expression divergence

East African cichlid fishes have diversified in an explosive fashion, but the (epi)genetic basis of the phenotypic diversity of these fishes remains largely unknown. Although transposable elements (TEs) have been associated with phenotypic variation in cichlids, little is known about their transcriptional activity and epigenetic silencing. Here, we describe dynamic patterns of TE expression in African cichlid gonads and during early development. Orthology inference revealed an expansion of piwil1 genes in Lake Malawi cichlids, likely driven by PiggyBac TEs...

The beneficial effect of social interaction in mitigating the incidence of post-stroke depression (PSD) and ameliorating depressive symptoms has been consistently demonstrated through preclinical and clinical studies. However, the underlying relationship with oxytocin requires further investigation. In light of this, the present study aimed to explore the protective effect of pair housing on the development of PSD and the potential relationship with oxytocin receptors. The PSD model was induced by middle cerebral artery occlusion (MCAO) for 50 min, followed by 4-week isolated housing and restrained stress...

The monoamine transporters, including the serotonin transporter (SERT), dopamine transporter (DAT), and norepinephrine transporter (NET), are the therapeutic targets for the treatment of many neuropsychiatric disorders. Despite significant progress in characterizing the structures and transport mechanisms of these transporters, the regulation of their transport functions through dimerization or oligomerization remains to be understood. In the present study, we identified a conserved intramolecular ion-pair at the third extracellular loop (EL3) connecting TM5 and TM6 that plays a critical but divergent role in the modulation of dimerization and transport functions among the monoamine transporters...

Glypicans are linked to various aspects of neoplastic behavior, and their therapeutic value has been proposed in different cancers. Here, we have systematically assessed the impact of GPC4 on cancer progression through functional genomics and transcriptomic analyses across a broad range of cancers. Survival analysis using TCGA cancer patient data reveals divergent effects of GPC4 expression across various cancer types, revealing elevated GPC4 expression levels to be associated with both poor and favorable prognoses in a cancer-dependent manner...

In the human genome, two short open reading frames (ORFs) separated by a transcriptional silencer and a small intervening sequence stem from the gene SMIM45 . The two ORFs show different translational characteristics, and they also show divergent patterns of evolutionary development. The studies presented here describe the evolution of the components of SMIM45 . One ORF consists of an ultra-conserved 68 amino acid (aa) sequence, whose origins can be traced beyond the evolutionary age of divergence of the elephant shark, ~462 MYA...

Baleen whales (Mysticeti) possess the necessary anatomical structures and genetic elements for olfaction. Nevertheless, the olfactory receptor gene ( OR ) repertoire has undergone substantial degeneration in the cetacean lineage following the divergence of the Artiodactyla and Cetacea. The functionality of highly degenerated mysticete OR s within their olfactory epithelium remains unknown. In this study, we extracted total RNA from the nasal mucosae of common minke whales ( Balaenoptera acutorostrata ) to investigate OR s' localized expression...

The family of phosphatidylethanolamine-binding proteins (PEBPs) participates in various plant biological processes, mainly flowering regulation and seed germination. In cucurbit crops, several PEBP genes have been recognized to be responsible for flowering time. However, the investigation of PEBP family members across the genomes of cucurbit species has not been reported, and their conservation and divergence in structure and function remain largely unclear. Herein, PEBP genes were identified from seven cucurbit crops and were used to perform a comparative genomics analysis...

Limb-conformation defects significantly influence equine performance and welfare, necessitating thorough investigation for effective management. This study examines the prevalence and genetic parameters of 14 limb-conformation defects in Menorca Purebred horses using data from 1120 records (509 animals with an average age of 101.87 ± 1.74 months) collected between 2015 and 2023. Defects were evaluated using a three-class scale by three appraisers, and a Bayesian approach via Gibbs sampling was employed to estimate genetic parameters including gender, birth period, stud selection criteria, evaluation age and appraiser as fixed effects...

Calcitonin (CT) and calcitonin gene-related peptide (CGRP) are critical regulators of calcium balance and have extensive implications for vertebrate physiological processes. This study explores the CT and CGRP signaling systems in chickens through cloning and characterization of the chicken calcitonin receptor (CTR) and calcitonin receptor-like receptor (CLR), together with three receptor activity-modifying proteins (RAMPs). We illuminated the functional roles for chickens between the receptors examined alone and in RAMP-associated complexes using luciferase reporter assays...

The Tubby-like proteins (TLPs) gene family is a group of transcription factors found in both animals and plants. In this study, we identified twelve B. distachyon TLPs, divided into six groups based on conserved domains and evolutionary relationships. We predicted cis-regulatory elements involved in light, hormone, and biotic and abiotic stresses. The expression patterns in response to light and hormones revealed that BdTLP3 , 4 , 7 , and 14 are involved in light responses, and BdTLP1 is involved in ABA responses...

