Regulatory Variations Research Articles

Glucocorticoids and HPA axis regulation in the stress-obesity connection: A comprehensive overview of biological, physiological and behavioural dimensions.

Chronic stress, characterized by increased long-term exposure to the glucocorticoid hormone cortisol, is increasingly linked to obesity development. Still, various knowledge gaps persist, including on underlying pathophysiological mechanisms. The aim of the current review is to provide the latest insights on the connection between stress and obesity. We discuss three biological stress systems-the autonomic nervous system, the hypothalamus-pituitary-adrenal (HPA) axis and the immune system-and their link with obesity, with a particular focus on the HPA axis. The role of cortisol and its regulatory variations (including glucocorticoid rhythmicity and altered sensitivity) in adipose tissue biology and obesity development is discussed. Moreover, we highlight the physiological, affective, cognitive and behavioural dimensions of the stress response offering a deeper understanding of how stress contributes to obesity development and vice versa. Finally, stress as a treatment target for obesity is discussed. We conclude that the link between stress and obesity is complex and multifaceted, influenced by physiological, affective, cognitive and behavioural stress response mechanisms, which especially when chronically present, play a key role in the development of obesity and associated cardiometabolic diseases. This necessitates integrated approaches tailored to individual needs, including lifestyle modifications, behavioural interventions, psychosocial support and possible additional pharmacological interventions.

The value of decentralized clinical trials: Inclusion, accessibility, and innovation.

In this Review, we explore the transformative potential of decentralized clinical trials (DCTs) in addressing the limitations of traditional randomized controlled trials (RCTs). We highlight the merits of DCTs fostering greater inclusivity, efficiency, and adaptability. We emphasize the challenges of RCTs, including limited participant diversity and logistical barriers, geographical constraints, and mistrust in research institutions, showing how DCTs are preferred in addressing these challenges by utilizing remote digital technologies and community providers to enable broader, more inclusive participation. Furthermore, we underscore the potential of DCTs for democratizing clinical research. We also stress the importance of addressing unresolved challenges, including data security and privacy, remote patient monitoring, and regulatory variations. Research is needed to devise standardized protocols to streamline DCT processes, explore its long-term impacts on patient outcomes, and overcome challenges through equitable stakeholder engagement.

Dynamic patterns of gene expressional and regulatory variations in cotton heterosis.

Although the application of heterosis has significantly increased crop yield over the past century, the mechanisms underlying this phenomenon still remain obscure. Here, we applied transcriptome sequencing to unravel the impacts of parental expression differences and transcriptomic reprogramming in cotton heterosis. A high-quality transcriptomic atlas covering 15 developmental stages and tissues was constructed for XZM2, an elite hybrid of upland cotton (Gossypium hirsutum L.), and its parental lines, CRI12 and J8891. This atlas allowed us to identify gene expression differences between the parents and to characterize the transcriptomic reprogramming that occurs in the hybrid. Our analysis revealed abundant gene expression differences between the parents, with pronounced tissue specificity; a total of 1,112 genes exhibited single-parent expression in at least one tissue. It also illuminated transcriptomic reprogramming in the hybrid XZM2, which included both additive and non-additive expression patterns. Coexpression networks between parents and hybrid constructed via weighted gene coexpression network analysis identified modules closely associated with fiber development. In particular, key regulatory hub genes involved in fiber development showed high-parent dominant or over dominant patterns in the hybrid, potentially driving the emergence of heterosis. Finally, high-depth resequencing data was generated and allele-specific expression patterns examined in the hybrid, enabling the dissection of cis- and trans-regulation contributions to the observed expression differences. Parental transcriptional differences and transcriptomic reprogramming in the hybrid, especially the non-additive upregulation of key genes, play an important role in shaping heterosis. Collectively, these findings provide new insights into the molecular basis of heterosis in cotton.

