Recent advances in single-cell sequencing assays for the transposase-accessibility chromatin (scATAC-seq) technique have provided cell-specific chromatin accessibility landscapes of cis-regulatory elements, providing deeper insights into cellular sta...
Meishan pigs are a well-known indigenous pig breed in China characterized by a high fertility. Notably, the number of endometrial grands is significantly higher in Meishan pigs than Duroc pigs. The characteristics of the endometrial tissue are relate...
Transcription factors are managers of the cellular factory, and key components to many diseases. Many non-coding single nucleotide polymorphisms affect transcription factors, either by directly altering the protein or its functional activity at indiv...
Human fungal pathogens often encounter fungicidal stress upon host invasion, but they can swiftly adapt by transcriptional reprogramming that enables pathogen survival. Fungal immune evasion is tightly connected to chromatin regulation. Hence, fungal...
Light is an essential environmental factor for Sparassis latifolia primordia formation, but the molecular mechanism is still unclear. In this study, differential expression profiling of light-induced primordia formation (LIPF) was established by inte...
Jeryak is the F1 generation of the cross between Gannan yak and Jersey cattle, which has the advantages of fast growth and high adaptability. The growth and development of skeletal muscle is closely linked to meat production and the quality of meat....
Next-generation sequencing technologies have revolutionised the study of biological systems by enabling the examination of a broad range of tissues. Its application to single-cell genomics has generated a dynamic and evolving field with a vast amount...
Breast cancer is a heterogeneous disease composed of various biologically distinct subtypes, each characterized by unique molecular features. Its formation and progression involve a complex, multistep process that includes the accumulation of numerou...
Cortisol, the main glucocorticoid in teleost, plays a central role in mediating the physiological response to stress by regulating metabolism, immune function, and growth. While its transcriptional effects are well known, its role in modulating chrom...
Drought resistance in plants is influenced by multiple signaling pathways that involve various transcription factors, many target genes, and multiple types of epigenetic modifications. Studies on epigenetic modifications of drought focus on DNA methy...
In recent years, there has been a growing interest in profiling multiomic modalities within individual cells simultaneously. One such example is integrating combined single-cell RNA sequencing (scRNA-seq) data and single-cell transposase-accessible c...
Meat production traits in pigs are critical economic characteristics, primarily influenced by the formation and development of skeletal muscle. Skeletal muscle development is regulated by a complex transcriptional network, which partly relies on chro...
Pimpled eggs have defective shells, which severely impacts hatching rates and transportation safety. In this study, we constructed single-cell resolution transcriptomic and chromatin accessibility maps from uterine tissues of chickens using single-ce...
Single-cell RNA-seq data contains a lot of dropouts hampering downstream analyses due to the low number and inefficient capture of mRNAs in individual cells. Here, we present Epi-Impute, a computational method for dropout imputation by reconciling ex...
Fruit color, a defining characteristic in mulberry, varies markedly across cultivars, ranging from black and red to pink and white. However, the regulatory mechanisms governing pigmentation during fruit development remain poorly characterized. In thi...
The gaseous hormone ethylene plays pivotal roles in plant growth and development. The rate-limiting enzyme of ethylene biosynthesis in seed plants is 1-aminocyclopropane-1-carboxylic acid (ACC) synthase (ACS). ACS proteins are encoded by a multigene...
Single-cell ATAC-seq (scATAC-seq), as the updating of ATAC-seq, provides a novel method for probing open chromatin sites. Currently, research of scATAC-seq is faced with the problem of high dimensionality and the inherent sparsity of the generated da...
Retinoic acid (RA) plays a critical role in initiating meiosis in primordial germ cells (PGC), yet the specific mechanisms of its interaction with PGC remain unclear. In this study, we used an in vitro feeder-free culture system with chicken PGC as a...
Salinity serves as an important environmental factor in ecosystems, driving the evolution of adaptive strategies in euryhaline species. The Pacific white shrimp, Litopenaeus vannamei, is a representative euryhaline species. However, the molecular mec...
During the postnatal stages, skeletal muscle development undergoes a series of meticulously regulated alterations in gene expression. However, limited studies have employed chromatin accessibility to unravel the underlying molecular mechanisms govern...
Mast cells can recognize foot-and-mouth disease virus-like particles (FMDV-VLPs) via mannose receptors (MRs) to produce differentially expressed cytokines. The regulatory role of chromatin accessibility in this process is unclear. Bone marrow-derived...
Molting is a critical physiological process for the growth and development of Eriocheir sinensis. Any disruption in this process can significantly affect both survival rates and crab quality. The regulatory mechanisms of molting vary across different...
The gaseous hormone ethylene plays a pivotal role in plant growth and development. In seed plants, the key rate-limiting enzyme that controls ethylene biosynthesis is ACC synthase (ACS). ACS has, for a long time, been believed to be a single-activity...
Lilac (Syringa spp.) is a widely cultivated ornamental plant prized for its fragrant aroma and attractive flower colors. However, the molecular mechanisms governing its flower pigmentation remain poorly understood. In this study, we performed integra...
Skeletal muscle satellite cells, the resident stem cells in pig skeletal muscle, undergo proliferation and differentiation to enable muscle tissue repair. The proliferative and differentiative abilities of these cells gradually decrease during in vit...
