Structural Basis for the Calmodulin-Mediated Activation of eEF-2K

Translation is a highly energy consumptive process tightly regulated for optimal protein quality and adaptation to energy and nutrient availability. A key facilitator of this process is the α-kinase eEF-2K that specifically phosphorylates the GTP-dependent translocase eEF-2, thereby reducing its affinity for the ribosome and suppressing the elongation phase of protein synthesis. eEF-2K activation requires calmodulin binding and auto-phosphorylation at the primary stimulatory site, T348. Biochemical studies have predicted that calmodulin activates eEF-2K through a unique allosteric process mechanistically distinct from other calmodulin-dependent kinases. Here we resolve the atomic details of this mechanism through a 2.3 Å crystal structure of the heterodimeric complex of calmodulin with the functional core of eEF-2K (eEF-2KTR). This structure, which represents the activated T348-phosphorylated state of eEF-2KTR, highlights how through an intimate association with the calmodulin C-lobe, the kinase creates a spine that extends from its N-terminal calmodulin-targeting motif through a conserved regulatory element to its active site. Modification of key spine residues has deleterious functional consequences.

A deep generative model for multi-view profiling of single-cell RNA-seq and ATAC-seq data

Here, we present a multi-modal deep generative model, the single-cell Multi-View Profiler (scMVP), which is designed for handling sequencing data that simultaneously measure gene expression and chromatin accessibility in the same cell, including SNARE-seq, sci-CAR, Paired-seq, SHARE-seq, and Multiome from 10X Genomics. scMVP generates common latent representations for dimensionality reduction, cell clustering, and developmental trajectory inference and generates separate imputations for differential analysis and cis-regulatory element identification. scMVP can help mitigate data sparsity issues with imputation and accurately identify cell groups for different joint profiling techniques with common latent embedding, and we demonstrate its advantages on several realistic datasets.

Dynamic Regulation of Lipid Metabolism in the Placenta of in Vitro and in Vivo Models of Gestational Diabetes Mellitus

Background: The purpose of this study was to investigate lipid metabolism in the placenta of Gestational diabetes mellitus (GDM) individuals and to evaluate its effect on the fetus. Methods: We examined the expression of lipogenesis- and lipolysis-related proteins in the in vitro and in vivo GDM placenta models. Results: The levels of sterol regulatory element binding protein-1c (SREBP-1c) were increased, and fat accumulated more during early hyperglycemia, indicating that lipogenesis was stimulated. When hyperglycemia was further extended, lipolysis was activated due to the phosphorylation of hormone-sensitive lipase (HSL) and expression of adipose triglyceride lipase (ATGL). In the animal model of GDM and in the placenta of GDM patients during the extended stage of GDM, the expression of SREBP-1c decreased and the deposition of fat increased. Similar to the results obtained in the in vitro study, lipolysis was enhanced in the animal and human placenta of extended GDM. Conclusion: These results suggest that fat synthesis may be stimulated by lipogenesis in the placenta when the blood glucose level is high. Subsequently, the accumulated fat can be degraded by lipolysis and more fat and its metabolites can be delivered to the fetus when the GDM condition is extended at the late stage of gestation. Imbalanced fat metabolism in the placenta and fetus of GDM patients can cause metabolic complications in the fetus, including fetal macrosomia, obesity, and type 2 diabetes mellitus.

Three classes of epigenomic regulators converge to hyperactivate the essential maternal gene deadhead within a heterochromatin mini-domain

The formation of a diploid zygote is a highly complex cellular process that is entirely controlled by maternal gene products stored in the egg cytoplasm. This highly specialized transcriptional program is tightly controlled at the chromatin level in the female germline. As an extreme case in point, the massive and specific ovarian expression of the essential thioredoxin Deadhead (DHD) is critically regulated in Drosophila by the histone demethylase Lid and its partner, the histone deacetylase complex Sin3A/Rpd3, via yet unknown mechanisms. Here, we identified Snr1 and Mod(mdg4) as essential for dhd expression and investigated how these epigenomic effectors act with Lid and Sin3A to hyperactivate dhd. Using Cut&Run chromatin profiling with a dedicated data analysis procedure, we found that dhd is intriguingly embedded in an H3K27me3/H3K9me3-enriched mini-domain flanked by DNA regulatory elements, including a dhd promoter-proximal element essential for its expression. Surprisingly, Lid, Sin3a, Snr1 and Mod(mdg4) impact H3K27me3 and this regulatory element in distinct manners. However, we show that these effectors activate dhd independently of H3K27me3/H3K9me3, and that dhd remains silent in the absence of these marks. Together, our study demonstrates an atypical and critical role for chromatin regulators Lid, Sin3A, Snr1 and Mod(mdg4) to trigger tissue-specific hyperactivation within a unique heterochromatin mini-domain.

