Zoological Research最新文献

{"title":"LncRNA pol-lnc78 as a ceRNA regulates antibacterial responses via suppression of pol-miR-n199-3p-mediated SARM down-regulation in <i>Paralichthys</i> <i>olivaceus</i>.","authors":"Xian-Hui Ning, Bing Han, Ye Peng, Shao-Wu Yin","doi":"10.24272/j.issn.2095-8137.2022.520","DOIUrl":"10.24272/j.issn.2095-8137.2022.520","url":null,"abstract":"<p><p>Long non-coding RNAs (lncRNAs) function as key modulators in mammalian immunity, particularly due to their involvement in lncRNA-mediated competitive endogenous RNA (ceRNA) crosstalk. Despite their recognized significance in mammals, research on lncRNAs in lower vertebrates remains limited. In the present study, we characterized the first immune-related lncRNA (pol-lnc78) in the teleost Japanese flounder ( <i>Paralichthys</i> <i>olivaceus</i>). Results indicated that pol-lnc78 acted as a ceRNA for pol-miR-n199-3p to target the sterile alpha and armadillo motif-containing protein (SARM), the fifth discovered member of the Toll/interleukin 1 (IL-1) receptor (TIR) adaptor family. This ceRNA network regulated the antibacterial responses of flounder via the Toll-like receptor (TLR) signaling pathway. Specifically, SARM acted as a negative regulator and exacerbated bacterial infection by inhibiting the expression of inflammatory cytokines IL-1β and tumor necrosis factor-α (TNF-α). Pol-miR-n199-3p reduced SARM expression by specifically interacting with the 3' untranslated region (UTR), thereby promoting SARM-dependent inflammatory cytokine expression and protecting the host against bacterial dissemination. Furthermore, pol-lnc78 sponged pol-miR-n199-3p to ameliorate the inhibition of SARM expression. During infection, the negative regulators pol-lnc78 and SARM were significantly down-regulated, while pol-miR-n199-3p was significantly up-regulated, thus favoring host antibacterial defense. These findings provide novel insights into the mechanisms underlying fish immunity and open new horizons to better understand ceRNA crosstalk in lower vertebrates.</p>","PeriodicalId":48636,"journal":{"name":"Zoological Research","volume":"1 1","pages":"25-35"},"PeriodicalIF":4.9,"publicationDate":"2024-01-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10839655/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"68882311","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Combined ATAC-seq, RNA-seq, and GWAS analysis reveals glycogen metabolism regulatory network in Jinjiang oyster ( <i>Crassostrea ariakensis</i>).","authors":"Biao Wu, Xi Chen, Jie Hu, Zhen-Yuan Wang, Yan Wang, Da-You Xu, Hao-Bing Guo, Chang-Wei Shao, Li-Qing Zhou, Xiu-Jun Sun, Tao Yu, Xiao-Mei Wang, Yan-Xin Zheng, Guang-Yi Fan, Zhi-Hong Liu","doi":"10.24272/j.issn.2095-8137.2023.021","DOIUrl":"10.24272/j.issn.2095-8137.2023.021","url":null,"abstract":"<p><p>Glycogen serves as the principal energy reserve for metabolic processes in aquatic shellfish and substantially contributes to the flavor and quality of oysters. The Jinjiang oyster ( <i>Crassostrea ariakensis</i>) is an economically and ecologically important species in China. In the present study, RNA sequencing (RNA-seq) and assay for transposase-accessible chromatin using sequencing (ATAC-seq) were performed to investigate gene expression and chromatin accessibility variations in oysters with different glycogen contents. Analysis identified 9 483 differentially expressed genes (DEGs) and 7 215 genes with significantly differential chromatin accessibility (DCAGs) were obtained, with an overlap of 2 600 genes between them. Notably, a significant proportion of these genes were enriched in pathways related to glycogen metabolism, including \"Glycogen metabolic process\" and \"Starch and sucrose metabolism\". In addition, genome-wide association study (GWAS) identified 526 single nucleotide polymorphism (SNP) loci associated with glycogen content. These loci corresponded to 241 genes, 63 of which were categorized as both DEGs and DCAGs. This study enriches basic research data and provides insights into the molecular mechanisms underlying the regulation of glycogen metabolism in <i>C. ariakensis</i>.