Diversification and conservation of DNA binding specificities of SPL family of transcription factors.

SQUAMOSA Promoter-Binding Protein-Like (SPL) transcription factors play vital roles in plant development and stress responses. In this study, we report a comprehensive DNA Affinity Purification sequencing (DAP-seq) analysis for 14 of the 16 SPL transcription factors in , providing valuable insights into their DNA-binding specificities. We performed Gene Ontology (GO) analysis of the target genes to reveal their convergent and diverse biological functions among SPL family proteins.

Transcription factor binding site divergence across maize inbred lines drives transcriptional and phenotypic variation.

Regulatory elements are important constituents of plant genomes that have shaped ancient and modern crops. Their identification, function, and diversity in crop genomes however are poorly characterized, thus limiting our ability to harness their power for further agricultural advances using induced or natural variation. Here, we use DNA affinity purification-sequencing (DAP-seq) to map transcription factor (TF) binding events for 200 maize TFs belonging to 30 distinct families and heterodimer pairs in two distinct inbred lines historically used for maize hybrid plant production, providing empirical binding site annotation for 5.

Robust discovery of gene regulatory networks from single-cell gene expression data by Causal Inference Using Composition of Transactions.

Gene regulatory networks (GRNs) drive organism structure and functions, so the discovery and characterization of GRNs is a major goal in biological research. However, accurate identification of causal regulatory connections and inference of GRNs using gene expression datasets, more recently from single-cell RNA-seq (scRNA-seq), has been challenging. Here we employ the innovative method of Causal Inference Using Composition of Transactions (CICT) to uncover GRNs from scRNA-seq data.

MYB24 orchestrates terpene and flavonol metabolism as light responses to anthocyanin depletion in variegated grape berries.

Variegation is a rare type of mosaicism not fully studied in plants, especially fruits. We examined red and white sections of grape (Vitis vinifera cv. 'Béquignol') variegated berries and found that accumulation of products from branches of the phenylpropanoid and isoprenoid pathways showed an opposite tendency.

Double DAP-seq uncovered synergistic DNA binding of interacting bZIP transcription factors.

Many eukaryotic transcription factors (TF) form homodimer or heterodimer complexes to regulate gene expression. Dimerization of BASIC LEUCINE ZIPPER (bZIP) TFs are critical for their functions, but the molecular mechanism underlying the DNA binding and functional specificity of homo- versus heterodimers remains elusive. To address this gap, we present the double DNA Affinity Purification-sequencing (dDAP-seq) technique that maps heterodimer binding sites on endogenous genomic DNA.

Transcription Factor Dynamics in Cross-Regulation of Plant Hormone Signaling Pathways.

Cross-regulation between hormone signaling pathways is indispensable for plant growth and development. However, the molecular mechanisms by which multiple hormones interact and co-ordinate activity need to be understood. Here, we generated a cross-regulation network explaining how hormone signals are integrated from multiple pathways in etiolated Arabidopsis () seedlings.

Kartogenin (KGN)/synthetic melanin nanoparticles (SMNP) loaded theranostic hydrogel scaffold system for multiparametric magnetic resonance imaging guided cartilage regeneration.

Cartilage regeneration after injury is still a great challenge in clinics, which suffers from its avascularity and poor proliferative ability. Herein we designed a novel biocompatible cellulose nanocrystal/GelMA (gelatin-methacrylate anhydride)/HAMA (hyaluronic acid-methacrylate anhydride)-blended hydrogel scaffold system, loaded with synthetic melanin nanoparticles (SMNP) and a bioactive drug kartogenin (KGN) for theranostic purpose. We found that the SMNP-KGN/Gel showed favorable mechanical property, thermal stability, and distinct magnetic resonance imaging (MRI) contrast enhancement.

First Plant Cell Atlas symposium report.

