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

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

Local Moment Formation in the Periodic Anderson Model with Superconducting Correlations

We study local moment formation in the presence of superconducting correlations among the f-electrons in the periodic Anderson model. Local moments form if the Coulomb interaction U>U_cr. We find that U_cr is considerably stronger in the presence of superconducting correlations than in the non-superconducting system. Our study is done for various values of the f-level energy and electronic density. The smallest critical U_cr values occur for the case where the number of f- electrons per site is equal to one. In the presence of d-wave superconducting correlations we find that local moment formation presents a quantum phase transition as function of pressure. This quantum phase transition separates a region where local moments and d-wave superconductivity coexist from another region characterized by a superconducting ground state with no local moments. We discuss the possible relevance of these results to experimental studies of the competition between magnetic order and superconductivity in CeCu_2Si_2.Comment: 4 pages. accepted for publication in Phys. Rev.

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

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

Multifractal scaling in the Bak-Tang-Wiesenfeld Sandpile and edge events

An analysis of moments and spectra shows that, while the distribution of avalanche areas obeys finite size scaling, that of toppling numbers is universally characterized by a full, nonlinear multifractal spectrum. Rare, large avalanches dissipating at the border influence the statistics very sensibly. Only once they are excluded from the sample, the conditional toppling distribution for given area simplifies enough to show also a well defined, multifractal scaling. The resulting picture brings to light unsuspected, novel physics in the model.Comment: 5 pages, 4 figure

Stochastic processes and conformal invariance

We discuss a one-dimensional model of a fluctuating interface with a dynamic exponent $z=1$. The events that occur are adsorption, which is local, and desorption which is non-local and may take place over regions of the order of the system size. In the thermodynamic limit, the time dependence of the system is given by characters of the $c=0$ conformal field theory of percolation. This implies in a rigorous way a connection between CFT and stochastic processes. The finite-size scaling behavior of the average height, interface width and other observables are obtained. The avalanches produced during desorption are analyzed and we show that the probability distribution of the avalanche sizes obeys finite-size scaling with new critical exponents.Comment: 4 pages, 6 figures, revtex4. v2: change of title and minor correction