Enter exitrons

Staiger D, Simpson GG. Enter exitrons. Genome Biology. 2015;16(1): 136.Exitrons are exon-like introns located within protein-coding exons. Removal or retention of exitrons through alternative splicing increases proteome complexity and thus adds to phenotypic diversity

The SERRATE protein is involved in alternative splicing in <em>Arabidopsis thaliana</em>

Howalternative splicing (AS) is regulated in plants has not yet been elucidated. Previously, we have shown that the nuclear cap-binding protein complex (AtCBC) is involved in AS in Arabidopsis thaliana. Here we show that both subunits of AtCBC (AtCBP20 and AtCBP80) interact with SERRATE (AtSE), a protein involved in the microRNA biogenesis pathway. Moreover, using a high-resolution reverse transcript-ase-polymerase chain reaction AS system we have found that AtSE influences AS in a similar way to the cap-binding complex (CBC), preferentially affecting selection of 50 splice site of first introns. The AtSE protein acts in cooperation with AtCBC: many changes observed in the mutant lacking the correct SERRATE activity were common to those observed in the cbp mutants. Interestingly, significant changes in AS of some genes were also observed in other mutants of plant microRNA biogenesis pathway, hyl1-2 and dcl1-7, but a majority of them did not cor-respond to the changes observed in the se-1mutant. Thus, the role of SERRATE in AS regulation is distinct from that of HYL1andDCL1, and is similar to the regu-lation of AS in which CBC is involved

Revisiting Politicide: State Annihilation in Israel/Palestine

State annihilation is a persistent concern in Israel/Palestine. While the specter of Israel’s destruction increasingly haunts Israeli public political debates, the actual materialization of Palestinian statehood seems to be permanently suspended, caught in an ever-protracted process of state-building. The current paper claims that to understand the unfolding of the discursive formations, as well as the spatial dimensions of conflict and control in Israel/Palestine, we should explicate the workings of the processes of politicide. Politicide, in this regard, denotes the eradication of the political existence of a group and sabotaging the turning of a community of people into a polity. This analysis suggests that the insistence that the State of Israel is under threat of extinction should be understood as a speech act, a performative reiteration, which allows for the securitization of Israeli rule in the occupied Palestinian territory, a securitization which then serves to rationalize the ongoing concrete politicide of the Palestinians. Elaborating on the concept of politicide, and diverging from defining it solely through the use of brute violence, this examination suggests that what is often overlooked in discussions of politicide are the seemingly more benign means of its implementation, the micro-power mechanisms of spatial control, prohibitions and regulations

T-DNA insertion mutants reveal complex expression patterns of the aldehyde dehydrogenase 3H1 locus in Arabidopsis thaliana

The Arabidopsis thaliana aldehyde dehydrogenase 3H1 gene (ALDH3H1; AT1G44170) belongs to family 3 of the plant aldehyde dehydrogenase superfamily. The full-length transcript of the corresponding gene comprises an open reading frame of 1583 bp and encodes a protein of 484 amino acid residues. Gene expression studies have shown that this transcript accumulates mainly in the roots of 4-week-old plants following abscisic acid, dehydration, and NaCl treatments. The current study provided experimental data that the ALDH3H1 locus generates at least five alternative transcript variants in addition to the previously described ALDH3H1 mRNA. The alternative transcripts accumulated in wild-type plants at a low level but were upregulated in a mutant that carried a T-DNA insertion in the first exon of the gene. Expression of the transcript isoforms involved alternative gene splicing combined with an alternative promoter. The transcript isoforms were differentially expressed in the roots and shoots and showed developmental stage- and tissue-specific expression patterns. These data support the hypothesis that alternative isoforms produced by gene splicing or alternative promoters regulate the abundance of the constitutively spliced and functional variants

Gut CD4+ T cell phenotypes are a continuum molded by microbes, not by TH archetypes

