Expression analysis of transcription factors in sugarcane during cold stress

Transcription factors (TF) are a wide class of genes in plants, and these can regulate the expression of other genes in response to various environmental stresses (biotic and abiotic). In the current study, transcription factor activity in sugarcane was examined during cold stress. Initially, RNA transcript reads of two sugarcane cultivars (ROC22 and GT08-1108) under cold stress were downloaded from SRA NCBI database. The reads were aligned into a reference genome and the differential expression analyses were performed with the R/Bioconductor edgeR package. Based on our analyses in the ROC22 cultivar, 963 TF genes were significantly upregulated under cold stress among a total of 5649 upregulated genes, while 293 TF genes were downregulated among a total of 3,289 downregulated genes. In the GT08-1108 cultivar, 974 TF genes were identified among 5,649 upregulated genes and 283 TF genes were found among 3,289 downregulated genes. Most transcription factors were annotated with GO categories related to protein binding, transcription factor binding, DNA-sequence-specific binding, transcription factor complex, transcription factor activity in RNA polymerase II, the activity of nucleic acid binding transcription factor, transcription corepressor activity, sequence-specific regulatory region, the activity of transcription factor of RNA polymerase II, transcription factor cofactor activity, transcription factor activity from plastid promoter, transcription factor activity from RNA polymerase I promoter, polymerase II and RNA polymerase III. The findings of above results will help to identify differentially expressed transcription factors during cold stress. It also provides a comprehensive analysis of the regulation of the transcription activity of many genes. Therefore, this study provides the molecular basis for improving cold tolerance in sugarcane and other economically important grasses.

The transcription factor activity gradient (TAG) model: contemplating a contact-independent mechanism for enhancer–promoter communication

How distal cis-regulatory elements (e.g., enhancers) communicate with promoters remains an unresolved question of fundamental importance. Although transcription factors and cofactors are known to mediate this communication, the mechanism by which diffusible molecules relay regulatory information from one position to another along the chromosome is a biophysical puzzle—one that needs to be revisited in light of recent data that cannot easily fit into previous solutions. Here we propose a new model that diverges from the textbook enhancer–promoter looping paradigm and offer a synthesis of the literature to make a case for its plausibility, focusing on the coactivator p300.

Novel Irreversible Menin Inhibitor, BMF-219, Shows Potent Single Agent Activity in Clinically Relevant DLBCL Cells