The Plant Cell Atlas (PCA) community hosted a virtual symposium on December 9 and 10, 2021 on single cell and spatial omics technologies. The conference gathered almost 500 academic, industry, and government leaders to identify the needs and directions of the PCA community and to explore how establishing a data synthesis center would address these needs and accelerate progress. This report details the presentations and discussions focused on the possibility of a data synthesis center for a PCA and the expected impacts of such a center on advancing science and technology globally.

Elucidating the biology of transcription factor-DNA interaction for accurate identification of cis-regulatory elements.

Transcription factors (TFs) play a critical role in determining cell fate decisions by integrating developmental and environmental signals through binding to specific cis-regulatory modules and regulating spatio-temporal specificity of gene expression patterns. Precise identification of functional TF binding sites in time and space not only will revolutionize our understanding of regulatory networks governing cell fate decisions but is also instrumental to uncover how genetic variations cause morphological diversity or disease. In this review, we discuss recent advances in mapping TF binding sites and characterizing the various parameters underlying the complexity of binding site recognition by TFs.

Direct regulation of shikimate, early phenylpropanoid, and stilbenoid pathways by Subgroup 2 R2R3-MYBs in grapevine.

The stilbenoid pathway is responsible for the production of resveratrol in grapevine (Vitis vinifera L.). A few transcription factors (TFs) have been identified as regulators of this pathway but the extent of this control has not been deeply studied.

Vision, challenges and opportunities for a Plant Cell Atlas.

With growing populations and pressing environmental problems, future economies will be increasingly plant-based. Now is the time to reimagine plant science as a critical component of fundamental science, agriculture, environmental stewardship, energy, technology and healthcare. This effort requires a conceptual and technological framework to identify and map all cell types, and to comprehensively annotate the localization and organization of molecules at cellular and tissue levels.

Potentials of single-cell genomics in deciphering cellular phenotypes.

Single-cell genomics, particularly single-cell transcriptome profiling by RNA sequencing have transformed the possibilities to relate genes to functions, structures, and eventually phenotypes. We can now observe changes in each cell's transcriptome and among its neighborhoods, interrogate the sequence of transcriptional events, and assess their influence on subsequent events. This paradigm shift in biology enables us to infer causal relationships in these events with high accuracy.

Dextran methacrylate hydrogel microneedles loaded with doxorubicin and trametinib for continuous transdermal administration of melanoma.

Microneedles (MNs) technology has many advantages and is an ideal local transdermal drug delivery method. Here we synthesized photocrosslinkable dextran methacrylate (DexMA), and its degree of substitution is 5 % higher than the previous method. We used DexMA hydrogel for the first time to develop a new type of MNs for continuous transdermal administration.

Injectable supramolecular gelatin hydrogel loading of resveratrol and histatin-1 for burn wound therapy.

Prolonged inflammatory response and insufficient vascularization cause delayed and poor wound healing. In this study, we fabricated a supramolecular host-guest gelatin (HGM) hydrogel loaded with resveratrol (Res) and histatin-1 (His-1) to suppress inflammation and promote vascularization at skin burn wound sites. The HGM hydrogel showed good properties of shear-thinning and injectability, thereby allowing easy in situ injection and fast adaption to irregular wounds.

Functionalized GO Nanovehicles with Nitric Oxide Release and Photothermal Activity-Based Hydrogels for Bacteria-Infected Wound Healing.

Bacteria-infected wounds are attracting increasing attention, as antibiotic misuse and multidrug-resistant bacteria complicate their treatment. Herein, we reported a photothermal activity-based drug consisting of β-cyclodextrin (βCD)-functionalized graphene oxide (GO) near-infrared light-responsive nanovehicles combined with the nitric oxide donor BNN6, in a methacrylate-modified gelatin (GelMA)/hyaluronic acid graft dopamine (HA-DA) hydrogel. The synergistic effects of photothermal and gas therapies are expected to improve antibacterial efficiency and reduce drug resistance.