Reference-free inferring of transcriptomic events in cancer cells on single-cell data

BackgroundCancerous cells’ identity is determined via a mixture of multiple factors such as genomic variations, epigenetics, and the regulatory variations that are involved in transcription. The differences in transcriptome expression as well as abnormal structures in peptides determine phenotypical differences. Thus, bulk RNA-seq and more recent single-cell RNA-seq data (scRNA-seq) are important to identify pathogenic differences. In this case, we rely on k-mer decomposition of sequences to identify pathogenic variations in detail which does not need a reference, so it outperforms more traditional Next-Generation Sequencing (NGS) analysis techniques depending on the alignment of the sequences to a reference.ResultsVia our alignment-free analysis, over esophageal and glioblastoma cancer patients, high-frequency variations over multiple different locations (repeats, intergenic regions, exons, introns) as well as multiple different forms (fusion, polyadenylation, splicing, etc.) could be discovered. Additionally, we have analyzed the importance of less-focused events systematically in a classic transcriptome analysis pipeline where these events are considered as indicators for tumor prognosis, tumor prediction, tumor neoantigen inference, as well as their connection with respect to the immune microenvironment.ConclusionsOur results suggest that esophageal cancer (ESCA) and glioblastoma processes can be explained via pathogenic microbial RNA, repeated sequences, novel splicing variants, and long intergenic non-coding RNAs (lincRNAs). We expect our application of reference-free process and analysis to be helpful in tumor and normal samples differential scRNA-seq analysis, which in turn offers a more comprehensive scheme for major cancer-associated events.

Haplotype-resolved chromosomal-level genome assembly reveals regulatory variations in mulberry fruit anthocyanin content.

Understanding the intricate regulatory mechanisms underlying the anthocyanin content (AC) in fruits and vegetables is crucial for advanced biotechnological customization. In this study, we generated high-quality haplotype-resolved genome assemblies for two mulberry cultivars: the high-AC 'Zhongsang5801' (ZS5801) and the low-AC 'Zhenzhubai' (ZZB). Additionally, we conducted a comprehensive analysis of genes associated with AC production. Through genome-wide association studies (GWAS) on 112 mulberry fruits, we identified MaVHAG3, which encodes a vacuolar-type H+-ATPase G3 subunit, as a key gene linked to purple pigmentation. To gain deeper insights into the genetic and molecular processes underlying high AC, we compared the genomes of ZS5801 and ZZB, along with fruit transcriptome data across five developmental stages, and quantified the accumulation of metabolic substances. Compared to ZZB, ZS5801 exhibited significantly more differentially expressed genes (DEGs) related to anthocyanin metabolism and higher levels of anthocyanins and flavonoids. Comparative analyses revealed expansions and contractions in the flavonol synthase (FLS) and dihydroflavonol 4-reductase (DFR) genes, resulting in altered carbon flow. Co-expression analysis demonstrated that ZS5801 displayed more significant alterations in genes involved in late-stage AC regulation compared to ZZB, particularly during the phase stage. In summary, our findings provide valuable insights into the regulation of mulberry fruit AC, offering genetic resources to enhance cultivars with higher AC traits.

Green supply chain management influence on theeconomic and environmental aspectsin China.

In China's rapid industrial development, the adoption and impact of green supply chain practices (GSCP) have become pivotal. This research employs a non-radial, non-angle SBM-DEA model to examine the intricate relationship between environmental sustainability and economic advancement. The observation suggests that companies adopting the global sustainable consumption and production (GSCP) framework demonstrate a more substantial alignment with China's sustainable goals. However, this alignment is accompanied by a fundamental conflict between the need for economic growth and the need for environmental caution. This study highlights China's sincere efforts to adhere to global ecological norms, as the environmental outcomes (ENVO) demonstrated. The findings on organizational culture (O.C.) present a complex depiction of China's direction, highlighting the intersection between its longstanding traditions with the pressing demands of modern environmentally sustainable corporate practices. The presence of regulatory variations across provinces highlights the regional differences within the nation, thus causing organizations to adopt adaptable environmental policies. The complex network of supply chains in China and the careful management of financial resources underscore the diverse range of difficulties and opportunities that firms face. This research ultimately provides a comprehensive understanding of the crucial balancing process that characterizes China's path toward environmental sustainability. It highlights the importance of effectively managing these factors, since it is essential for enterprises to achieve enduring and sustainable success.

The PFAS controversy part-2: Global perspectives and regulatory variations

The PFAS controversy part-2: Global perspectives and regulatory variations

Gene communities in co-expression networks across different tissues.

