Distinct core promoter codes drive transcription initiation at key developmental transitions in a marine chordate

BACKGROUND: Development is largely driven by transitions between transcriptional programs. The initiation of transcription at appropriate sites in the genome is a key component of this and yet few rules governing selection are known. Here, we used cap analysis of gene expression (CAGE) to generate bp-resolution maps of transcription start sites (TSSs) across the genome of Oikopleura dioica, a member of the closest living relatives to vertebrates. RESULTS: Our TSS maps revealed promoter features in common with vertebrates, as well as striking differences, and uncovered key roles for core promoter elements in the regulation of development. During spermatogenesis there is a genome-wide shift in mode of transcription initiation characterized by a novel core promoter element. This element was associated with > 70% of male-specific transcription, including the use of cryptic internal promoters within operons. In many cases this led to the exclusion of trans-splice sites, revealing a novel mechanism for regulating which mRNAs receive the spliced leader. Binding of the cell cycle regulator, E2F1, is enriched at the TSS of maternal genes in endocycling nurse nuclei. In addition, maternal promoters lack the TATA-like element found in zebrafish and have broad, rather than sharp, architectures with ordered nucleosomes. Promoters of ribosomal protein genes lack the highly conserved TCT initiator. We also report an association between DNA methylation on transcribed gene bodies and the TATA-box. CONCLUSIONS: Our results reveal that distinct functional promoter classes and overlapping promoter codes are present in protochordates like in vertebrates, but show extraordinary lineage-specific innovations. Furthermore, we uncover a genome-wide, developmental stage-specific shift in the mode of TSS selection. Our results provide a rich resource for the study of promoter structure and evolution in Metazoa

A Review of DUSP26: Structure, Regulation and Relevance in Human Disease

Dual specificity phosphatases (DUSPs) play a crucial role in the regulation of intracellular signalling pathways, which in turn influence a broad range of physiological processes. DUSP malfunction is increasingly observed in a broad range of human diseases due to deregulation of key pathways, most notably the MAP kinase (MAPK) cascades. Dual specificity phosphatase 26 (DUSP26) is an atypical DUSP with a range of physiological substrates including the MAPKs. The residues that govern DUSP26 substrate specificity are yet to be determined; however, recent evidence suggests that interactions with a binding partner may be required for DUSP26 catalytic activity. DUSP26 is heavily implicated in cancer where, akin to other DUSPs, it displays both tumour-suppressive and -promoting properties, depending on the context. Here we review DUSP26 by evaluating its transcriptional patterns, protein crystallographic structure and substrate binding, as well as its physiological role(s) and binding partners, its role in human disease and the development of DUSP26 inhibitors

Draft genome sequences of two <em>Micromonospora </em>strains isolated from the root nodules of <em>Alnus glutinosa</em>

\ua9 2024 American Society for Microbiology. All rights reserved.In this paper, the draft genomes of Micromonospora RTGN7 and RTP1Z1, derived from Alnus glutinosa root nodules, are reported. The assembly of RTGN7 is 6.6 Mbp, composed of 59 contigs, with an N50 of 321,872. RTP1Z1’s assembly is 6.3 Mbp, composed of 151 contigs, with an N50 of 76,442 bp

Complexity as Fitness for Evolved Cellular Automata Update Rules

We investigate the state change behavior of one-dimensional cellular automata during the solution of the binary density-classification task. Update rules of high, low and un- known fitness are applied to cellular au- tomata, thereby providing examples of high and low rates of successful classification. A spread factor, ω, is introduced and investi- gated as a numerical marker of state change behavior. The nature of ω describes complex or particle-like behavior on the part of the cellular automata over the middle region of initial configuration density-distribution, but breaks down at the ends. Because of the lim- itation on ω, a related jump-out term, jot, is selected for incorporation into the finess func- tion for genetic algorithm evolution of update rules. The inclusion of jot in the fitness func- tion significantly reduces the number of gen- erations required to reach high rates of suc- cessful classification (≥90%)