Egg yolk phosphatidylcholine is more effective than soybean phosphatidylcholine in improving dyslipidemia of obesity in mice fed a high-fat diet

This study aimed to evaluate the effects of dietary egg yolk phosphatidylcholine (EPC) and soybean phosphatidylcholine (SPC) on obesity mice fed a high-fat diet (HFD). After 60 days of dietary intervention, the effects were evaluated by biochemical indices and serum lipidomic analysis. EPC and SPC markedly reduced serum total cholesterol, serum triacylglycerol (TAG) and low-density lipoprotein cholesterol, while increased high-density lipoprotein cholesterol. EPC was more effective in reducing malondialdehyde and superoxide dismutase in liver than SPC. Main lipids including glycerophospholipids, TAG, sphingolipids and fatty acyls were significantly modified by EPC. Compared with HFD, EPC increased 10 main differential lipids such as phosphatidyl ethanolamine (22:6_20:0). The expressions of related protein including sterol-regulatory element binding proteins sterol-regulatory element binding proteins (SREBP-1c) and peroxisome proliferator-activated receptor α (PPAR-α) were significantly down-regulated with EPC treatment. Therefore, EPC was more effective than SPC in improving obesity by regulating glycerophospholipid metabolism.

Learning the histone codes of gene regulation with large genomic windows and three-dimensional chromatin interactions using transformer

The quantitative characterization of the transcriptional control by histone modifications (HMs) has been challenged by many computational studies, but still most of them exploit only partial aspects of intricate mechanisms involved in gene regulation, leaving a room for improvement. We present Chromoformer, a new transformer-based deep learning architecture that achieves the state-of-the-art performance in the quantitative deciphering of the histone codes of gene regulation. The core essence of Chromoformer architecture lies in the three variants of attention operation, each specialized to model individual hierarchy of three-dimensional (3D) transcriptional regulation including (1) histone codes at core promoters, (2) pairwise interaction between a core promoter and a distal cis-regulatory element mediated by 3D chromatin interactions, and (3) the collective effect of the pairwise cis-regulations. In-depth interpretation of the trained model behavior based on attention scores suggests that Chromoformer adaptively exploits the distant dependencies between HMs associated with transcription initiation and elongation. We also demonstrate that the quantitative kinetics of transcription factories and polycomb group bodies, in which the coordinated gene regulation occurs through spatial sequestration of genes with regulatory elements, can be captured by Chromoformer. Together, our study shows the great power of attention-based deep learning as a versatile modeling approach for the complex epigenetic landscape of gene regulation and highlights its potential as an effective toolkit that facilitates scientific discoveries in computational epigenetics.

Intragenic proviral elements support transcription of defective HIV-1 proviruses

HIV-1 establishes a persistent proviral reservoir by integrating into the genome of infected host cells. Current antiretroviral treatments do not target this persistent population of proviruses which include latently infected cells that upon treatment interruption can be reactivated to contribute to HIV-1 rebound. Deep sequencing of persistent HIV proviruses has revealed that greater than 90% of integrated HIV genomes are defective and unable to produce infectious virions. We hypothesized that intragenic elements in the HIV genome support transcription of aberrant HIV-1 RNAs from defective proviruses that lack long terminal repeats (LTRs). Using an intact provirus detection assay, we observed that resting CD4+ T cells and monocyte-derived macrophages (MDMs) are biased towards generating defective HIV-1 proviruses. Multiplex reverse transcription droplet digital PCR identified env and nef transcripts which lacked 5’ untranslated regions (UTR) in acutely infected CD4+ T cells and MDMs indicating transcripts are generated that do not utilize the promoter within the LTR. 5’UTR-deficient env transcripts were also identified in a cohort of people living with HIV (PLWH) on ART, suggesting that these aberrant RNAs are produced in vivo. Using 5’ rapid amplification of cDNA ends (RACE), we mapped the start site of these transcripts within the Env gene. This region bound several cellular transcription factors and functioned as a transcriptional regulatory element that could support transcription and translation of downstream HIV-1 RNAs. These studies provide mechanistic insights into how defective HIV-1 proviruses are persistently expressed to potentially drive inflammation in PLWH.