With the recent availability of tissue-specific gene expression data, e.g., provided by the GTEx Consortium, there is interest in comparing gene co-expression patterns across tissues. One promising approach to this problem is to use a multilayer network analysis framework and perform multilayer community detection. Communities in gene co-expression networks reveal groups of genes similarly expressed across individuals, potentially involved in related biological processes responding to specific environmental stimuli or sharing common regulatory variations. We construct a multilayer network in which each of the four layers is an exocrine gland tissue-specific gene co-expression network. We develop methods for multilayer community detection with correlation matrix input and an appropriate null model. Our correlation matrix input method identifies five groups of genes that are similarly co-expressed in multiple tissues (a community that spans multiple layers, which we call a generalist community) and two groups of genes that are co-expressed in just one tissue (a community that lies primarily within just one layer, which we call a specialist community). We further found gene co-expression communities where the genes physically cluster across the genome significantly more than expected by chance (on chromosomes 1 and 11). This clustering hints at underlying regulatory elements determining similar expression patterns across individuals and cell types. We suggest that KRTAP3-1, KRTAP3-3, and KRTAP3-5 share regulatory elements in skin and pancreas. Furthermore, we find that CELA3A and CELA3B share associated expression quantitative trait loci in the pancreas. The results indicate that our multilayer community detection method for correlation matrix input extracts biologically interesting communities of genes.

Dietary Exposure and Risk Assessment of Beta-Agonist Residues in Commercial Beef and Pork in Taiwan.

Beta-agonists (β-agonists) in meat products in one's diet raise concerns about the possibility of foodborne illness. It may also lead to discomfort, such as headaches and occasional irregular heartbeats, which might be linked to a heightened concern for cardiovascular issues. Taiwan's high demand for meat and reliance on imported meat products from certain countries where β-agonists are permitted has raised concerns. Recent import border checks and monitoring of meat products in the market have revealed the concentration of non-compliance with β-agonist residue regulations, which is ten ppb. This study aims to analyze the concentration of β-agonist residues in meat products sold in Taiwan and assess the current levels of exposure and dietary risk for consumers. The study analyzed 1415 samples of domestically produced and imported livestock products from supermarkets, traditional markets, and bulk stores in New Taipei City between 2019 and 2023. The samples were analyzed using the method for detecting 21 β-agonists based on the Taiwan Food and Drug Administration's specifications. Estimated daily intake (EDI) of β-agonists for different age groups and the target hazard quotient (THQ) were used to assess dietary exposure and risk. The results showed that all 1415 samples were compliant with regulations. Among them, 43 beef samples showed residues of ractopamine originating from the United States, with residue concentrations ranging from 1 to 10 μg/kg and an average residue concentration of 3.3 ± 1.9 μg/kg. Under average consumption, the highest EDI for the exposed population was observed in the 6-12 age group, with values of 0.1469 μg/kg/day, 0.0734 μg/kg/day, and 0.0242 μg/kg/day for the three residue concentrations (maximum detected residue, maximum allowable residue, and average detected residue, respectively). The THQs for ractopamine in imported beef samples were all less than 1, indicating no health hazards at the current intake levels of each age group and the residue concentrations in commercially available beef. Despite the findings, traders need to acknowledge regulatory variations between Taiwan and exporting countries when importing meat products. Traders should provide inspection reports to monitor β-agonist residue levels in imports or explore sourcing beef from countries with β-agonist bans.

Evolutionary analysis of conserved non-coding elements subsequent to whole-genome duplication in opium poppy.

Whole-genome duplication (WGD) leads to the duplication of both coding and non-coding sequences within an organism's genome, providing an abundant supply of genetic material that can drive evolution, ultimately contributing to plant adaptation and speciation. Although non-coding sequences contain numerous regulatory elements, they have been understudied compared to coding sequences. In order to address this gap, we explored the evolutionary patterns of regulatory sequences, coding sequences and transcriptomes using conserved non-coding elements (CNEs) as regulatory element proxies following the recent WGD event in opium poppy (Papaver somniferum). Our results showed similar evolutionary patterns in subgenomes of regulatory and coding sequences. Specifically, the biased or unbiased retention of coding sequences reflected the same pattern as retention levels in regulatory sequences. Further, the divergence of gene expression patterns mediated by regulatory element variations occurred at a more rapid pace than that of gene coding sequences. However, gene losses were purportedly dependent on relaxed selection pressure in coding sequences. Specifically, the rapid evolution of tissue-specific benzylisoquinoline alkaloid production in P. somniferum was associated with regulatory element changes. The origin of a novel stem-specific ACR, which utilized ancestral cis-elements as templates, is likely to be linked to the evolutionary trajectory behind the transition of the PSMT1-CYP719A21 cluster from high levels of expression solely in P. rhoeas root tissue to its elevated expression in P. somniferum stem tissue. Our findings demonstrate that rapid regulatory element evolution can contribute to the emergence of new phenotypes and provide valuable insights into the high evolvability of regulatory elements.

