ETS1, a Target Gene of the EWSR1::FLI1 Fusion Oncoprotein, Regulates the Expression of the Focal Adhesion Protein TENSIN3.

The mechanistic basis for the metastasis of Ewing sarcomas remains poorly understood, as these tumors harbor few mutations beyond the chromosomal translocation that initiates the disease. Instead, the epigenome of Ewing sarcoma cells reflects the regulatory state of genes associated with the DNA-binding activity of the fusion oncoproteins EWSR1::FLI1 or EWSR1::ERG. In this study, we examined the EWSR1::FLI1/ERG's repression of transcription factor genes, concentrating on those that exhibit a broader range of expression in tumors than in Ewing sarcoma cell lines.

The peptide GOLVEN10 alters root development and noduletaxis in Medicago truncatula.

The conservation of GOLVEN (GLV)/ROOT MERISTEM GROWTH FACTOR (RGF) peptide encoding genes across plant genomes capable of forming roots or root-like structures underscores their potential significance in the terrestrial adaptation of plants. This study investigates the function and role of GOLVEN peptide-coding genes in Medicago truncatula. Five out of fifteen GLV/RGF genes were notably upregulated during nodule organogenesis and were differentially responsive to nitrogen deficiency and auxin treatment.

ETS1, a target gene of the EWSR1::FLI1 fusion oncoprotein, regulates the expression of the focal adhesion protein TENSIN3.

The mechanistic basis for the metastasis of Ewing sarcomas remains poorly understood, as these tumors harbor few mutations beyond the chromosomal translocation that initiates the disease. Instead, the epigenome of Ewing sarcoma (EWS) cells reflects the regulatory state of genes associated with the DNA binding activity of the fusion oncoproteins EWSR1::FLI1 or EWSR1::ERG. In this study, we examined the EWSR1::FLI1/ERG's repression of transcription factor genes, concentrating on those that exhibit a broader range of expression in tumors than in EWS cell lines.

Annotated genome sequence of a fast-growing diploid clone of red alder (Alnus rubra Bong.).

Red alder (Alnus rubra Bong.) is an ecologically significant and important fast-growing commercial tree species native to western coastal and riparian regions of North America, having highly desirable wood, pigment, and medicinal properties. We have sequenced the genome of a rapidly growing clone.

Comparative Genome Analyses of Plant Rust Pathogen Genomes Reveal a Confluence of Pathogenicity Factors to Quell Host Plant Defense Responses.

Switchgrass rust caused by () has the ability to significantly affect the biomass yield of switchgrass, an important biofuel crop in the United States. A comparative genome analysis of with rust pathogen genomes infecting monocot cereal crops wheat, barley, oats, maize and sorghum revealed the presence of larger structural variations contributing to their genome sizes. A comparative alignment of the rust pathogen genomes resulted in the identification of collinear and syntenic relationships between and ; 21-0 ( 21) and Ug99 ( Ug99) and between 21 and ().

Fungi Modulate the Switchgrass Root Transcriptome to Circumvent Host Defenses and Establish a Symbiotic Relationship.

The fungal family Serendipitaceae encompasses root-associated lineages with endophytic, ericoid, orchid, and ectomycorrhizal lifestyles. Switchgrass is an important bioenergy crop for cellulosic ethanol production owing to high biomass production on marginal soils otherwise unfit for food crop cultivation. The aim of this study was to investigate the host plant responses to spp.

PIP-SNP: a pipeline for processing SNP data featured as linkage disequilibrium bin mapping, genotype imputing and marker synthesizing.

Genome-wide association study data analyses often face two significant challenges: (i) high dimensionality of single-nucleotide polymorphism (SNP) genotypes and (ii) imputation of missing values. SNPs are not independent due to physical linkage and natural selection. The correlation of nearby SNPs is known as linkage disequilibrium (LD), which can be used for LD conceptual SNP bin mapping, missing genotype inferencing and SNP dimension reduction.

Distinguishing HapMap Accessions Through Recursive Set Partitioning in Hierarchical Decision Trees.