Introduction: Diffuse large B-cell lymphoma (DLBCL) is the most common subtype of Non-Hodgkin Lymphoma. Double Hit Lymphomas (DHL) and Double Expresser Lymphomas (DEL) are high grade B-cell lymphomas (HGBLs) that have high MYC and BCL2 dependency. DHL harbor translocations of MYC and BCL2 (or BCL6 less frequently), which lead to increased cell growth and survival. Standard R-CHOP therapy is inadequate and results in poor patient outcomes. Novel targeted agents, which inhibit MYC and BCL2 are currently under investigation; however, there is no established standard-of-care for these highly aggressive lymphomas. Menin is a scaffold protein that is essential for cancers driven by oncogenic MLL-fusions, such as in acute leukemias. At present, the role of menin in DLBCL is not well described. A recent study demonstrated that MYC and menin co-localize on chromatin, leading to menin-mediated enhancement of MYC target gene expression in cancer cells. However, the relationship between menin and MYC and the direct effect of menin inhibition on MYC in liquid tumors has not been examined. Here, we demonstrate the ability of BMF-219, a novel, selective, orally bioavailable, irreversible inhibitor of menin, to modulate MYC expression in leukemia cells as the basis for exploring activity of the molecule in DLBCL cells. Methods: MOLM-13 cells incubated with BMF-219 for 6 and 24 hours at 0.5 μM and 1 μM were analyzed by RNA-seq on the Illumina NextSeq 550 platform. Differentially expressed genes were identified through DeSeq2 negative binomial model analysis. Transcription factor activity inference of differentially expressed genes was calculated using a published statistical framework and algorithm. DLBCL DHL cell lines, DB and Toledo, were treated with BMF-219 as monotherapy, and in combination with ABT-199, at a concentration range of 0.01 μM to 3 μM for a 4-day duration. Cell viability was measured using CellTiter Glo and IC 50 values were calculated. Results: RNA-seq analysis of MOLM-13 cells treated with BMF-219 showed a marked reduction of MYC transcript levels by ~25-fold at 6 hours of treatment at both concentrations tested, and ~110-fold and ~220-fold at 0.5 μM and 1 μM BMF-219 treatment, respectively, at 24 hours. Additionally, MYC and its co-factor, MAX, emerged as top candidates in transcription factor activity inference analysis based on ChIP-seq GEO repository datasets and differential expression of MOLM-13 cells treated with BMF-219 at 24 hours. These results prompted an examination of the effects of BMF-219 on lymphoid malignancies known to be highly dependent on MYC aberrations. Single-agent BMF-219 reduced >90% of cell viability in both DB and Toledo cells, at 1.0 μM and 0.36 μM, respectively. The IC 50 values of BMF-219 were calculated as 0.32 μM and 0.29 μM for DB and Toledo, respectively. Two reversible menin inhibitors tested were less effective in reducing growth of DHL cell lines. One reversible menin inhibitor exhibited IC 50 values of 3 μM and 1.5 μM in DB and Toledo, respectively, while neither cell line was sensitive to the other reversible compound. Given that a 20-fold reduction in BCL2 transcript occurred in MOLM-13 cells at 24 hours of 0.5 μM BMF-219 exposure, we investigated whether a combination of BCL2 inhibitor, ABT-199, with BMF-219 could further reduce cell viability of DHL cells. ABT-199 as a single agent reduced viability of Toledo cells, but not DB cells, at 0.33 μM. By contrast, the combination of BMF-219 and ABT-199 synergistically killed both DB and Toledo cells. Combination treatment using both inhibitors at 0.33 μM killed >80% of DB cells and 100% of Toledo cells. These results demonstrate that DLBCL DHL cells are sensitive to menin inhibition. Of note, initial data has indicated that multiple myeloma cells also manifest responses to BMF-219 similar to DHL DLBCL. Conclusions: Collectively, our study demonstrates the unique ability of BMF-219's irreversible menin inhibition, which leads to marked killing of DHL cells. BMF-219, as a single agent, substantially reduces MYC and BCL2 gene expression in liquid tumor cells, providing a molecular basis for targeting DLBCL and other tumors with these aberrations. Additionally, BMF-219 offers single agent as well as treatment synergy when combined with ABT-199 in DHL cells. These data serve as initial pre-clinical evidence for employing irreversible menin inhibition as a promising therapeutic strategy in DHL DLBCL. Disclosures Somanath: Biomea Fusion, Inc.: Consultancy, Current Employment, Current equity holder in publicly-traded company. Lu: Biomea Fusion Inc.: Current Employment, Current equity holder in publicly-traded company. Law: Biomea Fusion Inc.: Current Employment, Current equity holder in publicly-traded company, Current holder of individual stocks in a privately-held company, Current holder of stock options in a privately-held company. Archer: Biomea Fusion: Current Employment, Current holder of stock options in a privately-held company. Cacovean: Abbvie: Current equity holder in publicly-traded company; Lyell Imunopharma: Current equity holder in publicly-traded company; CytomX: Current equity holder in publicly-traded company; Iovance: Current equity holder in publicly-traded company, Ended employment in the past 24 months; Biomea Fusion: Current Employment, Current equity holder in publicly-traded company. Palmer: Nyrada, Inc.: Consultancy, Current equity holder in publicly-traded company, Membership on an entity's Board of Directors or advisory committees; Exopharm: Consultancy; Biomea Fusion Inc.: Consultancy, Current equity holder in publicly-traded company. Kinoshita: Biomea Fusion INC.,: Current Employment, Current equity holder in publicly-traded company, Current holder of individual stocks in a privately-held company, Current holder of stock options in a privately-held company, Patents & Royalties. Butler: Biomea Fusion Inc.: Current Employment, Current equity holder in publicly-traded company.

H3K9me selectively blocks transcription factor activity and ensures differentiated tissue integrity

The developmental role of histone H3K9 methylation (H3K9me), which typifies heterochromatin, remains unclear. In Caenorhabditis elegans, loss of H3K9me leads to a highly divergent upregulation of genes with tissue and developmental-stage specificity. During development H3K9me is lost from differentiated cell type-specific genes and gained at genes expressed in earlier developmental stages or other tissues. The continuous deposition of H3K9me2 by the SETDB1 homolog MET-2 after terminal differentiation is necessary to maintain repression. In differentiated tissues, H3K9me ensures silencing by restricting the activity of a defined set of transcription factors at promoters and enhancers. Increased chromatin accessibility following the loss of H3K9me is neither sufficient nor necessary to drive transcription. Increased ATAC-seq signal and gene expression correlate at a subset of loci positioned away from the nuclear envelope, while derepressed genes at the nuclear periphery remain poorly accessible despite being transcribed. In conclusion, H3K9me deposition can confer tissue-specific gene expression and maintain the integrity of terminally differentiated muscle by restricting transcription factor activity.