Cannabinoid exposure in rat adolescence reprograms the initial behavioral, molecular, and epigenetic response to cocaine.

The initial response to an addictive substance can facilitate repeated use: That is, individuals experiencing more positive effects are more likely to use that drug again. Increasing evidence suggests that psychoactive cannabinoid use in adolescence enhances the behavioral effects of cocaine. However, despite the behavioral data, there is no neurobiological evidence demonstrating that cannabinoids can also alter the brain's initial molecular and epigenetic response to cocaine.

Big Data to the Bench: Transcriptome Analysis for Undergraduates.

Next-generation sequencing (NGS)-based methods are revolutionizing biology. Their prevalence requires biologists to be increasingly knowledgeable about computational methods to manage the enormous scale of data. As such, early introduction to NGS analysis and conceptual connection to wet-lab experiments is crucial for training young scientists.

Preparation and characterisation of a novel silk fibroin/hyaluronic acid/sodium alginate scaffold for skin repair.

To mimic the natural structure of tissue extracellular matrix, a novel silk fibroin (SF)/hyaluronic acid (HA)/sodium alginate (SA) composite scaffold (92% in porosity) was prepared by freeze-drying. Fourier-transform infrared spectroscopy and Raman spectra indicated interactions among SF, HA, and SA molecules. Scanning electron microscopy showed that the prepared SF/HA/SA scaffold had soft, elastic characteristics, with an average pore diameter of 93 μm.

Piecing together cis-regulatory networks: insights from epigenomics studies in plants.

5-Methylcytosine, a chemical modification of DNA, is a covalent modification found in the genomes of both plants and animals. Epigenetic inheritance of phenotypes mediated by DNA methylation is well established in plants. Most of the known mechanisms of establishing, maintaining and modifying DNA methylation have been worked out in the reference plant Arabidopsis thaliana.

Network modeling of kinase inhibitor polypharmacology reveals pathways targeted in chemical screens.

Small molecule screens are widely used to prioritize pharmaceutical development. However, determining the pathways targeted by these molecules is challenging, since the compounds are often promiscuous. We present a network strategy that takes into account the polypharmacology of small molecules in order to generate hypotheses for their broader mode of action.

Mapping genome-wide transcription-factor binding sites using DAP-seq.

To enable low-cost, high-throughput generation of cistrome and epicistrome maps for any organism, we developed DNA affinity purification sequencing (DAP-seq), a transcription factor (TF)-binding site (TFBS) discovery assay that couples affinity-purified TFs with next-generation sequencing of a genomic DNA library. The method is fast, inexpensive, and more easily scaled than chromatin immunoprecipitation sequencing (ChIP-seq). DNA libraries are constructed using native genomic DNA from any source of interest, preserving cell- and tissue-specific chemical modifications that are known to affect TF binding (such as DNA methylation) and providing increased specificity as compared with in silico predictions based on motifs from methods such as protein-binding microarrays (PBMs) and systematic evolution of ligands by exponential enrichment (SELEX).

CrY2H-seq: a massively multiplexed assay for deep-coverage interactome mapping.

Broad-scale protein-protein interaction mapping is a major challenge given the cost, time, and sensitivity constraints of existing technologies. Here, we present a massively multiplexed yeast two-hybrid method, CrY2H-seq, which uses a Cre recombinase interaction reporter to intracellularly fuse the coding sequences of two interacting proteins and next-generation DNA sequencing to identify these interactions en masse. We applied CrY2H-seq to investigate sparsely annotated Arabidopsis thaliana transcription factors interactions.

A transcription factor hierarchy defines an environmental stress response network.

Environmental stresses are universally encountered by microbes, plants, and animals. Yet systematic studies of stress-responsive transcription factor (TF) networks in multicellular organisms have been limited. The phytohormone abscisic acid (ABA) influences the expression of thousands of genes, allowing us to characterize complex stress-responsive regulatory networks.