Decoding co-/post-transcriptional complexities of plant transcriptomes and epitranscriptome using next-generation sequencing technologies

Next-generation sequencing (NGS) technologies – Illumina RNA-seq, Pacific Biosciences isoform sequencing (PacBio Iso-seq), and Oxford Nanopore direct RNA sequencing (DRS) - have revealed the complexity of plant transcriptomes and their regulation at the co-/posttranscriptional level. Global analysis of mature mRNAs, transcripts from nuclear run-on assays, and nascent chromatin-bound mRNAs using short as well as full-length and single-molecule DRS reads have uncovered potential roles of different forms of RNA polymerase II during the transcription process, and the extent of co-transcriptional pre-mRNA splicing and polyadenylation. These tools have also allowed mapping of transcriptome-wide start sites in cap-containing RNAs, poly(A) site choice, poly(A) tail length, and RNA base modifications. Analysis of a large number of plant transcriptomes using high-throughput short and long reads under different conditions has established that diverse abiotic and biotic stresses and environmental cues such as light, which regulates many aspects of plant growth and development, have a profound impact on gene expression at the co-/post-transcriptional level. The emerging theme from these studies is that reprogramming of gene expression in response to developmental cues and stresses at the co-/post transcriptional level likely plays a crucial role in eliciting appropriate responses for optimal growth and plant survival under adverse conditions. Although the mechanisms by which developmental cues and different stresses regulate co-/posttranscriptional splicing are largely unknown, a few recent studies are beginning to provide some insights into these mechanisms. These studies indicate that the external cues target spliceosomal and splicing regulatory proteins to modulate alternative splicing. In this review, we provide an overview of recent discoveries on the dynamics and complexities of plant transcriptomes, mechanistic insights into splicing regulation, and discuss critical gaps in co-/post-transcriptional research that need to be addressed using diverse genomic and biochemical approaches

Metastasizing placental site trophoblastic tumor: Immunohistochemical and DNA analysis 2 case reports and a review of the literature

Placental-site trophoblastic tumor (PSTT) is a rare form of gestational trophoblastic neoplasia. The clinical behaviour of PSTT is usually benign, but sometimes it can be highly malignant with late recurrence and metastasis. We describe two cases of PSTT with pulmonary metastasis in patients aged 35 and 29 years respectively. The mitotic rate was elevated to 9 and 13 mitotic figures per 10 high-power fields respectively. Immunohistochemical staining showed a predominance of human placental lactogen (hPL) positive cells when compared with human chorionic gonadotropin (hCG) reactive cells in one case, and a reverse pattern in the other one. DNA measurement in one case showed an aneuploid tumor with a tetraploid DNA peak. The clinical behaviour of PSTT remains unpredictable, and there are no reliable means of predicting clinical outcom

Deciphering the Plant Splicing Code: Experimental and Computational Approaches for Predicting Alternative Splicing and Splicing Regulatory Elements

Extensive alternative splicing (AS) of precursor mRNAs (pre-mRNAs) in multicellular eukaryotes increases the protein-coding capacity of a genome and allows novel ways to regulate gene expression. In flowering plants, up to 48% of intron-containing genes exhibit AS. However, the full extent of AS in plants is not yet known, as only a few high-throughput RNA-Seq studies have been performed. As the cost of obtaining RNA-Seq reads continues to fall, it is anticipated that huge amounts of plant sequence data will accumulate and help in obtaining a more complete picture of AS in plants. Although it is not an onerous task to obtain hundreds of millions of reads using high-throughput sequencing technologies, computational tools to accurately predict and visualize AS are still being developed and refined. This review will discuss the tools to predict and visualize transcriptome-wide AS in plants using short-reads and highlight their limitations. Comparative studies of AS events between plants and animals have revealed that there are major differences in the most prevalent types of AS events, suggesting that plants and animals differ in the way they recognize exons and introns. Extensive studies have been performed in animals to identify cis-elements involved in regulating AS, especially in exon skipping. However, few such studies have been carried out in plants. Here, we review the current state of research on splicing regulatory elements (SREs) and briefly discuss emerging experimental and computational tools to identify cis-elements involved in regulation of AS in plants. The availability of curated alternative splice forms in plants makes it possible to use computational tools to predict SREs involved in AS regulation, which can then be verified experimentally. Such studies will permit identification of plant-specific features involved in AS regulation and contribute to deciphering the splicing code in plants

Energy constrained sandpile models

We study two driven dynamical systems with conserved energy. The two automata contain the basic dynamical rules of the Bak, Tang and Wiesenfeld sandpile model. In addition a global constraint on the energy contained in the lattice is imposed. In the limit of an infinitely slow driving of the system, the conserved energy $E$ becomes the only parameter governing the dynamical behavior of the system. Both models show scale free behavior at a critical value $E_c$ of the fixed energy. The scaling with respect to the relevant scaling field points out that the developing of critical correlations is in a different universality class than self-organized critical sandpiles. Despite this difference, the activity (avalanche) probability distributions appear to coincide with the one of the standard self-organized critical sandpile.Comment: 4 pages including 3 figure