</p>","PeriodicalId":48636,"journal":{"name":"Zoological Research","volume":"1 1","pages":"201-214"},"PeriodicalIF":4.9,"publicationDate":"2024-01-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10839670/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"68882536","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Indian monsoon drove the dispersal of the <i>thoracica</i> group of <i>Scytodes</i> spitting spiders.","authors":"Yu-Fa Luo, Shu-Qiang Li","doi":"10.24272/j.issn.2095-8137.2023.364","DOIUrl":"10.24272/j.issn.2095-8137.2023.364","url":null,"abstract":"<p><p>We examined the global biogeography of the <i>Scytodes</i> <i>thoracica</i> group of spitting spiders based on 23 years of sampling at the species level (61 species in the <i>thoracica</i> group and 84 species of <i>Scytodes</i>) using DNA data from six loci. Our results indicated that the <i>thoracica</i> group initially dispersed from Southeast Asia to East Africa between 46.5 and 33.0 million years ago, and dispersal events intensified between Southeast/South Asia and East/South Africa from the early to late Miocene. The timing of these events indicates that Asian-African faunal exchange of the <i>thoracica</i> group was driven by the Indian monsoon, and the pattern of dispersal suggests that colonialization took root when the Indian monsoon shifted from a North-South direction to an East-West direction from the middle Eocene.</p>","PeriodicalId":48636,"journal":{"name":"Zoological Research","volume":"45 1","pages":"152-159"},"PeriodicalIF":4.9,"publicationDate":"2024-01-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10839671/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139513896","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Unexpected divergence in magnetoreceptor MagR from robin and pigeon linked to two sequence variations.","authors":"Shun Wang, Peng Zhang, Fan Fei, Tianyang Tong, Xiujuan Zhou, Yajie Zhou, Jing Zhang, Mengke Wei, Yanqi Zhang, Lei Zhang, Yulong Huang, Lin Zhang, Xin Zhang, Tiantian Cai, Can Xie","doi":"10.24272/j.issn.2095-8137.2023.138","DOIUrl":"10.24272/j.issn.2095-8137.2023.138","url":null,"abstract":"<p><p>Birds exhibit extraordinary mobility and remarkable navigational skills, obtaining guidance cues from the Earth's magnetic field for orientation and long-distance movement. Bird species also show tremendous diversity in navigation strategies, with considerable differences even within the same taxa and among individuals from the same population. The highly conserved iron and iron-sulfur cluster binding magnetoreceptor (MagR) protein is suggested to enable animals, including birds, to detect the geomagnetic field and navigate accordingly. Notably, MagR is also implicated in other functions, such as electron transfer and biogenesis of iron-sulfur clusters, raising the question of whether variability exists in its biochemical and biophysical features among species, particularly birds. In the current study, we conducted a comparative analysis of MagR from two different bird species, including the migratory European robin and the homing pigeon. Sequence alignment revealed an extremely high degree of similarity between the MagRs of these species, with only three sequence variations. Nevertheless, two of these variations underpinned significant differences in metal binding capacity, oligomeric state, and magnetic properties. These findings offer compelling evidence for the marked differences in MagR between the two avian species, potentially explaining how a highly conserved protein can mediate such diverse functions.</p>","PeriodicalId":48636,"journal":{"name":"Zoological Research","volume":"45 1","pages":"69-78"},"PeriodicalIF":4.9,"publicationDate":"2024-01-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10839668/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138812760","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Endogenous biosynthesis of docosahexaenoic acid (DHA) regulates fish oocyte maturation by promoting pregnenolone production.","authors":"Yi Li, Xuehui Li, Ding Ye, Ru Zhang, Chengjie Liu, Mudan He, Houpeng Wang, Wei Hu, Yonghua Sun","doi":"10.24272/j.issn.2095-8137.2023.032","DOIUrl":"10.24272/j.issn.2095-8137.2023.032","url":null,"abstract":"<p><p>Omega-3 polyunsaturated fatty acids (n-3 PUFAs), particularly docosahexaenoic acid (22:6n-3, DHA), play crucial roles in the reproductive health of vertebrates, including humans. Nevertheless, the underlying mechanism related to this phenomenon remains largely unknown. In this study, we employed two zebrafish genetic models, i.e., <i>elovl2</i> ^<i>-/-</i> mutant as an endogenous DHA-deficient model and <i>fat1</i> (omega-3 desaturase encoding gene) transgenic zebrafish as an endogenous DHA-rich model, to investigate the effects of DHA on oocyte maturation and quality. Results show that the <i>elovl2</i> ^<i>-/-</i> mutants had much lower fecundity and poorer oocyte quality than the wild-type controls, while the <i>fat1</i> zebrafish had higher fecundity and better oocyte quality than wild-type controls. DHA deficiency in <i>elovl2</i> ^<i>-/-</i> embryos led to defects in egg activation, poor microtubule stability, and reduced pregnenolone levels. Further study revealed that DHA promoted pregnenolone synthesis by enhancing transcription of <i>cyp11a1</i>, which encodes the cholesterol side-chain cleavage enzyme, thereby stabilizing microtubule assembly during oogenesis. In turn, the hypothalamic-pituitary-gonadal axis was enhanced by DHA. In conclusion, using two unique genetic models, our findings demonstrate that endogenously synthesized DHA promotes oocyte maturation and quality by promoting pregnenolone production via transcriptional regulation of <i>cyp11a1</i>.