The HapMap (haplotype map) projects have produced valuable genetic resources in life science research communities, allowing researchers to investigate sequence variations and conduct genome-wide association study (GWAS) analyses. A typical HapMap project may require sequencing hundreds, even thousands, of individual lines or accessions within a species. Due to limitations in current sequencing technology, the genotype values for some accessions cannot be clearly called.

LegumeIP V3: from models to crops-an integrative gene discovery platform for translational genomics in legumes.

Legumes have contributed to human health, sustainable food and feed production worldwide for centuries. The study of model legumes has played vital roles in deciphering key genes, pathways, and networks regulating biological mechanisms and agronomic traits. Along with emerging breeding technology such as genome editing, translation of the knowledge gained from model plants to crops is in high demand.

Iron-Sulfur Cluster Protein NITROGEN FIXATION S-LIKE1 and Its Interactor FRATAXIN Function in Plant Immunity.

Iron-sulfur (Fe-S) clusters are inorganic cofactors that are present in all kingdoms of life as part of a large number of proteins involved in several cellular processes, including DNA replication and metabolism. In this work, we demonstrate an additional role for two Fe-S cluster genes in biotic stress responses in plants. Eleven Fe-S cluster genes, including the - () and its interactor (), when silenced in , compromised nonhost resistance to pv.

: A Web Server for Designing Effective and Specific Plant siRNAs with Genome-Wide Off-Target Assessment.

We report an advanced web server, the plant-specific small noncoding RNA interference tool , which can be used to design a pool of small interfering RNAs (siRNAs) for highly effective, specific, and nontoxic gene silencing in plants. In developing this tool, we integrated the transcript dataset of plants, several rules governing gene silencing, and a series of computational models of the biological mechanism of the RNA interference (RNAi) pathway. The designed pool of siRNAs can be used to construct a long double-strand RNA and expressed through virus-induced gene silencing (VIGS) or synthetic transacting siRNA vectors for gene silencing.

Insertional mutagenesis of Brachypodium distachyon using the Tnt1 retrotransposable element.

Brachypodium distachyon is an annual C3 grass used as a monocot model system in functional genomics research. Insertional mutagenesis is a powerful tool for both forward and reverse genetics studies. In this study, we explored the possibility of using the tobacco retrotransposon Tnt1 to create a transposon-based insertion mutant population in B.

The CLE53-SUNN genetic pathway negatively regulates arbuscular mycorrhiza root colonization in Medicago truncatula.

Plants and arbuscular mycorrhizal fungi (AMF) engage in mutually beneficial symbioses based on a reciprocal exchange of nutrients. The beneficial character of the symbiosis is maintained through a mechanism called autoregulation of mycorrhization (AOM). AOM includes root-to-shoot-to-root signaling; however, the molecular details of AOM are poorly understood.

MtSSPdb: The Small Secreted Peptide Database.

A growing number of small secreted peptides (SSPs) in plants are recognized as important regulatory molecules with roles in processes such as growth, development, reproduction, stress tolerance, and pathogen defense. Recent discoveries further implicate SSPs in regulating root nodule development, which is of particular significance for legumes. SSP-coding genes are frequently overlooked, because genome annotation pipelines generally ignore small open reading frames, which are those most likely to encode SSPs.

GPU empowered pipelines for calculating genome-wide kinship matrices with ultra-high dimensional genetic variants and facilitating 1D and 2D GWAS.

Genome-wide association study (GWAS) is a powerful approach that has revolutionized the field of quantitative genetics. Two-dimensional GWAS that accounts for epistatic genetic effects needs to consider the effects of marker pairs, thus quadratic genetic variants, compared to one-dimensional GWAS that accounts for individual genetic variants. Calculating genome-wide kinship matrices in GWAS that account for relationships among individuals represented by ultra-high dimensional genetic variants is computationally challenging.

Identification and Functional Investigation of Genome-Encoded, Small, Secreted Peptides in Plants.