Generic Sandpile Models Have Directed Percolation Exponents

We study sandpile models with stochastic toppling rules and having sticky grains so that with a non-zero probability no toppling occurs, even if the local height of pile exceeds the threshold value. Dissipation is introduced by adding a small probability of particle loss at each toppling. Generically, for models with a preferred direction, the avalanche exponents are those of critical directed percolation clusters. For undirected models, avalanche exponents are those of directed percolation clusters in one higher dimension.Comment: 4 pages, 4 figures, minor change

Scale-free energy dissipation and dynamic phase transition in stochastic sandpiles

We study numerically scaling properties of the distribution of cumulative energy dissipated in an avalanche and the dynamic phase transition in a stochastic directed cellular automaton [B. Tadi\'c and D. Dhar, Phys. Rev. Lett. {\bf 79}, 1519 (1997)] in d=1+1 dimensions. In the critical steady state occurring for the probability of toppling $p\ge p^\star$= 0.70548, the dissipated energy distribution exhibits scaling behavior with new scaling exponents $\tau_E$ and D_E for slope and cut-off energy, respectively, indicating that the sandpile surface is a fractal. In contrast to avalanche exponents, the energy exponents appear to be p- dependent in the region $p^\star \le p <1$, however the product $(\tau_E-1)D_E$ remains universal. We estimate the roughness exponent of the transverse section of the pile as $\chi =0.44\pm 0.04$. Critical exponents characterizing the dynamic phase transition at $p^\star$ are obtained by direct simulation and scaling analysis of the survival probability distribution and the average outflow current. The transition belongs to a new universality class with the critical exponents $\nu_\| =\gamma =1.22 \pm 0.02$, $\beta =0.56\pm 0.02$ and $\nu_\bot = 0.761 \pm 0.029$, with apparent violation of hyperscaling. Generalized hyperscaling relation leads to $\beta + \beta ^\prime = (d-1)\nu_\bot$, where $\beta ^\prime = 0.195 \pm 0.012$ is the exponent governed by the ultimate survival probability

The Bak-Tang-Wiesenfeld sandpile model around the upper critical dimension

We consider the Bak-Tang-Wiesenfeld sandpile model on square lattices in different dimensions (D>=6). A finite size scaling analysis of the avalanche probability distributions yields the values of the distribution exponents, the dynamical exponent, and the dimension of the avalanches. Above the upper critical dimension D_u=4 the exponents equal the known mean field values. An analysis of the area probability distributions indicates that the avalanches are fractal above the critical dimension.Comment: 7 pages, including 9 figures, accepted for publication in Physical Review

Numerical Determination of the Avalanche Exponents of the Bak-Tang-Wiesenfeld Model

We consider the Bak-Tang-Wiesenfeld sandpile model on a two-dimensional square lattice of lattice sizes up to L=4096. A detailed analysis of the probability distribution of the size, area, duration and radius of the avalanches will be given. To increase the accuracy of the determination of the avalanche exponents we introduce a new method for analyzing the data which reduces the finite-size effects of the measurements. The exponents of the avalanche distributions differ slightly from previous measurements and estimates obtained from a renormalization group approach.Comment: 6 pages, 6 figure

Mean-field behavior of the sandpile model below the upper critical dimension

We present results of large scale numerical simulations of the Bak, Tang and Wiesenfeld sandpile model. We analyze the critical behavior of the model in Euclidean dimensions $2\leq d\leq 6$. We consider a dissipative generalization of the model and study the avalanche size and duration distributions for different values of the lattice size and dissipation. We find that the scaling exponents in $d=4$ significantly differ from mean-field predictions, thus suggesting an upper critical dimension $d_c\geq 5$. Using the relations among the dissipation rate $\epsilon$ and the finite lattice size $L$, we find that a subset of the exponents displays mean-field values below the upper critical dimensions. This behavior is explained in terms of conservation laws.Comment: 4 RevTex pages, 2 eps figures embedde

Crossover phenomenon in self-organized critical sandpile models

We consider a stochastic sandpile where the sand-grains of unstable sites are randomly distributed to the nearest neighbors. Increasing the value of the threshold condition the stochastic character of the distribution is lost and a crossover to the scaling behavior of a different sandpile model takes place where the sand-grains are equally transferred to the nearest neighbors. The crossover behavior is numerically analyzed in detail, especially we consider the exponents which determine the scaling behavior.Comment: 6 pages, 9 figures, accepted for publication in Physical Review