RNA turnover and chromatin-dependent gene silencing

Over the last few years, there has been a convergence of two seemingly disparate fields of study: chromatin-dependent gene silencing and RNA turnover. In contrast to RNA turnover mechanisms that operate on a truly posttranscriptional level, we are at the beginning of studies leading the way toward a model in which RNA turnover mechanisms are also involved in chromatin-dependent gene regulation. In particular, data from a variety of organisms have shown that the assembly of silent chromatin coincides with the presence or absence of non-protein-coding RNAs (ncRNAs). These range from long ncRNAs that have been classically implicated in the regulation of dosage compensation and genomic imprinting to small ncRNAs which are involved in heterochromatin assembly via the RNA interference (RNAi) pathway. This raises the question of how common ncRNAs are used to control gene expression at the level of chromatin. It is known at least, that they are present, as recent findings indicate that transcription of eukaryotic genomes is much more widespread than previously anticipated. However, the existence of a ncRNA does not prove its biological significance. Thus, a future challenge will be to distinguish the ncRNAs that are in some way meaningful to the organism from those that arise from the imperfect fidelity of the transcription machinery. Finally, no matter whether functional or not, RNAs transcribed from supposedly silent chromatin seem to be processed rapidly. Recent data from both fission and budding yeast suggest that chromatin-dependent gene silencing is achieved, at least in part, through RNA turnover mechanisms that use components of the RNAi pathway as well as polyadenylation-dependent RNA decay. Hence, silent chromatin is not only controlled transcriptionally, but also on co- and posttranscriptional level

Efficient downregulation of immunoglobulin μ mRNA with premature translation-termination codons requires the 5′-half of the VDJ exon

Premature translation-termination codons (PTCs) elicit rapid degradation of the mRNA by a process called nonsense-mediated mRNA decay (NMD). NMD appears to be significantly more efficient for mRNAs of genes belonging to the immunoglobulin superfamily, which frequently acquire PTCs during VDJ rearrangment, than for mRNAs of other genes. To identify determinants for efficient NMD, we developed a minigene system derived from a mouse immunoglobulin μ gene (Ig-μ) and measured the effect of PTCs at different positions on the mRNA level. This revealed that PTCs located downstream of the V-D junction in the VDJ exon of Ig-μ minigenes and of endogenous Ig-μ genes elicit very strong mRNA downregulation, whereas NMD efficiency decreases gradually further upstream in the V segment where a PTC was inserted. Interestingly, two PTCs are in positions where they usually do not trigger NMD (<50 nt from the 3′-most 5′ splice site) still resulted in reduced mRNA levels. Using a set of hybrid constructs comprised of Ig-μ and an inefficient substrate for NMD, we identified a 177 nt long element in the V segment that is necessary for efficient downregulation of PTC-containing hybrid transcripts. Moreover, deletion of this NMD-promoting element from the Ig-μ minigene results in loss of strong NM

Chromatin-associated ncRNA activities

RNA transcripts that do not code for proteins have been long known to lie at the heart of many biological processes, such as splicing and translation. Yet their full potential has only been appreciated recently and non-coding RNAs (ncRNAs) are now attracting increasing attention. Pioneering work in yeast and plant systems has revealed that non-coding RNAs can have a major influence on the deposition of histone and DNA modifications. This can introduce heritable variation into gene expression and, thus, be the basis of epigenetic phenomena. Mechanistically, such processes have been studied extensively in the fission yeast Schizosaccharomyces pombe, providing an important conceptual framework for possible modes of action of ncRNAs also in other organisms. In this review, we highlight mechanistic insights into chromatin-associated ncRNA activities gained from work with fission yeast, and we draw parallels to studies in other eukaryotes that indicate evolutionary conservatio

Dicer and Hsp104 Function in a Negative Feedback Loop to Confer Robustness to Environmental Stress