Genetic Testing for Prostate Cancer, Urothelial Cancer, and Kidney Cancer

As genetic testing plays an increasingly salient role in the realm of cancer diagnosis, prognostication, and treatment, this review aims to elucidate the current landscape and future directions of genetic testing in genitourinary cancers, with a focus on prostate cancer, urothelial carcinoma, and renal cell carcinoma. With the increasing adoption of next-generation sequencing technology, the utilization and access to genetic testing in real-world settings have become critical for practicing urologists and genitourinary oncologists, especially after the approval of poly(ADP-ribose) polymerase inhibitors for prostate cancer and the utilization of immune checkpoint inhibitors. In this rapidly evolving field, this review underscores the clinical value of interpreting genetic variations and the importance of distinguishing between germline and somatic mutations, for whom testing can be prescribed, and which genes should be tested. While the current modus operandi predominantly relies on exome sequencing, we posit that the future of genetic testing in genitourinary cancers will see an expansion to encompass whole-genome sequencing, accounting for structural and regulatory variations that impact gene expression. In the upcoming era of liquid biopsies, we envisage an increase in noninvasive cancer genetic testing for the purposes of diagnosis, prognosis, treatment response, and progression monitoring, supplementing the gold-standard tissue biopsies that provide histologic information. Ultimately, thoroughly interpreting genetic testing results and the subsequent treatment implications necessitates a multidisciplinary approach. This review strives to offer urologists a comprehensive perspective on genetic testing in these prevalent urological cancers, contributing to improved diagnosis, prognosis, and treatment decision-making.

Hypergraph factorization for multi-tissue gene expression imputation

Integrating gene expression across tissues and cell types is crucial for understanding the coordinated biological mechanisms that drive disease and characterize homoeostasis. However, traditional multi-tissue integration methods either cannot handle uncollected tissues or rely on genotype information, which is often unavailable and subject to privacy concerns. Here we present HYFA (hypergraph factorization), a parameter-efficient graph representation learning approach for joint imputation of multi-tissue and cell-type gene expression. HYFA is genotype agnostic, supports a variable number of collected tissues per individual, and imposes strong inductive biases to leverage the shared regulatory architecture of tissues and genes. In performance comparison on Genotype–Tissue Expression project data, HYFA achieves superior performance over existing methods, especially when multiple reference tissues are available. The HYFA-imputed dataset can be used to identify replicable regulatory genetic variations (expression quantitative trait loci), with substantial gains over the original incomplete dataset. HYFA can accelerate the effective and scalable integration of tissue and cell-type transcriptome biorepositories.

Hybrid allele-specific ChIP-seq analysis identifies variation in brassinosteroid-responsive transcription factor binding linked to traits in maize

BackgroundGenetic variation in regulatory sequences that alter transcription factor (TF) binding is a major cause of phenotypic diversity. Brassinosteroid is a growth hormone that has major effects on plant phenotypes. Genetic variation in brassinosteroid-responsive cis-elements likely contributes to trait variation. Pinpointing such regulatory variations and quantitative genomic analysis of the variation in TF-target binding, however, remains challenging. How variation in transcriptional targets of signaling pathways such as the brassinosteroid pathway contributes to phenotypic variation is an important question to be investigated with innovative approaches.ResultsHere, we use a hybrid allele-specific chromatin binding sequencing (HASCh-seq) approach and identify variations in target binding of the brassinosteroid-responsive TF ZmBZR1 in maize. HASCh-seq in the B73xMo17 F1s identifies thousands of target genes of ZmBZR1. Allele-specific ZmBZR1 binding (ASB) has been observed for 18.3% of target genes and is enriched in promoter and enhancer regions. About a quarter of the ASB sites correlate with sequence variation in BZR1-binding motifs and another quarter correlate with haplotype-specific DNA methylation, suggesting that both genetic and epigenetic variations contribute to the high level of variation in ZmBZR1 occupancy. Comparison with GWAS data shows linkage of hundreds of ASB loci to important yield and disease-related traits.ConclusionOur study provides a robust method for analyzing genome-wide variations of TF occupancy and identifies genetic and epigenetic variations of the brassinosteroid response transcription network in maize.