</p>","PeriodicalId":48636,"journal":{"name":"Zoological Research","volume":"1 1","pages":"176-188"},"PeriodicalIF":4.9,"publicationDate":"2024-01-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10839667/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"68882637","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Full T-cell activation and function in teleosts require collaboration of first and co-stimulatory signals.","authors":"Wei Liang, Kang Li, Haiyou Gao, Kunming Li, Jiansong Zhang, Qian Zhang, Xinying Jiao, Jialong Yang, Xiumei Wei","doi":"10.24272/j.issn.2095-8137.2023.053","DOIUrl":"10.24272/j.issn.2095-8137.2023.053","url":null,"abstract":"<p><p>Mammalian T-cell responses require synergism between the first signal and co-stimulatory signal. However, whether and how dual signaling regulates the T-cell response in early vertebrates remains unknown. In the present study, we discovered that the Nile tilapia ( <i>Oreochromis</i> <i>niloticus</i>) encodes key components of the LAT signalosome, namely, LAT, ITK, GRB2, VAV1, SLP-76, GADS, and PLC-γ1. These components are evolutionarily conserved, and CD3ε mAb-induced T-cell activation markedly increased their expression. Additionally, at least ITK, GRB2, and VAV1 were found to interact with LAT for signalosome formation. Downstream of the first signal, the NF-κB, MAPK/ERK, and PI3K-AKT pathways were activated upon CD3ε mAb stimulation. Furthermore, treatment of lymphocytes with CD28 mAbs triggered the AKT-mTORC1 pathway downstream of the co-stimulatory signal. Combined CD3ε and CD28 mAb stimulation enhanced ERK1/2 and S6 phosphorylation and elevated NFAT1, c-Fos, IL-2, CD122, and CD44 expression, thereby signifying T-cell activation. Moreover, rather than relying on the first or co-stimulatory signal alone, both signals were required for T-cell proliferation. Full T-cell activation was accompanied by marked apoptosis and cytotoxic responses. These findings suggest that tilapia relies on dual signaling to maintain an optimal T-cell response, providing a novel perspective for understanding the evolution of the adaptive immune system.</p>","PeriodicalId":48636,"journal":{"name":"Zoological Research","volume":"1 1","pages":"13-24"},"PeriodicalIF":4.9,"publicationDate":"2024-01-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10839663/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"68882847","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Comprehensive analysis of the gut microbiome and post-translational modifications elucidates the route involved in microbiota-host interactions.","authors":"Hai-Yang Wang, Lan-Xiang Liu, Xue-Yi Chen, Yang-Dong Zhang, Wen-Xia Li, Wen-Wen Li, Lian Wang, Xiao-Long Mo, Hong Wei, Ping Ji, Peng Xie","doi":"10.24272/j.issn.2095-8137.2023.008","DOIUrl":"10.24272/j.issn.2095-8137.2023.008","url":null,"abstract":"<p><p>The gut microbiome interacts with the host to maintain body homeostasis, with gut microbial dysbiosis implicated in many diseases. However, the underlying mechanisms of gut microbe regulation of host behavior and brain functions remain unclear. This study aimed to elucidate the influence of gut microbiota on brain functions via post-translational modification mechanisms in the presence or absence of bacteria without any stimulation. We conducted succinylome analysis of hippocampal proteins in germ-free (GF) and specific pathogen-free (SPF) mice and metagenomic analysis of feces from SPF mice. These results were integrated with previously reported hippocampal acetylome and phosphorylome data from the same batch of mice. Subsequent bioinformatics analyses revealed 584 succinylation sites on 455 proteins, including 54 up-regulated succinylation sites on 91 proteins and 99 down-regulated sites on 51 proteins in the GF mice compared to the SPF mice. We constructed a panoramic map of gut microbiota-regulated succinylation, acetylation, and phosphorylation, and identified cross-talk and relative