Elucidating the Molecular Mechanism of Cis-Regulation by the Long Noncoding RNA LincRNA-p21

Pervasive transcription is a hallmark of mammalian genomes. Although protein-coding genes span only a small fraction of the genome, more than two-thirds is transcribed, yielding thousands of noncoding transcripts whose expression exhibits a tight correlation with cell type, disease state, and other biological phenomena. A subset of these transcripts, termed long noncoding RNAs (lncRNAs) on account of their length (\u3e200 nucleotides) and lack of apparent coding potential, have been shown to play functional roles in processes ranging from immune signaling to organogenesis. In contrast to trans-acting lncRNAs, which may operate in either the nucleus or cytoplasm, cis-acting lncRNAs remain at their site of transcription and regulate the expression of nearby protein-coding genes. These lncRNAs have been proposed to act through three main mechanisms: (1) the RNA molecule may interact with protein factors to enact transcriptional activation or repression; (2) the act of lncRNA transcription may increase the local concentration of RNA polymerase II or chromatin-modifying factors; or (3) DNA elements within a lncRNA locus may directly regulate the expression of both the lncRNA and its neighboring gene. Deconvolving these interlinked mechanisms has proven challenging and necessitates the development and implementation of new experimental techniques. In this work, we used a suite of independent molecular and genetic approaches, including a novel ribozyme-based tool for targeted transcript degradation, to expand our understanding of the molecular “logic” through which cis-acting lncRNAs enact gene regulation. We focused on the p53-inducible lncRNA LincRNA-p21, which acts in cis to reinforce the expression of the nearby protein-coding gene and key p53 target p21/Cdkn1a. To identify the functional element of cis-regulation at this locus, we generated four mouse strains harboring complementary LincRNA-p21 loss-of-function mutations that allowed us to separately examine the importance of the LincRNA-p21 transcriptional process and the underlying DNA sequence. This parallel genetic approach demonstrated that full-length LincRNA-p21 transcription, processing, and accumulation are dispensable for cis-regulation and revealed a requirement for a conserved sequence element within exon 1. Further experiments with molecular tools suggested that active transcription through this conserved region promotes p21 expression, implicating a dual role for the transcriptional process and sequence elements within the locus. This comprehensive functional dissection of a single lncRNA locus attests to the regulatory potential of lncRNA loci and further reveals the biological significance of pervasive genomic transcription

I\u27m a Barbie Girl, In a Barbie World

Writings and artwork examining beauty standards in advertising and fashion (including The Disney Effect ), eating disorders, dieting, and cosmetic surgery.https://digitalcommons.chapman.edu/feminist_zines/1015/thumbnail.jp

Dust and grit matter: abrasives of different size lead to opposing dental microwear textures in experimentally fed sheep (Ovis aries)

External abrasives ingested along with the herbivore diet are considered main contributors to dental wear, though how the different sizes and concentrations of these abrasives influence wear remains unclear. Dental microwear texture analysis (DMTA) is an establishedmethod for dietary reconstructionwhich describes a tooth’s surface topography on a micrometre scale. The method has yielded conflicting results as to the effect of external abrasives. In the present study, a feeding experiment was performed on sheep (Ovis aries) fed seven diets of different abrasiveness. Our aim was to discern the individual effects of size (4, 50 and 130 μm) and concentration (0%,4% and 8% of dry matter) of abrasives on dental wear, applying DMTA to four tooth positions. Microwear textures differed between individual teeth, but surprisingly, showed no gradient along the molar tooth row, and the strongest differentiation of experimental groups was achieved when combining data of all maxillary molars. Overall, a pattern of increasing height, volume and complexity of the tooth’s microscopic surface appeared with increasing size of dietary abrasives, and when compared with the control, the small abrasive diets showed a polishing effect. The results indicate that the size of dietary abrasives is more important for dental microwear texture traces than their concentration, and that different sizes can have opposing effects on the dietary signal. The latter finding possibly explains conflicting evidence from previous experimental DMTA applications. Further exploration is required to understand whether and how microscopic traces created by abrasives translate quantitatively to tissue loss