Hundreds to thousands of small secreted peptides (SSPs) are encoded in plant genomes but have been overlooked, and most remain unannotated and unstudied. Despite their low profile, they have been found to confer dramatic effects on growth and development of plants. With the growing appreciation of their significance, the development of appropriate methods to identify and functionally assess the myriad SSPs encoded in plant genomes has become critical.

Draft Genome Sequence Resource of Switchgrass Rust Pathogen, Isolate Ard-01.

is an important biotrophic fungal pathogen that causes rust disease in switchgrass. Lack of genomic resources for has hampered the progress toward developing effective disease resistance against this pathogen. Therefore, we have sequenced the whole genome of and generated a framework to understand pathogenicity mechanisms and identify effectors, repeat element invasion, genome evolution, and comparative genomics among spp.

A microRNA biogenesis-like pathway for producing phased small interfering RNA from a long non-coding RNA in rice.

Phased small interfering RNAs (phasiRNAs) are a class of non-coding RNAs that perform essential functions in plants. Unlike microRNA biogenesis from a hairpin structure, the production of phasiRNAs usually requires a phase initiator and an RNA-dependent RNA polymerase (RDR) to form double-strand RNAs. By using full-length rice cDNA (KL-cDNA) to identify phasiRNA loci, we found that a putative non-coding sequence with a long hairpin structure generates the phasiRNAs, which we name Long Hairpin-structure containing non-coding RNA (LHR).

GWASpro: a high-performance genome-wide association analysis server.

Summary: We present GWASpro, a high-performance web server for the analyses of large-scale genome-wide association studies (GWAS). GWASpro was developed to provide data analyses for large-scale molecular genetic data, coupled with complex replicated experimental designs such as found in plant science investigations and to overcome the steep learning curves of existing GWAS software tools. GWASpro supports building complex design matrices, by which complex experimental designs that may include replications, treatments, locations and times, can be accounted for in the linear mixed model.

2D association and integrative omics analysis in rice provides systems biology view in trait analysis.

The interactions among genes and between genes and environment contribute significantly to the phenotypic variation of complex traits and may be possible explanations for missing heritability. However, to our knowledge no existing tool can address the two kinds of interactions. Here we propose a novel linear mixed model that considers not only the additive effects of biological markers but also the interaction effects of marker pairs.

psRNATarget: a plant small RNA target analysis server (2017 release).

Plant regulatory small RNAs (sRNAs), which include most microRNAs (miRNAs) and a subset of small interfering RNAs (siRNAs), such as the phased siRNAs (phasiRNAs), play important roles in regulating gene expression. Although generated from genetically distinct biogenesis pathways, these regulatory sRNAs share the same mechanisms for post-translational gene silencing and translational inhibition. psRNATarget was developed to identify plant sRNA targets by (i) analyzing complementary matching between the sRNA sequence and target mRNA sequence using a predefined scoring schema and (ii) by evaluating target site accessibility.

JRmGRN: joint reconstruction of multiple gene regulatory networks with common hub genes using data from multiple tissues or conditions.

Motivation: Joint reconstruction of multiple gene regulatory networks (GRNs) using gene expression data from multiple tissues/conditions is very important for understanding common and tissue/condition-specific regulation. However, there are currently no computational models and methods available for directly constructing such multiple GRNs that not only share some common hub genes but also possess tissue/condition-specific regulatory edges.

Results: In this paper, we proposed a new graphic Gaussian model for joint reconstruction of multiple gene regulatory networks (JRmGRN), which highlighted hub genes, using gene expression data from several tissues/conditions.

Genome-Wide Identification of Peptides Involved in Macronutrient Responses and Nodulation.

Growing evidence indicates that small, secreted peptides (SSPs) play critical roles in legume growth and development, yet the annotation of SSP-coding genes is far from complete. Systematic reannotation of the genome identified 1,970 homologs of established SSP gene families and an additional 2,455 genes that are potentially novel SSPs, previously unreported in the literature. The expression patterns of known and putative SSP genes based on 144 RNA sequencing data sets covering various stages of macronutrient deficiencies and symbiotic interactions with rhizobia and mycorrhiza were investigated.