SummaryEpigenetic mechanisms can be influenced by environmental cues and thus evoke phenotypic variation. This plasticity can be advantageous for adaptation but also detrimental if not tightly controlled. Although having attracted considerable interest, it remains largely unknown if and how environmental cues such as temperature trigger epigenetic alterations. Using fission yeast, we demonstrate that environmentally induced discontinuous phenotypic variation is buffered by a negative feedback loop that involves the RNase Dicer and the protein disaggregase Hsp104. In the absence of Hsp104, Dicer accumulates in cytoplasmic inclusions and heterochromatin becomes unstable at elevated temperatures, an epigenetic state inherited for many cell divisions after the heat stress. Loss of Dicer leads to toxic aggregation of an exogenous prionogenic protein. Our results highlight the importance of feedback regulation in building epigenetic memory and uncover Hsp104 and Dicer as homeostatic controllers that buffer environmentally induced stochastic epigenetic variation and toxic aggregation of prionogenic proteins

Modeling deadwood for rockfall mitigation assessments in windthrow areas

Studying how deadwood mitigates the rockfall hazard in mountain forests is key to understanding the influence of climate-induced disturbances on the protective capacity of mountain forests. Both experimental quantification and numerical process modeling are needed to address this question. Modeling provides detailed insights into the rock–deadwood interaction and can therefore be used to develop effective forest management strategies. Here, we introduce an automatic deadwood generator (ADG) for assessing the impact of fresh woody storm debris on the protective capacity of a forest stand against rockfall. The creation of various deadwood scenarios allows us to directly quantify the mitigation potential of deadwood. To demonstrate the functionality of the proposed ADG method, we compare deadwood log patterns, deadwood effective height, and mesoscale surface ruggedness observed in field surveys in a natural windthrow area with their simulated counterparts. Specifically, we consider two sites near Lake Klöntal, Switzerland, where a major windthrow event occurred in 2019. We perform rockfall simulations for the time (a) before, (b) directly after, and (c) 10 years after the windthrow event. We further compare the results with (d) a simulation with complete clearing of the thrown wood: in other words, a scenario with no standing forest remaining. We showcase an integration of deadwood into rockfall simulations with realistic deadwood configurations alongside a diameter at breast height (DBH)- and rot-fungi-dependent maximum deadwood breaking energy. Our results confirm the mitigation effect of deadwood, which significantly reduces the jump heights and velocities of 400 kg rocks. Our modeling results suggest that, even a decade after the windthrow event, deadwood has a stronger protective effect against rockfall than that provided by standing trees. We conclude that an ADG can contribute to the decision-making involved in forest and deadwood management after disturbances.</p

Single Cell RNA-Sequencing of Pluripotent States Unlocks Modular Transcriptional Variation

SummaryEmbryonic stem cell (ESC) culture conditions are important for maintaining long-term self-renewal, and they influence cellular pluripotency state. Here, we report single cell RNA-sequencing of mESCs cultured in three different conditions: serum, 2i, and the alternative ground state a2i. We find that the cellular transcriptomes of cells grown in these conditions are distinct, with 2i being the most similar to blastocyst cells and including a subpopulation resembling the two-cell embryo state. Overall levels of intercellular gene expression heterogeneity are comparable across the three conditions. However, this masks variable expression of pluripotency genes in serum cells and homogeneous expression in 2i and a2i cells. Additionally, genes related to the cell cycle are more variably expressed in the 2i and a2i conditions. Mining of our dataset for correlations in gene expression allowed us to identify additional components of the pluripotency network, including Ptma and Zfp640, illustrating its value as a resource for future discovery

Zc3h13/Flacc is required for adenosine methylation by bridging the mRNA binding factor Rbm15/Spenito to the m6A machinery component Wtap/Fl(2)d

N6-methyladenosine (m6A) is the most abundant mRNA modification in eukaryotes, playing crucial roles in multiple biological processes. m6A is catalyzed by the activity of Mettl3, which depends on additional proteins whose precise functions remain poorly understood. Here we identified Flacc/Zc3h13 as a novel interactor of m6A methyltransferase complex components in Drosophila and mouse. Like other components of this complex, Flacc controls m6A levels and is involved in sexdetermination in Drosophila. We demonstrate that Flacc promotes m6A deposition by bridging Fl(2)d to the mRNA binding factor Nito. Altogether, our work advances our molecular understanding of conservation and regulation of the m6A machinery

Distinctive features of lincRNA gene expression suggest widespread RNA-independent functions.