Complexity as Fitness for Evolved Cellular Automata Update Rules

We investigate the state change behavior of one-dimensional cellular automata during the solution of the binary density-classification task. Update rules of high, low and un- known fitness are applied to cellular au- tomata, thereby providing examples of high and low rates of successful classification. A spread factor, ω, is introduced and investi- gated as a numerical marker of state change behavior. The nature of ω describes complex or particle-like behavior on the part of the cellular automata over the middle region of initial configuration density-distribution, but breaks down at the ends. Because of the lim- itation on ω, a related jump-out term, jot, is selected for incorporation into the finess func- tion for genetic algorithm evolution of update rules. The inclusion of jot in the fitness func- tion significantly reduces the number of gen- erations required to reach high rates of suc- cessful classification (≥90%)

Complexity as Fitness for Evolved Cellular Automata Update Rules

We investigate the state change behavior of one-dimensional cellular automata during the solution of the binary density-classification task. Update rules of high, low and un- known fitness are applied to cellular au- tomata, thereby providing examples of high and low rates of successful classification. A spread factor, ω, is introduced and investi- gated as a numerical marker of state change behavior. The nature of ω describes complex or particle-like behavior on the part of the cellular automata over the middle region of initial configuration density-distribution, but breaks down at the ends. Because of the lim- itation on ω, a related jump-out term, jot, is selected for incorporation into the finess func- tion for genetic algorithm evolution of update rules. The inclusion of jot in the fitness func- tion significantly reduces the number of gen- erations required to reach high rates of suc- cessful classification (≥90%)

Analysis of the giant genomes of Fritillaria (Liliaceae) indicates that a lack of DNA removal characterizes extreme expansions in genome size.

This is an open access article under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.Plants exhibit an extraordinary range of genome sizes, varying by > 2000-fold between the smallest and largest recorded values. In the absence of polyploidy, changes in the amount of repetitive DNA (transposable elements and tandem repeats) are primarily responsible for genome size differences between species. However, there is ongoing debate regarding the relative importance of amplification of repetitive DNA versus its deletion in governing genome size. Using data from 454 sequencing, we analysed the most repetitive fraction of some of the largest known genomes for diploid plant species, from members of Fritillaria. We revealed that genomic expansion has not resulted from the recent massive amplification of just a handful of repeat families, as shown in species with smaller genomes. Instead, the bulk of these immense genomes is composed of highly heterogeneous, relatively low-abundance repeat-derived DNA, supporting a scenario where amplified repeats continually accumulate due to infrequent DNA removal. Our results indicate that a lack of deletion and low turnover of repetitive DNA are major contributors to the evolution of extremely large genomes and show that their size cannot simply be accounted for by the activity of a small number of high-abundance repeat families.Thiswork was supported by the Natural Environment ResearchCouncil (grant no. NE/G017 24/1), the Czech Science Fou nda-tion (grant no. P501/12/G090), the AVCR (grant no.RVO:60077344) and a Beatriu de Pinos postdoctoral fellowshipto J.P. (grant no. 2011-A-00292; Catalan Government-E.U. 7thF.P.)

Effect of retained chlorine in ENCAT™ 30 catalysts on the development of encapsulated Pd: insights from in situ Pd K, L₃ and Cl K-edge XAS

In situ X-ray absorption spectroscopy (XAS) and Pd K, LIII, and Cl K-edges shows that Cl can be present in significant amounts in ENCAT™ 30 catalysts and that it can severely retard Pd nanoparticle (NP) development in flowing solvents. We also show that whilst polymeric encapsulation protects the Pd against solvent induced agglomeration of Pd nanoparticles the evidence suggests it does not prevent the formation PdHx through reaction with the aqeous ethanol solvent, and that, as received, ENCAT™ 30 NP catalysts are not, for the most part, comprised of nanoparticulate Pd0 irrespective of the presence of Cl

Effects of Cl on the reduction of supported PdO in ethanol/water solvent mixtures

The reduction of γ-Al2O3-supported PdO in flowing aqueous ethanol was investigated. Quick EXAFS (QEXAFS) performed at the Pd K-edge reveals that the presence of Cl can have a profound effect on the reduction process. At low loadings of Pd (1 wt-%), the size dependency of the process is inverted, compared to Cl-free samples. The extent of reduction was found to be dependent on loading/particles size. It is shown, using in situ QEXAFS at the Cl K- and Pd L3-edges, that residual Cl is not removed by the flowing solvent mixture, even at an elevated temperature of 350 K. The origins of these behaviours are discussed in terms of the differing effects that Cl may have when bonded to oxidic or reduced metal centres and the results were compared to earlier observations made on the effects of Cl on commercial polyurea encapsulated Pd ENCAT™ NP 30 catalysts