Effects of Transgenerational Plasticity on Morphological and Physiological Properties of Stoloniferous Herb Centella asiatica Subjected to High/Low Light

Environmentally induced transgenerational plasticity can increase success of progeny and thereby be adaptive if progeny experiences the similarly parental environment. The ecological and evolutionary significance of transgenerational plasticity in plant has been studied mainly in the context of sexual generations. A pot experiment using the stoloniferous herb Centella asiatica was conducted to investigate the effects of high/low light treatment experienced by parental ramets (F0 generation) on morphological and physiological properties of offspring ramets (F2 generation) as well as growth performance. Light environment experienced by parental ramets (F0 generation) significantly influenced petiole length, specific petiole length, internode length of stolon, leaf area, specific leaf area (SLA), leaf nitrogen and chlorophyll contents, potential maximum net photosynthetic rate (Pmax) in offspring ramets subjected to parental or non-parental environments even after they were detached from the parental ramets. Potential maximum net photosynthetic rate (Pmax) of offspring ramets (F2 generation) from parental ramets (F0 generation) subjected to low light treatment was significantly greater than that of offspring ramets (F2 generation) from parental ramets (F0 generation) subjected to high light treatment. Potential maximum net photosynthetic rate (Pmax) of offspring ramets (F2 generation) subjected to parental light environment was greater than that of offspring ramets (F2 generation) subjected to non-parental light environment. The greatest biomass accumulation and total stolon length were observed in offspring ramets (F2 generation) subjected to low light treatment as parental ramets (F0 generation) experienced. When parental ramets (F0 generation) were subjected to low light treatment, biomass accumulation and total stolon length of offspring ramets (F2 generation) experiencing parental light environment were significantly greater than those of offspring ramets (F2 generation) experiencing non-parental light environment. Opposite pattern was observed in offspring ramets (F2 generation) from parental ramets subjected to high light treatment. Our work provides evidence that transgenerational plasticity through both morphological and physiological flexibility was triggered across vegetative generations for stoloniferous herb C. asiatica subjected to high/low light treatment. The transgenerational plasticity can allow offspring ramets to present adaptive phenotype early without lag time in response to the current environment. Thus, it is very important for clonal plants in adapting temporally and spatially heterogeneous habitats

CRISPR Explorer: A fast and intuitive tool for designing guide RNA for genome editing

The RNA-guided CRISPR-Cas9 (clustered, regularly interspaced, short palindromic repeat-CRISPR-associated 9) system has become a revolutionary technology for targeted genome engineering. The critical step of this technology requires the design of a highly specific and efficient guide RNA (gRNA) that will guide the Cas9 nuclease to the complementary DNA target sequence. CRISPR-Explorer is a new and user-friendly web server for selecting optimal CRISPR sites. It implements the latest scoring schemes of gRNA specificity and efficiency based on published empirical studies. The gRNA design results are generated instantly, thus removing wait times. The user can visualize the high-quality gRNAs with detailed design information through an interactive genome browser. Furthermore, the user can define and specify the parameters for gRNA selection in the Batch Design mode, which recognizes various input formats. CRISPR Explorer is freely accessible at: http://crisprexplorer.org

Plasma Cell Fate Is Orchestrated by Elaborate Changes in Genome Compartmentalization and Inter-chromosomal Hubs.

The transition from the follicular B to the plasma cell stage is associated with large-scale changes in cell morphology. Here, we examine whether plasma cell development is also associated with changes in nuclear architecture. We find that the onset of plasma cell development is concomitant with a decline in remote genomic interactions; a gain in euchromatic character at loci encoding for factors that specify plasma cell fate, including Prdm1 and Atf4; and establishment of de novo inter-chromosomal hubs. We find that, in developing plasma cells and concurrent with transcriptional silencing, the Ebf1 locus repositions from an euchromatic to peri-centromeric heterochromatic environment. Finally, we find that inter-chromosomal hubs are enriched for the deposition of either H3K27Ac or H3K27me3. These data indicate that plasma cell fate is orchestrated by elaborate changes in genome topology and that epigenetic marks, linked with super-enhancers or transcriptionally repressed regions, are enriched at inter-chromosomal hubs

Profiling of Stem/Progenitor Cell Regulatory Genes of the Synovial Joint by Genome-Wide RNA-Seq Analysis