The Hypolipidemic Effect of Dalbergia odorifera T. C. Chen Leaf Extract on Hyperlipidemic Rats and Its Mechanism Investigation Based on Network Pharmacology

Objective. The aim of this study was to explore the hypolipidemic effect and mechanism of Dalbergia odorifera T. C. Chen leaf extract. Methods. The hypolipidemic effect of D. odorifera leaf extract was investigated using a hyperlipidemic rat model. Then, its mechanism was predicted using network pharmacology methods and verified using western blotting. Results. Compared with the levels in the model group, the serum levels of triglyceride (TG), total cholesterol (TC), and low-density lipoprotein cholesterol (LDL-C) decreased significantly, whereas the serum level of high-density lipoprotein cholesterol (HDL-C) increased dramatically after treatment with the extract. The degrees of hepatocyte steatosis and inflammatory infiltration were markedly attenuated in vivo. Then, its hyperlipidemic mechanism was predicted using network pharmacology-based analysis. Thirty-five key targets, including sterol regulatory element-binding protein cleavage-activating protein (SCAP), sterol regulatory element-binding protein-2 (SREBP-2), 3-hydroxy-3-methylglutaryl-coenzyme A reductase (HMGCR), low-density lipoprotein receptor (LDLR), and ten signaling pathways, were associated with hyperlipidemia. Finally, it was verified that the extract downregulated the protein levels of SCAP, SREBP-2, and HMGCR, and upregulated protein levels of LDLR. Conclusion. These findings provided additional evidence of the hypolipidemic effect of D. odorifera leaf extract.

Genome-Wide cis-Regulatory Element Based Discovery of Auxin-Responsive Genes in Higher Plant

Auxin has a profound impact on plant physiology and participates in almost all aspects of plant development processes. Auxin exerts profound pleiotropic effects on plant growth and differentiation by regulating the auxin response genes’ expressions. The classical auxin reaction is usually mediated by auxin response factors (ARFs), which bind to the auxin response element (AuxRE) in the promoter region of the target gene. Experiments have generated only a limited number of plant genes with well-characterized functions. It is still unknown how many genes respond to exogenous auxin treatment. An economical and effective method was proposed for the genome-wide discovery of genes responsive to auxin in a model plant, Arabidopsis thaliana (A. thaliana). Our method relies on cis-regulatory-element-based targeted gene finding across different promoters in a genome. We first exploit and analyze auxin-specific cis-regulatory elements for the transcription of the target genes, and then identify putative auxin responsive genes whose promoters contain the elements in the collection of over 25,800 promoters in the A. thaliana genome. Evaluating our result by comparing with a published database and the literature, we found that this method has an accuracy rate of 65.2% (309/474) for predicting candidate genes responsive to auxin. Chromosome distribution and annotation of the putative auxin-responsive genes predicted here were also mined. The results can markedly decrease the number of identified but merely potential auxin target genes and also provide useful clues for improving the annotation of gene that lack functional information.

Altered HIV-1 mRNA Splicing Due to Drug-Resistance-Associated Mutations in Exon 2/2b

The underlying molecular mechanism and their general effect on the replication capacity of HIV 1 drug-resistance-associated mutations is often poorly understood. To elucidate the effect of two such mutations located in a region with a high density of spicing regulatory elements on the HIV-1-splicing outcome, bioinformatic predictions were combined with transfection and infection experiments. Results show that the previously described R263K drug-resistance-associated integrase mutation has additionally a severe effect on the ESE2b splicing regulatory element (SRE) in exon 2b, which causes loss of SD2b recognition. This was confirmed by an R263R silent mutation with a similar predicted effect on the exon 2b SRE. In contrast, a V260I mutation and its silent counterpart with a lower effect on ESS2b did not exhibit any differences in the splicing pattern. Since HIV-1 highly relies on a balanced splicing reaction, changes in the splicing outcome can contribute to changes in viral replication and might add to the effect of escape mutations toward antiviral drugs. Thus, a classification of mutations purely addressing proteins is insufficient.