A statistical approach to identify regulatory DNA variations

A statistical approach to identify regulatory DNA variations

ESG principles and social responsibility

In the face of escalating global challenges such as climate change, social inequality, and governance failures, corporations are increasingly adopting Environmental, Social, and Governance (ESG) principles and emphasizing Corporate Social Responsibility (CSR). This paper critically examines the integration of ESG principles into CSR strategies within the contemporary corporate landscape. We address challenges such as inconsistent reporting standards, data quality and availability, integration of ESG into investment decisions, conflicts between short-term financial results and long-term ESG goals, and regulatory variations across countries. Our findings underscore the need for harmonized ESG reporting standards and regulatory frameworks, the importance of comprehensive stakeholder engagement, and the necessity of viewing sustainability as a long-term strategic objective. The paper provides an in-depth understanding of how corporations can navigate these challenges, thereby aligning their operations with global sustainability goals and enhancing their societal impact. This analysis will benefit corporate leaders, policy-makers, investors, and scholars interested in the evolving intersections of ESG principles and CSR.

Combined population transcriptomic and genomic analysis reveals cis-regulatory differentiation of non-coding RNAs in maize.

Long intergenic non-coding RNA (lincRNA), cis-acting expression quantitative trait locus (cis-eQTL), maize, regulatory evolution. The law of genetic variation during domestication explains the evolutionary mechanism and provides a theoretical basis for improving existing varieties of maize. Previous studies focused on exploiting regulatory variations controlling the expression of protein-coding genes rather than of non-protein-coding genes. Here, we examined the genetic and evolutionary features of long non-coding RNAs from intergenic regions (long intergenic non-coding RNAs, lincRNAs) using population-scale transcriptome data and identified 1168 lincRNAs with cis-acting expression quantitative trait loci (cis-eQTLs). We found that lincRNAs are more likely to be regulated by cis-eQTLs, which exert stronger effects than the protein-coding genes. During maize domestication and improvement, upregulated alleles of lincRNAs, which originated from both standing variation and new mutation, accumulate more frequently and show larger effect sizes than the coding genes. A stronger signature of genetic differentiation was observed in their regulatory regions compared to those of randomly sampled lincRNAs. In addition, we found that cis-regulatory differentiation of lincRNAs is related to the sequence conservation of lincRNA transcripts. Non-conserved lincRNAs moretend to gain upregulated alleles and show a stronger relationship with selected traits than conserved lincRNAs between maize and its wild relatives. Our findings in maize improve the understanding of cis-regulatory variation in lincRNA genes during domestication and improvement and provide an effective approach for prioritizing candidates for further investigation.

Identification of transcriptional regulatory variants in pig duodenum, liver, and muscle tissues.

In humans and livestock species, genome-wide association studies (GWAS) have been applied to study the association between variants distributed across the genome and a phenotype of interest. To discover genetic polymorphisms affecting the duodenum, liver, and muscle transcriptomes of 300 pigs from 3 different breeds (Duroc, Landrace, and Large White), we performed expression GWAS between 25,315,878 polymorphisms and the expression of 13,891 genes in duodenum, 12,748 genes in liver, and 11,617 genes in muscle. More than 9.68 × 1011 association tests were performed, yielding 14,096,080 significantly associated variants, which were grouped in 26,414 expression quantitative trait locus (eQTL) regions. Over 56% of the variants were within 1 Mb of their associated gene. In addition to the 100-kb region upstream of the transcription start site, we identified the importance of the 100-kb region downstream of the 3'UTR for gene regulation, as most of the cis-regulatory variants were located within these 2 regions. We also observed 39,874 hotspot regulatory polymorphisms associated with the expression of 10 or more genes that could modify the protein structure or the expression of a regulator gene. In addition, 2 motifs (5'-GATCCNGYGTTGCYG-3' and a poly(A) sequence) were enriched across the 3 tissues within the neighboring sequences of the most significant single-nucleotide polymorphisms in each cis-eQTL region. The 14 million significant associations obtained in this study are publicly available and have enabled the identification of expression-associated cis-, trans-, and hotspot regulatory variants within and across tissues, thus shedding light on the molecular mechanisms of regulatory variations that shape end-trait phenotypes.