Eukaryotic genomes produce RNAs lacking protein-coding potential, with enigmatic roles. We integrated three approaches to study large intervening noncoding RNA (lincRNA) gene functions. First, we profiled mouse embryonic stem cells and neural precursor cells at single-cell resolution, revealing lincRNAs expressed in specific cell types, cell subpopulations, or cell cycle stages. Second, we assembled a transcriptome-wide atlas of nuclear lincRNA degradation by identifying targets of the exosome cofactor Mtr4. Third, we developed a reversible depletion system to separate the role of a lincRNA gene from that of its RNA. Our approach distinguished lincRNA loci functioning in trans from those modulating local gene expression. Some genes express stable and/or abundant lincRNAs in single cells, but many prematurely terminate transcription and produce lincRNAs rapidly degraded by the nuclear exosome. This suggests that besides RNA-dependent functions, lincRNA loci act as DNA elements or through transcription. Our integrative approach helps distinguish these mechanisms

Knee Extensors Muscle Plasticity Over a 5-Years Rehabilitation Process After Open Knee Surgery

We investigated molecular and cellular parameters which set metabolic and mechanical functioning of knee extensor muscles in the operated and contralateral control leg of 9 patients with a chronically insufficient anterior cruciate ligament (ACL; 26.6 ± 8.3 years, 8 males, 1 female) after open reconstructive surgery (week 0), after ambulant physiotherapy under cast immobilization (week 9), succeeding rehabilitation training (up to week 26), and subsequent voluntary physical activity (week 260). Clinical indices of knee function in the operated leg were improved at 52 weeks and remained at a comparable level at week 260. CSA of the quadriceps (-18%), MCSA of muscle fibers (-24%), and capillary-to-fiber ratio (-24%) in m. vastus lateralis from the ACL insufficient leg were lower at week 0 than reference values in the contralateral leg at week 260. Slow type fiber percentage (-35%) and mitochondrial volume density (-39%) were reduced in m. vastus lateralis from the operated leg at weeks 9 and 26. Composition alterations in the operated leg exceeded those in the contralateral leg and, with the exception of the volume density of subsarcolemmal mitochondria, returned to the reference levels at week 260. Leg-specific deterioration of metabolic characteristics in the vasti from the operated leg was reflected by the down-regulation of mitochondrial respiration complex I-III markers (-41–57%) at week 9. After rehabilitation training at week 26, the specific Y397 phosphorylation of focal adhesion kinase (FAK), which is a proxy for mechano-regulation, was elevated by 71% in the operated leg but not in the contralateral leg, which had performed strengthening type exercise during ambulant physiotherapy. Total FAK protein and Y397 phosphorylation levels were lowered in both legs at week 26 resulting in positive correlations with mitochondrial volume densities and mitochondrial protein levels. The findings emphasize that a loss of mechanical and metabolic characteristics in knee extensor muscle remains detectable years after untreated ACL rupture, which may be aggravated in the post-operative phase by the deterioration of slow-oxidative characteristics after reconstruction due to insufficient load-bearing muscle activity. The reestablishment of muscle composition subsequent to years of voluntary physical activity reinforces that slow-to-fast fiber transformation is reversible in humans

Silent chromatin at the middle and ends: lessons from yeasts

Eukaryotic centromeres and telomeres are specialized chromosomal regions that share one common characteristic: their underlying DNA sequences are assembled into heritably repressed chromatin. Silent chromatin in budding and fission yeast is composed of fundamentally divergent proteins tat assemble very different chromatin structures. However, the ultimate behaviour of silent chromatin and the pathways that assemble it seem strikingly similar among Saccharomyces cerevisiae (S. cerevisiae), Schizosaccharomyces pombe (S. pombe) and other eukaryotes. Thus, studies in both yeasts have been instrumental in dissecting the mechanisms that establish and maintain silent chromatin in eukaryotes, contributing substantially to our understanding of epigenetic processes. In this review, we discuss current models for the generation of heterochromatic domains at centromeres and telomeres in the two yeast species