Synovial joints suffer from arthritis and trauma that may be severely debilitative. Despite robust investigations in the roles of individual genes in synovial joint development and arthritis, little is known about global profiles of genes that regulate stem/progenitor cells of a synovial joint. The temporomandibular joint is a poorly understood synovial arthrosis with few clinical treatment options. Here, we isolated the articular and mature zones of the mandibular condyle by laser capture microdissection, performed genome-wide profiling, and analyzed molecular signaling pathways relevant to stem/progenitor cell functions. A total of 804 genes were differentially expressed between the articular and mature zones. Pathway analyses revealed 29 enriched signaling pathways, including the PI3K-Akt, Wnt, and Toll-like receptor signaling pathways that may regulate stem/progenitor cell homeostasis and differentiation into the chondrocyte lineage. Upstream regulator analyses further predicted potential upstream key regulators such as Xbp1, Nupr1, and Hif1a, and associated underlying mechanism networks were described. Among the multiple candidates of growth and transcriptional factors that may regulate stem/progenitor cells, we immunolocalized Sox9, Ihh, Frzb, Dkk1, Lgr5, and TGFβ3 in the articular and mature zones. These findings provide a comprehensive genetic mapping of growth and transcriptional genes in the articular and mature zones of a synovial joint condyle. Differentially expressed genes may play crucial roles in the regulation of stem/progenitor cells in development, homeostasis, and tissue regeneration

RNA-Seq Characterization of Spinal Cord Injury Transcriptome in Acute/Subacute Phases: A Resource for Understanding the Pathology at the Systems Level

<div><p>Spinal cord injury (SCI) is a devastating neurological disease without effective treatment. To generate a comprehensive view of the mechanisms involved in SCI pathology, we applied RNA-Sequencing (RNA-Seq) technology to characterize the temporal changes in global gene expression after contusive SCI in mice. We sequenced tissue samples from acute and subacute phases (2 days and 7 days after injury) and systematically characterized the transcriptomes with the goal of identifying pathways and genes critical in SCI pathology. The top enriched functional categories include “inflammation response,” “neurological disease,” “cell death and survival” and “nervous system development.” The top enriched pathways include LXR/RXR Activation and Atherosclerosis Signaling, etc. Furthermore, we developed a systems-based analysis framework in order to identify key determinants in the global gene networks of the acute and sub-acute phases. Some candidate genes that we identified have been shown to play important roles in SCI, which demonstrates the validity of our approach. There are also many genes whose functions in SCI have not been well studied and can be further investigated by future experiments. We have also incorporated pharmacogenomic information into our analyses. Among the genes identified, the ones with existing drug information can be readily tested in SCI animal models. Therefore, in this study we have described an example of how global gene profiling can be translated to identifying genes of interest for functional tests in the future and generating new hypotheses. Additionally, the RNA-Seq enables splicing isoform identification and the estimation of expression levels, thus providing useful information for increasing the specificity of drug design and reducing potential side effect. In summary, these results provide a valuable reference data resource for a better understanding of the SCI process in the acute and sub-acute phases.</p> </div

The top canonical pathways enriched in the differentially expressed genes.

<p>(A) Top 15 canonical pathways enriched in top 10% up/down-regulated genes of 2D/CTR and 7D/CTR are shown. The –log(P value) of the enrichment of each canonical pathway was plotted. (B) LXR/RXR Activation pathway up-regulated genes are colored pink. The color of a gene reflects its fold change. The higher the fold change the deeper the color.</p

The expression of macrophage marker genes in both acute and subacute phases of SCI.

<p>Expression profile of the common macrophage marker Itgam (A), M1 specific marker CD86 (B) and M2 specific marker Arg1(C) during the time-course of SCI. P values were calculated by one-way ANOVA. GSEA analysis: differential gene expression was ranked by fold change (x-axis: 2D vs control (D), 7D vs control (E), 7D vs 2D (F)). The most up-regulated genes are shown on the left side (red), while the most up-regulated genes were shown on the right side (blue). Black bars represent the positions of the M1 vs M2 up-regulated signature genes in the ranked list. Enrichment score (ES, Y-axis) reflects the degree the genes are overrepresented. When the distribution is at random, the enrichment score is zero. Enrichment of signature genes at the top of the ranked list results in a large positive deviation of the ES from zero. NES, normalized enrichment score; FDR, false discovery rate-adjusted q value.</p

Single-swap editing for the correction of common Duchenne muscular dystrophy mutations

Duchenne muscular dystrophy (DMD) is a fatal X-linked recessive disease of progressive muscle weakness and wasting caused by the absence of dystrophin protein. Current gene therapy approaches using antisense oligonucleotides require lifelong dosing and have limited efficacy in restoring dystrophin production. A gene editing approach could permanently correct the genome and restore dystrophin protein expression. Here, we describe single-swap editing, in which an adenine base editor edits a single base pair at a splice donor site or splice acceptor site to enable exon skipping or reframing. In human induced pluripotent stem cell-derived cardiomyocytes, we demonstrate that single-swap editing can enable beneficial exon skipping or reframing for the three most therapeutically relevant exons—DMD exons 45, 51, and 53—which could be beneficial for 30% of all DMD patients. Furthermore, an adeno-associated virus delivery method for base editing components can efficiently restore dystrophin production locally and systemically in skeletal and cardiac muscles of a DMD mouse model containing a deletion of Dmd exon 44. Our studies demonstrate single-swap editing as a potential gene editing therapy for common DMD mutations