Genomic innovation and regulatory rewiring during evolution of the cotton genus Gossypium.

Phenotypic diversity and evolutionary innovation ultimately trace to variation in genomic sequence and rewiring of regulatory networks. Here, we constructed a pan-genome of the Gossypium genus using ten representative diploid genomes. We document the genomic evolutionary history and the impact of lineage-specific transposon amplification on differential genome composition. The pan-3D genome reveals evolutionary connections between transposon-driven genome size variation and both higher-order chromatin structure reorganization and the rewiring of chromatin interactome. We linked changes in chromatin structures to phenotypic differences in cotton fiber and identified regulatory variations that decode the genetic basis of fiber length, the latter enabled by sequencing 1,005 transcriptomes during fiber development. We showcase how pan-genomic, pan-3D genomic and genetic regulatory data serve as a resource for delineating the evolutionary basis of spinnable cotton fiber. Our work provides insights into the evolution of genome organization and regulation and will inform cotton improvement by enabling regulome-based approaches.

ChromLoops: a comprehensive database for specific protein-mediated chromatin loops in diverse organisms.

Chromatin loops (or chromatin interactions) areimportant elements of chromatin structures. Disruption of chromatin loops is associated with many diseases, such as cancer and polydactyly. A few methods, including ChIA-PET, HiChIP and PLAC-Seq, have been proposed to detect high-resolution, specific protein-mediated chromatin loops. With rapid progress in 3D genomic research, ChIA-PET, HiChIP and PLAC-Seq datasets continue to accumulate, and effective collection and processing for these datasets are urgently needed. Here, we developed a comprehensive, multispecies and specific protein-mediated chromatin loop database (ChromLoops, https://3dgenomics.hzau.edu.cn/chromloops), which integrated 1030 ChIA-PET, HiChIP and PLAC-Seq datasets from 13 species, and documented 1491 416 813 high-quality chromatin loops. We annotated genes and regions overlapping with chromatin loop anchors with rich functional annotations, such as regulatory elements (enhancers, super-enhancers and silencers), variations (common SNPs, somatic SNPsand eQTLs), and transcription factor binding sites. Moreover, we identified genes with high-frequency chromatin interactions in the collected species. In particular, we identified genes with high-frequency interactions in cancer samples. We hope that ChromLoops will provide a new platform for studying chromatin interaction regulation in relation to biological processes and disease.

Evolutionary characterization of miR396s in Poaceae exemplified by their genetic effects in wheat and maize

MiR396s play important roles in regulating plant growth and stress response, and great potential for crop yield promotion was anticipated. For more comprehensive and precise understanding of miR396s in Poaceae, we analyzed the phylogenetic linkage, gene expression, and chromosomal distribution of miR396s in this study. Although the mature miR396s’ sequences were mostly conserved, differential expression patterns and chromosomal distribution were found among Poaceae species including the major cereal crops rice, wheat, and maize. Consistently, in comparison with rice, wheat and maize plants transformed with the target mimicry construct of miR396 (MIM396) exhibited differential effects on grain size and disease resistance. While the TaMIM396 plants showed increased grain size, panicle length and sensitivity to B. graminis, the ZmMIM396 plants didn’t show obvious changes in grain size and disease resistance. In Addition, several GROWTH-REGULATING FACTOR (GRF) genes in wheat and maize were repressed by miR396s, which could be reversed by MIM396, confirming the conserved regulatory roles of miR396 on GRFs. While providing new solution to enhance grain yield in wheat and revealing potential regulatory variations of miR396s in controlling grain size and disease resistance in different crops, this study gives clues to further explore miR396s’ functions in other Poaceae species.