CD4+ effector lymphocytes (Teff) are traditionally classified by the cytokines they produce. To determine the states that Teff cells actually adopt in frontline tissues in vivo, we applied single-cell transcriptome and chromatin analyses to colonic Teff cells in germ-free or conventional mice or in mice after challenge with a range of phenotypically biasing microbes. Unexpected subsets were marked by the expression of the interferon (IFN) signature or myeloid-specific transcripts, but transcriptome or chromatin structure could not resolve discrete clusters fitting classic helper T cell (TH) subsets. At baseline or at different times of infection, transcripts encoding cytokines or proteins commonly used as TH markers were distributed in a polarized continuum, which was functionally validated. Clones derived from single progenitors gave rise to both IFN-γ- and interleukin (IL)-17-producing cells. Most of the transcriptional variance was tied to the infecting agent, independent of the cytokines produced, and chromatin variance primarily reflected activities of activator protein (AP)-1 and IFN-regulatory factor (IRF) transcription factor (TF) families, not the canonical subset master regulators T-bet, GATA3 or RORγ

Medicago truncatula contains a second gene encoding a plastid located glutamine synthetase exclusively expressed in developing seeds

<p>Abstract</p> <p>Background</p> <p>Nitrogen is a crucial nutrient that is both essential and rate limiting for plant growth and seed production. Glutamine synthetase (GS), occupies a central position in nitrogen assimilation and recycling, justifying the extensive number of studies that have been dedicated to this enzyme from several plant sources. All plants species studied to date have been reported as containing a single, nuclear gene encoding a plastid located GS isoenzyme per haploid genome. This study reports the existence of a second nuclear gene encoding a plastid located GS in <it>Medicago truncatula</it>.</p> <p>Results</p> <p>This study characterizes a new, second gene encoding a plastid located glutamine synthetase (GS2) in <it>M. truncatula</it>. The gene encodes a functional GS isoenzyme with unique kinetic properties, which is exclusively expressed in developing seeds. Based on molecular data and the assumption of a molecular clock, it is estimated that the gene arose from a duplication event that occurred about 10 My ago, after legume speciation and that duplicated sequences are also present in closely related species of the Vicioide subclade. Expression analysis by RT-PCR and western blot indicate that the gene is exclusively expressed in developing seeds and its expression is related to seed filling, suggesting a specific function of the enzyme associated to legume seed metabolism. Interestingly, the gene was found to be subjected to alternative splicing over the first intron, leading to the formation of two transcripts with similar open reading frames but varying 5' UTR lengths, due to retention of the first intron. To our knowledge, this is the first report of alternative splicing on a plant GS gene.</p> <p>Conclusions</p> <p>This study shows that <it>Medicago truncatula </it>contains an additional GS gene encoding a plastid located isoenzyme, which is functional and exclusively expressed during seed development. Legumes produce protein-rich seeds requiring high amounts of nitrogen, we postulate that this gene duplication represents a functional innovation of plastid located GS related to storage protein accumulation exclusive to legume seed metabolism.</p

A practical guide to single-cell RNA-sequencing for biomedical research and clinical applications.

RNA sequencing (RNA-seq) is a genomic approach for the detection and quantitative analysis of messenger RNA molecules in a biological sample and is useful for studying cellular responses. RNA-seq has fueled much discovery and innovation in medicine over recent years. For practical reasons, the technique is usually conducted on samples comprising thousands to millions of cells. However, this has hindered direct assessment of the fundamental unit of biology-the cell. Since the first single-cell RNA-sequencing (scRNA-seq) study was published in 2009, many more have been conducted, mostly by specialist laboratories with unique skills in wet-lab single-cell genomics, bioinformatics, and computation. However, with the increasing commercial availability of scRNA-seq platforms, and the rapid ongoing maturation of bioinformatics approaches, a point has been reached where any biomedical researcher or clinician can use scRNA-seq to make exciting discoveries. In this review, we present a practical guide to help researchers design their first scRNA-seq studies, including introductory information on experimental hardware, protocol choice, quality control, data analysis and biological interpretation

Lessons from non-canonical splicing

Recent improvements in experimental and computational techniques that are used to study the transcriptome have enabled an unprecedented view of RNA processing, revealing many previously unknown non-canonical splicing events. This includes cryptic events located far from the currently annotated exons and unconventional splicing mechanisms that have important roles in regulating gene expression. These non-canonical splicing events are a major source of newly emerging transcripts during evolution, especially when they involve sequences derived from transposable elements. They are therefore under precise regulation and quality control, which minimizes their potential to disrupt gene expression. We explain how non-canonical splicing can lead to aberrant transcripts that cause many diseases, and also how it can be exploited for new therapeutic strategies