independence between the different types of post-translational modifications in modulating complicated intracellular pathways. Pearson correlation analysis indicated that 13 taxa, predominantly belonging to the Bacteroidetes phylum, were correlated with the biological functions of post-translational modifications. Positive correlations between these taxa and succinylation and negative correlations between these taxa and acetylation were identified in the modulation of intracellular pathways. This study highlights the hippocampal physiological changes induced by the absence of gut microbiota, and proteomic quantification of succinylation, phosphorylation, and acetylation, contributing to our understanding of the role of the gut microbiome in brain function and behavioral phenotypes.</p>","PeriodicalId":48636,"journal":{"name":"Zoological Research","volume":"1 1","pages":"95-107"},"PeriodicalIF":4.9,"publicationDate":"2024-01-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10839661/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"68882355","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Patterns and drivers of avian taxonomic and phylogenetic beta diversity in China vary across geographical backgrounds and dispersal abilities.","authors":"Jian-Chao Liang, Zhi-Feng Ding, Chun-Lin Li, Yi-Ming Hu, Zhi-Xin Zhou, Gan-Wen Lie, Xiao-Nan Niu, Wen-Bin Huang, Hui-Jian Hu, Xing-Feng Si","doi":"10.24272/j.issn.2095-8137.2023.076","DOIUrl":"10.24272/j.issn.2095-8137.2023.076","url":null,"abstract":"<p><p>Geographical background and dispersal ability may strongly influence assemblage dissimilarity; however, these aspects have generally been overlooked in previous large-scale beta diversity studies. Here, we examined whether the patterns and drivers of taxonomic beta diversity (TBD) and phylogenetic beta diversity (PBD) of breeding birds in China vary across (1) regions on both sides of the Hu Line, which demarcates China's topographical, climatic, economic, and social patterns, and (2) species with different dispersal ability. TBD and PBD were calculated and partitioned into turnover and nestedness components using a moving window approach. Variables representing climate, habitat heterogeneity, and habitat quality were employed to evaluate the effects of environmental filtering. Spatial distance was considered to assess the impact of dispersal limitation. Variance partitioning analysis was applied to assess the relative roles of these variables. In general, the values of TBD and PBD were high in mountainous areas and were largely determined by environmental filtering. However, different dominant environmental filters on either side of the Hu Line led to divergent beta diversity patterns. Specifically, climate-driven species turnover and habitat heterogeneity-related species nestedness dominated the regions east and west of the line, respectively. Additionally, bird species with stronger dispersal ability were more susceptible to environmental filtering, resulting in more homogeneous assemblages. Our results indicated that regions with distinctive geographical backgrounds may present different ecological factors that lead to divergent assemblage dissimilarity patterns, and dispersal ability determines the response of assemblages to these ecological factors. Identifying a single universal explanation for the observed pattern without considering these aspects may lead to simplistic or incomplete conclusions. Consequently, a comprehensive understanding of large-scale beta diversity patterns and effective planning of conservation strategies necessitate the consideration of both geographical background and species dispersal ability.</p>","PeriodicalId":48636,"journal":{"name":"Zoological Research","volume":"1 1","pages":"125-135"},"PeriodicalIF":4.9,"publicationDate":"2024-01-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10839669/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"68882864","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Cath-KP, a novel peptide derived from frog skin, prevents oxidative stress damage in a Parkinson's disease model.","authors":"Huanpeng Lu, Jinwei Chai, Zijian Xu, Jiena Wu, Songzhe He, Hang Liao, Peng Huang, Xiaowen Huang, Xi Chen, Haishan Jiang, Shaogang Qu, Xueqing Xu","doi":"10.24272/j.issn.2095-8137.2023.101","DOIUrl":"10.24272/j.issn.2095-8137.2023.101","url":null,"abstract":"<p><p>Parkinson's disease (PD) is a neurodegenerative condition that results in dyskinesia, with oxidative stress playing a pivotal role in its progression. Antioxidant peptides may thus present therapeutic potential for PD. In this