Snapshots of a protein folding intermediate

We have investigated the folding dynamics of Thermus thermophilus cytochrome c_(552) by time-resolved fluorescence energy transfer between the heme and each of seven site-specific fluorescent probes. We have found both an equilibrium unfolding intermediate and a distinct refolding intermediate from kinetics studies. Depending on the protein region monitored, we observed either two-state or three-state denaturation transitions. The unfolding intermediate associated with three-state folding exhibited native contacts in β-sheet and C-terminal helix regions. We probed the formation of a refolding intermediate by time-resolved fluorescence energy transfer between residue 110 and the heme using a continuous flow mixer. The intermediate ensemble, a heterogeneous mixture of compact and extended polypeptides, forms in a millisecond, substantially slower than the ∼100-μs formation of a burst-phase intermediate in cytochrome c. The surprising finding is that, unlike for cytochrome c, there is an observable folding intermediate, but no microsecond burst phase in the folding kinetics of the structurally related thermostable protein

Conformational changes in the expression domain of the Escherichia coli thiM riboswitch

The thiM riboswitch contains an aptamer domain that adaptively binds the coenzyme thiamine pyrophosphate (TPP). The binding of TPP to the aptamer domain induces structural rearrangements that are relayed to a second domain, the so-called expression domain, thereby interfering with gene expression. The recently solved crystal structures of the aptamer domains of the thiM riboswitches in complex with TPP revealed how TPP stabilizes secondary and tertiary structures in the RNA ligand complex. To understand the global modes of reorganization between the two domains upon metabolite binding the structure of the entire riboswitch in presence and absence of TPP needs to be determined. Here we report the secondary structure of the entire thiM riboswitch from Escherichia coli in its TPP-free form and its transition into the TPP-bound variant, thereby depicting domains of the riboswitch that serve as communication links between the aptamer and the expression domain. Furthermore, structural probing provides an explanation for the lack of genetic control exerted by a riboswitch variant with mutations in the expression domain that still binds TPP

Dental microwear texture analysis correlations in guinea pigs (Cavia porcellus) and sheep (Ovis aries) suggest that dental microwear texture signal consistency is species-specific

Dental microwear texture (DMT) analysis is used to differentiate abrasive dental wear patterns in many species fed different diets. Because DMT parameters all describe the same surface, they are expected to correlate with each other distinctively. Here, we explore the data range of, and correlations between, DMT parameters to increase the understanding of how this group of proxies records wear within and across species. The analysis was based on subsets of previously published DMT analyses in guinea pigs, sheep, and rabbits fed either a natural whole plant diet (lucerne, grass, bamboo) or pelleted diets with or without added quartz abrasives (guinea pigs and rabbits: up to 45 days, sheep: 17 months). The normalized DMT parameter range (P4: 0.69 0.25; M2: 0.83 0.16) and correlation coefficients (P4: 0.50 0.31; M2: 0.63 0.31) increased along the tooth row in guinea pigs, suggesting that strong correlations may be partially explained by data range. A comparison between sheep and guinea pigs revealed a higher DMT data range in sheep (0.93 0.16; guinea pigs: 0.47 0.29), but this did not translate into more substantial correlation coefficients (sheep: 0.35 0.28; guinea pigs: 0.55 0.32). Adding rabbits to an interspecies comparison of low abrasive dental wear (pelleted lucerne diet), the softer enamel of the hypselodont species showed a smaller data range for DMT parameters (guinea pigs 0.49 0.32, rabbit 0.19 0.18, sheep 0.78 0.22) but again slightly higher correlations coefficients compared to the hypsodont teeth (guinea pigs 0.55 0.31, rabbits 0.56 0.30, sheep 0.42 0.27). The findings suggest that the softer enamel of fast-replaced ever-growing hypselodont cheek teeth shows a greater inherent wear trace consistency, whereas the harder enamel of permanent and non-replaced enamel of hypsodont ruminant teeth records less coherent wear patterns. Because consistent diets were used across taxa, this effect cannot be ascribed to the random overwriting of individual wear traces on the more durable hypsodont teeth. This matches literature reports on reduced DMT pattern consistency on harder materials; possibly, individual wear events become more random in nature on harder material. Given the species-specific differences in enamel characteristics, the findings suggest a certain species-specificity of DMT patterns