MdVQ37 overexpression reduces basal thermotolerance in transgenic apple by affecting transcription factor activity and salicylic acid homeostasis

High temperature (HT) is one of the most important environmental stress factors and seriously threatens plant growth, development, and production. VQ motif-containing proteins are transcriptional regulators that have been reported to regulate plant growth and developmental processes, including responses to biotic and abiotic stresses. However, the relationships between VQ motif-containing proteins and HT stress have not been studied in depth in plants. In this study, transgenic apple (Malus domestica) plants overexpressing the apple VQ motif-containing protein-coding gene (MdVQ37) were exposed to HT stress, and the transgenic lines exhibited a heat-sensitive phenotype. In addition, physiological and biochemical studies revealed that, compared with WT plants, transgenic lines had lower enzymatic activity and photosynthetic capacity and lower amounts of nonenzymatic antioxidant system metabolites under HT stress. Transcriptome analysis revealed 1379 genes whose expression differed between the transgenic lines and WT plants. GO and KEGG pathway analyses showed that transcription factor activity and plant hormone signaling pathways were differentially influenced and enriched in the transgenic lines. Salicylic acid (SA) content analysis indicated that overexpression of MdVQ37 reduced the content of endogenous SA by regulating the expression of SA catabolism-related genes, which ultimately resulted in disruption of the SA-dependent signaling pathway under HT stress. The application of SA slightly increased the survival rate of the transgenic lines under HT stress. Taken together, our results indicate that apple MdVQ37 has a regulatory function in basal thermotolerance by modulating the activity of transcription factors and SA homeostasis. Overall, this study provides novel insights that improve our understanding of the various functions of VQ motif-containing proteins.

scBasset: Sequence-based modeling of single cell ATAC-seq using convolutional neural networks

1AbstractSingle cell ATAC-seq (scATAC) shows great promise for studying cellular heterogeneity in epigenetic landscapes, but there remain significant challenges in the analysis of scATAC data due to the inherent high dimensionality and sparsity. Here we introduce scBasset, a sequence-based convolutional neural network method to model scATAC data. We show that by leveraging the DNA sequence information underlying accessibility peaks and the expressiveness of a neural network model, scBasset achieves state-of-the-art performance across a variety of tasks on scATAC and single cell multiome datasets, including cell type identification, scATAC profile denoising, data integration across assays, and transcription factor activity inference.

Baseline pro-inflammatory gene expression in whole blood is related to adverse long-term outcomes after transcatheter aortic valve replacement: a case control study

Background Age-associated inflammation and immune system dysfunction have been implicated as mechanisms that increase risk for adverse long-term procedural outcomes in older adults. The purpose of this study was to investigate relationships between baseline inflammatory and innate antiviral gene expression and outcomes after transcatheter aortic valve replacement (TAVR) in older adults with severe aortic stenosis. Methods We performed a retrospective case–control study comparing pre-procedural pro-inflammatory and Type 1 interferon (IFN) gene expression in 48 controls with favorable outcomes (alive 1 year after TAVR with improved quality of life [QoL]) versus 48 individuals with unfavorable outcomes (dead by 1 year or alive at 1 year but with reduced QoL). Gene expression was evaluated in whole blood via (1) pre-defined composite scores of 19 inflammation-associated genes and 34 Type I IFN response genes, and (2) pro-inflammatory and antiviral transcription factor activity inferred from promotor based bioinformatics analyses of genes showing > 25% difference in average expression levels across groups. All analyses were adjusted for age, gender, body mass index, diabetes, immunosuppression, cardiovascular disease (CVD), and frailty. Results Relative to controls, those with unfavorable outcomes demonstrated higher expression of the pro-inflammatory gene composite prior to TAVR (p < 0.01) and bioinformatic indicators of elevated Nuclear Factor kB (p < 0.001) and Activator Protein 1 (p < 0.001) transcription factor activity, but no significant differences in Type I IFN-related gene expression. Conclusions These results demonstrate that a pro-inflammatory state prior to TAVR, independent of CVD severity and frailty status, is associated with worse long-term procedural outcomes.