Abiotic stresses pose significant challenges to wheat farming, yet exploiting the genetic variability within germplasm collections offers an opportunity to effectively address these challenges. In this study, we investigated the genetic diversity of key agronomic traits among twenty durum wheat cultivars, with the intention to pinpoint those better suited to semi-arid conditions. Field trials were conducted at the ITGC-FDPS Institute, Setif, Algeria, during the winter season of 2021/22. A completely randomized design was used with three replicates...

BACKGROUND: This study aims to explore how Russian society perceives children with cancer and their families to determine its potential as a tool for solving the social struggles of cancer-affected youth. METHODS: The study took place between 2019 and 2020 and involved 237 parents of cancer-affected children enrolled for inpatient treatment in 5 pediatric oncology clinics in the North Caucasus Federal District (Russia). The study exploits a specially designed questionnaire survey as its main research method...

Changes in gene regulatory elements play critical roles in human phenotypic divergence. However, identifying the base-pair changes responsible for the distinctive morphology of Homo sapiens remains challenging. Here, we report a noncoding single-nucleotide polymorphism (SNP), rs41298798, as a potential causal variant contributing to the morphology of the skull base and vertebral structures found in Homo sapiens. Screening for differentially regulated genes between Homo sapiens and extinct relatives revealed 13 candidate genes associated with basicranial development, with TBX1, implicated in DiGeorge syndrome, playing a pivotal role...

Gene regulatory divergence between species can result from cis-acting local changes to regulatory element DNA sequences or global trans-acting changes to the regulatory environment. Understanding how these mechanisms drive regulatory evolution has been limited by challenges in identifying trans-acting changes. We present a comprehensive approach to directly identify cis- and trans-divergent regulatory elements between human and rhesus macaque lymphoblastoid cells using assay for transposase-accessible chromatin coupled to self-transcribing active regulatory region (ATAC-STARR) sequencing...

Mechanisms underlying phenotypic divergence across species remain unresolved. In this issue of Cell Genomics, Hansen, Fong, et al.1 systematically dissect human and rhesus macaque gene expression divergence by screening tens of thousands of orthologous elements for enhancer activity in lymphoblastoid cell lines, revealing a much greater role for trans divergence at levels equal to those of cis effects, counter to the prevailing consensus in the field.

PURPOSE: Alterations of the NF1 tumor suppressor gene is the second most frequent genetic event in embryonal rhabdomyosarcoma (ERMS), but its associations with clinicopathologic features, outcome, or coexisting molecular events are not well defined. Additionally, NF1 alterations, mostly in the setting of neurofibromatosis type I (NF1), drive the pathogenesis of most malignant peripheral nerve sheath tumor with divergent RMS differentiation (also known as malignant triton tumor [MTT])...

Breast cancer is a highly heterogeneous disease with varied subtypes, prognoses and therapeutic responsiveness. Human leukocyte antigen class I (HLA-I) shapes the immunity and thereby influences the outcome of breast cancer. However, the implications of HLA-I variations in breast cancer remain poorly understood. In this study, we established a multiomics cohort of 1156 Chinese breast cancer patients for HLA-I investigation. We calculated four important HLA-I indicators in each individual, including HLA-I expression level, somatic HLA-I loss of heterozygosity (LOH), HLA-I evolutionary divergence (HED) and peptide-binding promiscuity (Pr)...

Macroautophagy/autophagy is an essential catabolic process that targets a wide variety of cellular components including proteins, organelles, and pathogens. ATG7, a protein involved in the autophagy process, plays a crucial role in maintaining cellular homeostasis and can contribute to the development of diseases such as cancer. ATG7 initiates autophagy by facilitating the lipidation of the ATG8 proteins in the growing autophagosome membrane. The noncanonical isoform ATG7(2) is unable to perform ATG8 lipidation; however, its cellular regulation and function are unknown...

The liquid crystal molecule 3-fluoro-4-(3,4,5-trifluorophenyl)phenyl 2,6-difluoro-4-( trans -5-n-propyl-1,3-dioxane-2-yl)benzoate (DIO) has attracted considerable interest owing to its unique ferroelectric nematic phase and extraordinarily high dielectric constant. To expand the DIO series, novel analogs with 1,3-dioxane units converted to ester units (EST analogs) were synthesized, and their physical properties were characterized. The EST analogs exhibited ferroelectric phases similar to those of the corresponding DIO analogs...

Thoracoabdominal MRI is limited by respiratory motion, especially in neonates who cannot perform breath-holds. To reduce motion blurring, radially-acquired MRI can be reconstructed from data acquired during specific respiratory phases ("hard-gating"), but this reduces image SNR. Various "soft-gating" reconstruction schemes have been proposed that incorporate data acquired outside the period of interest into reconstruction with diminished weighting. However, the choice of soft-gated weighting algorithm and parameters, and effect on image SNR and motion blurring, has not previously been explored...