study, a novel cathelicidin peptide (Cath-KP; GCSGRFCNLFNNRRPGRLTLIHRPGGDKRTSTGLIYV) was identified from the skin of the Asiatic painted frog ( <i>Kaloula pulchra</i>). Structural analysis using circular dichroism and homology modeling revealed a unique <i>αββ</i> conformation for Cath-KP. <i>In vitro</i> experiments, including free radical scavenging and ferric-reducing antioxidant analyses, confirmed its antioxidant properties. Using the 1-methyl-4-phenylpyridinium ion (MPP ⁺)-induced dopamine cell line and 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine (MPTP)-induced PD mice, Cath-KP was found to penetrate cells and reach deep brain tissues, resulting in improved MPP ⁺-induced cell viability and reduced oxidative stress-induced damage by promoting antioxidant enzyme expression and alleviating mitochondrial and intracellular reactive oxygen species accumulation through Sirtuin-1 (Sirt1)/Nuclear factor erythroid 2-related factor 2 (Nrf2) pathway activation. Both focal adhesion kinase (FAK) and p38 were also identified as regulatory elements. In the MPTP-induced PD mice, Cath-KP administration increased the number of tyrosine hydroxylase (TH)-positive neurons, restored TH content, and ameliorated dyskinesia. To the best of our knowledge, this study is the first to report on a cathelicidin peptide demonstrating potent antioxidant and neuroprotective properties in a PD model by targeting oxidative stress. These findings expand the known functions of cathelicidins, and hold promise for the development of therapeutic agents for PD.</p>","PeriodicalId":48636,"journal":{"name":"Zoological Research","volume":"1 1","pages":"108-124"},"PeriodicalIF":4.9,"publicationDate":"2024-01-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10839659/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"68882875","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Pig H3K4me3, H3K27ac, and gene expression profiles reveal reproductive tissue-specific activity of transposable elements.","authors":"Tao Jiang, Zhi-Min Zhou, Zi-Qi Ling, Qing Zhang, Zhong-Zi Wu, Jia-Wen Yang, Si-Yu Yang, Bin Yang, Lu-Sheng Huang","doi":"10.24272/j.issn.2095-8137.2023.060","DOIUrl":"10.24272/j.issn.2095-8137.2023.060","url":null,"abstract":"<p><p>Regulatory sequences and transposable elements (TEs) account for a large proportion of the genomic sequences of species; however, their roles in gene transcription, especially tissue-specific expression, remain largely unknown. Pigs serve as an excellent animal model for studying genomic sequence biology due to the extensive diversity among their wild and domesticated populations. Here, we conducted an integrated analysis using H3K27ac ChIP-seq, H3K4me3 ChIP-seq, and RNA-seq data from 10 different tissues of seven fetuses and eight closely related adult pigs. We aimed to annotate the regulatory elements and TEs to elucidate their associations with histone modifications and mRNA expression across different tissues and developmental stages. Based on correlation analysis between mRNA expression and H3K27ac and H3K4me3 peak activity, results indicated that H3K27ac exhibited stronger associations with gene expression than H3K4me3. Furthermore, 1.45% of TEs overlapped with either the H3K27ac or H3K4me3 peaks, with the majority displaying tissue-specific activity. Notably, a TE subfamily (LTR4C_SS), containing binding motifs for SIX1 and SIX4, showed specific enrichment in the H3K27ac peaks of the adult and fetal ovaries. RNA-seq analysis also revealed widespread expression of TEs in the exons or promoters of genes, including 4 688 TE-containing transcripts with distinct development stage-specific and tissue-specific expression. Of note, 1 967 TE-containing transcripts were enriched in the testes. We identified a long terminal repeat (LTR), MLT1F1, acting as a testis-specific alternative promoter in <i>SRPK2</i> (a cell cycle-related protein kinase) in our pig dataset. This element was also conserved in humans and mice, suggesting either an ancient integration of TEs in genes specifically expressed in the testes or parallel evolutionary patterns. Collectively, our findings demonstrate that TEs are deeply embedded in the genome and exhibit important tissue-specific biological functions, particularly in the reproductive organs.</p>","PeriodicalId":48636,"journal":{"name":"Zoological Research","volume":"1 1","pages":"138-151"},"PeriodicalIF":4.9,"publicationDate":"2024-01-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10839656/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"68882852","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}