Ligand-activated Retinoid X Receptors (RXRs) regulate gene networks essential for neural development, neuroinflammation, and metabolism. Understanding how RXR activation influences chromatin architecture and gene expression may reveal mechanisms rele...
Transcription factors play a key role in Penicillium expansum infection process. Although the crucial characteristics of some transcription factors of pathogenic fungi have been found, many transcription factors involved in P. expansum infections hav...
The Single-cell Assay for Transposase-Accessible Chromatin with high throughput sequencing (scATAC-seq) has gained increasing popularity in recent years, allowing for chromatin accessibility to be deciphered and gene regulatory networks (GRNs) to be...
Intramuscular fat (IMF) content plays a crucial role in determining pork quality. Recent studies have highlighted transcriptional mechanisms controlling adipogenesis in porcine IMF. However, the changes in chromatin accessibility during adipogenic di...
Light is an important environmental factor affecting the ripening and quality of strawberry fruit. Previous studies have shown that red light treatment can promote strawberry ripening. Gene expression is closely associated with chromatin openness, an...
Abstract: Optimizing feed efficiency through the feed conversion ratio (FCR) is paramount for economic viability and sustainability. In this study, we integrated RNA-seq, ATAC-seq, and genome-wide association study (GWAS) data to investigate key func...
Ascidian larvae undergo tail elongation and notochord lumenogenesis, making them an ideal model for investigating tissue morphogenesis in embryogenesis. The cellular and mechanical mechanisms of these processes have been studied; however, the underly...
Background/Objectives: Chromatin accessibility is closely associated with transcriptional regulation during maize (Zea mays) leaf development. However, its precise role in controlling gene expression at different developmental stages remains poorly u...
Recent advances in single-cell transposase-accessible chromatin using a sequencing assay (scATAC-seq) allow cellular heterogeneity dissection and regulatory landscape reconstruction with an unprecedented resolution. However, compared to bulk-sequenci...
Feed efficiency (FE) is a crucial trait in pig production that influences both economic viability and environmental sustainability. The jejunum, an essential organ for nutrient absorption, plays a significant role in determining FE by affecting how p...
Embryonic diapause is a common evolutionary adaptation observed across a wide range of organisms. Artemia is one of the classic animal models for diapause research. The current studies of Artemia diapause mainly focus on the induction and maintenance...
The Drosophila imaginal disc has been an excellent model for the study of developmental gene regulation. In particular, long non-coding RNAs (lncRNAs) have gained widespread attention in recent years due to their important role in gene regulation. Th...
The epigenetic regulation mechanism of porcine skeletal muscle development relies on the openness of chromatin and is also precisely regulated by transcriptional machinery. However, fewer studies have exploited the temporal changes in gene expression...
Although significant advancement has been made in the study of adipogenesis, knowledge about how chromatin accessibility regulates yak adipogenesis is lacking. We here described genome-wide dynamic chromatin accessibility in preadipocytes and adipocy...
Despite significant advances of the bovine epigenome investigation, new evidence for the epigenetic basis of fetal cartilage development remains lacking. In this study, the chondrocytes were isolated from long bone tissues of bovine fetuses at 90 day...
Cattle-yak, a crossbreed of yak and cattle, which can exhibit obvious heterosis and can adapt to the harsh environmental conditions of the Qinghai Tibet Plateau (QTP). However, F1 cattle-yak were found to be sterile because they were unable to produc...
Practices related to mitochondrial research have long been hindered by the presence of mitochondrial pseudogenes within the nuclear genome (NUMTs). Even though partially assembled human reference genomes like hg38 have included NUMTs compilation, the...
The snATAC + snRNA platform allows epigenomic profiling of open chromatin and gene expression with single-cell resolution. The most critical assay step is to isolate high-quality nuclei to proceed with droplet-base single nuclei isolation and barcodi...
Chromatin structure plays a pivotal role in maintaining the precise regulation of gene expression. Accessible chromatin regions act as the binding sites of transcription factors (TFs) and cis-elements. Therefore, information from these open regions w...
Background: According to the cancer stem cells (CSCs) hypothesis, a population of cancer cells with stem cell properties is responsible for tumor propagation, drug resistance, and disease recurrence. Study of the mechanisms responsible for lung CSCs...
Lung cancer is the worldwide leading cause of death from cancer. Epigenetic modifications such as methylation and changes in chromatin accessibility are major gene regulatory mechanisms involved in tumorigenesis and cellular lineage commitment. We ai...
Many efforts have been made to reveal the mechanisms underlying skeletal muscle development because of its importance in animals. However, knowledge on chromatin accessibility, a prerequisite for gene expression, remains limited. Here, dynamic change...
Osteosarcoma (OSA) is a highly aggressive bone tumor primarily affecting pediatric or adolescent humans and large-breed dogs. Canine OSA shares striking similarities with its human counterpart, making it an invaluable translational model for uncoveri...
Male breast cancer represents about 1% of all breast cancer diagnoses and, although there are some similarities between male and female breast cancer, the paucity of data available on male breast cancer makes it difficult to establish targeted therap...
Pasteurella multocida can cause goat hemorrhagic sepsis and endemic pneumonia. Respiratory epithelial cells are the first line of defense in the lungs during P. multocida infection. These cells act as a mechanical barrier and activate immune response...
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