetic reprogramming, or the resetting of most epigenetic marks, occurs twice. The first instance of reprogramming occurs in primordial germ cells and the second occurs following fertilization. These processes may be both passive and active. In order for epigenetic inheritance to occur the epigenetic modifications must be able to escape reprogramming. There are several examples supporting this non-Mendelian mechanism of inheritance including the prepacking of early developmental genes in histones instead of protamines in sperm, genomic imprinting via methylation marks, the retention of CenH3 in mammalian sperm and the inheritance of piwi-associated interfering RNAs. The ability of mammals to pass on epigenetic information to their progeny provides clear evidence that inheritance is not restricted to DNA sequence and epigenetics plays a key role in producing viable offspring

The stochastic order of probability measures on ordered metric spaces

The general notion of a stochastic ordering is that one probability distribution is smaller than a second one if the second attaches more probability to higher values than the first. Motivated by recent work on barycentric maps on spaces of probability measures on ordered Banach spaces, we introduce and study a stochastic order on the space of probability measures $\mathcal{P}(X)$, where $X$ is a metric space equipped with a closed partial order, and derive several useful equivalent versions of the definition. We establish the antisymmetry and closedness of the stochastic order (and hence that it is a closed partial order) for the case of a partial order on a Banach space induced by a closed normal cone with interior. We also consider order-completeness of the stochastic order for a cone of a finite-dimensional Banach space and derive a version of the arithmetic-geometric-harmonic mean inequalities in the setting of the associated probability space on positive matrices.Comment: 25 page

Epigenetic Modifications during Angiosperm Gametogenesis

Angiosperms do not contain a distinct germline, but rather develop gametes from gametophyte initials that undergo cell division. These gametes contain cells that give rise to an endosperm and the embryo. DNA methylation is decreased in the vegetative nucleus (VN) and central cell nuclei (CCN) resulting in expression of transposable elements (TEs). It is thought that the siRNAs produced in response to TE expression are able to travel to the sperm cells and egg cells (EC) from VN and CCN, respectively, in order to enforce silencing there. Demethylation during gametogenesis helps ensure that even newly integrated TEs are expressed and therefore silenced by the resulting siRNA production. A final form of epigenetic control is modification of histones, which includes accumulation of the H3 variant HTR10 in mature sperm that is then completely replaced following fertilization. In females, the histone isoforms present in the EC and CCN differ, potentially helping to differentiate the two components during gametogenesis

Transgenerational inheritance of epigenetic response to abiotic stress in Arabidopsis thaliana

xiv, 246 leaves : ill. ; 29 cmAbiotic stresses are one of the major limiting factors of plant growth and thus crop productivity. Exposure to these stresses, including temperature and UV, cause physiological and epigenetic changes in plants. Such changes may be inherited in the progeny of stressed plants, and may change their ability to respond to stress. To understand the ability of plants to inherit an epigenetic stress memory as well as the physiological manifestations of such a memory, we propagated both stressed and control plants and compared the progeny under both normal and stressed conditions. In addition to wild-type plants we used Dicer-like mutants dcl2, dcl3 and dcl4, as Dicers have been linked to RNA-directed DNA methylation, a form of epigenetic memory. These studies revealed that leaf number decreases in the progeny of stressed plants, and bolting occurs earlier in the progeny of temperature stressed plants but later in the progeny of UV-C stressed plants. Transposons were also re-activated in the progeny of stressed plants. While heat shock transcription factor 2A increased expression in the progeny of heat stressed plants, many genes involved in DNA repair and histone modifications decreased. DCL2 and DCL3 appeared to be more important in transgenerational stress memory than DCL4. However, all dcl plants were generally not significantly different than wild-type plants, indicating that a single DCL deficiency may be compensated for by another DCL

Transgenerational Adaptation to Heavy Metal Salts in Arabidopsis

Exposure to abiotic and biotic stress results in changes in plant physiology and triggers genomic instability. Recent reports suggest that the progeny of stressed plants also exhibit changes in genome stability, stress tolerance, and methylation. Here we analyzed whether exposure to Ni2+, Cd2+, and Cu2+ salts leads to transgenerational changes in homologous recombination frequency and stress tolerance. We found that the immediate progeny of stressed plants exhibited an increased rate of recombination. However, when the progeny of stressed plants was propagated without stress, recombination reverted to normal levels. Exposure of plants to heavy metals for five consecutive generations (S1–S5) resulted in recombination frequency being maintained at a high level. Skipping stress following two to three generations of propagation with 50 mM Ni2+ or Cd2+ did not decrease the recombination frequency, suggesting plant acclimation to upregulated recombination. Analysis of the progeny of plants exposed to Cu2+ and Ni2+ indicated higher stress tolerance to the heavy metal parental plants were exposed to. Tolerance was higher in plants propagated with stress for three to five generations, which resulted in longer roots than plants propagated on heavy metals for only one to two generations. Tolerance was also more prominent upon exposure to a higher concentration of salts. The progeny of stressed plants were also more tolerant to NaCl and methyl methane sulfonate

Patterns of genomic and phenomic diversity in wine and table grapes.

Grapes are one of the most economically and culturally important crops worldwide, and they have been bred for both winemaking and fresh consumption. Here we evaluate patterns of diversity across 33 phenotypes collected over a 17-year period from 580 table and wine grape accessions that belong to one of the world's largest grape gene banks, the grape germplasm collection of the United States Department of Agriculture. We find that phenological events throughout the growing season are correlated, and quantify the marked difference in size between table and wine grapes. By pairing publicly available historical phenotype data with genome-wide polymorphism data, we identify large effect loci controlling traits that have been targeted during domestication and breeding, including hermaphroditism, lighter skin pigmentation and muscat aroma. Breeding for larger berries in table grapes was traditionally concentrated in geographic regions where Islam predominates and alcohol was prohibited, whereas wine grapes retained the ancestral smaller size that is more desirable for winemaking in predominantly Christian regions. We uncover a novel locus with a suggestive association with berry size that harbors a signature of positive selection for larger berries. Our results suggest that religious rules concerning alcohol consumption have had a marked impact on patterns of phenomic and genomic diversity in grapes

Increases in Vein Length Compensate for Leaf Area Lost to Lobing in Grapevine

Premise:Leaf lobing and leaf size vary considerably across and within species,including among grapevines (Vitisspp.), some of the best‐studied leaves. Weexamined the relationship between leaf lobing and leaf area across grapevinepopulations that varied in extent of leaf lobing.Methods:We used homologous landmarking techniques to measure 2632 leavesacross 2 years in 476 unique, genetically distinct grapevines fromfive biparentalcrosses that vary primarily in the extent of lobing. We determined to what extent leafarea explained variation in lobing, vein length, and vein to blade ratio.Results:Although lobing was the primary source of variation in shape across theleaves we measured, leaf area varied only slightly as a function of lobing. Rather, leafarea increases as a function of total major vein length, total branching vein length, andvein to blade ratio. These relationships are stronger for more highly lobed leaves, withthe residuals for each model differing as a function of distal lobing.Conclusions:For leaves with different extents of lobing but the same area, the morehighly lobed leaves have longer veins and higher vein to blade ratios, allowing themto maintain similar leaf areas despite increased lobing. Thesefindings show howmore highly lobed leaves may compensate for what would otherwise result in areduced leaf area, allowing for increasedphotosynthetic capacity through similarleaf siz