Genomics最新文献

{"title":"High-resolution dissection of human cell type-specific enhancers in cis and trans activities","authors":"Meng Wang,&nbsp;Xiaoxu Yang,&nbsp;Qixi Wu","doi":"10.1016/j.ygeno.2025.110985","DOIUrl":"10.1016/j.ygeno.2025.110985","url":null,"abstract":"<div><div>The spatiotemporal-specific gene expression is regulated by cell type-specific regulatory elements. Here we selected the H3K4me1-associated DNA sequences as candidate enhancers in two different human cell lines and performed ChIP-STARR-seq to quantify the cell-type-specific enhancer activities with high-resolution. We investigated how the activity landscape of enhancers would change when transferred from native cells (<em>cis</em> activity) to another cell lines (<em>trans</em> activity). We obtained enhancers <em>cis</em> activity maps and <em>trans</em> activity maps in two different cell lines. The <em>cis</em> and <em>trans</em> activity maps enabled us to identify cell type-specific active enhancers, with enrichment of motifs of differentially expressed TFs. Comparisons between the <em>cis</em> and <em>trans</em> activity maps revealed general consistent regulatory property with different levels of activity in two cell lines, suggesting sequence intrinsic regulatory properties remain similar in different types of cells. This study provides a new perspective on sequence intrinsic enhancer activities in different types of cells.</div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"117 1","pages":"Article 110985"},"PeriodicalIF":3.4,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142927013","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Expansion of peripheral cytotoxic CD4+ T cells in Alzheimer's disease: New insights from multi-omics evidence","authors":"Jiongxue Chen ,&nbsp;Jiatian Xie ,&nbsp;Fuyin Deng ,&nbsp;Jinhua Cai ,&nbsp;Sitai Chen ,&nbsp;Xingrong Song ,&nbsp;Shangzhou Xia ,&nbsp;Qingyu Shen ,&nbsp;Xinying Guo ,&nbsp;Yamei Tang","doi":"10.1016/j.ygeno.2024.110976","DOIUrl":"10.1016/j.ygeno.2024.110976","url":null,"abstract":"<div><div>The significance of the adaptive immune response in Alzheimer's disease (AD) is increasingly recognized. We analyzed scRNA-Seq data from AD patients, revealing a notable rise in CD4 cytotoxic T cells (CD4-CTLs) in peripheral blood mononuclear cells (PBMCs), validated in vivo and in vitro. This rise correlates with cognitive decline in AD patients. We also identified transcription factors TBX21 and MYBL1 as key drivers of CD4-CTL expansion. Further analyses indicate these cells are terminally differentiated, showing clonal expansion, metabolic changes, and unique communication patterns. Mendelian randomization identified risk genes SRGN and ITGB1, suggesting their genetic regulation in CD4-CTLs may contribute to AD. To summarize, our findings characterize the expansion of CD4-CTLs in the PBMCs of AD patients, providing valuable understanding into the possible mechanisms involved in the expansion of CD4-CTLs in AD.</div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"117 1","pages":"Article 110976"},"PeriodicalIF":3.4,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142806497","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Evolutionary dynamics of repetitive elements and their relationship with genome size in Acrididae","authors":"Lina Zhao ,&nbsp;Hao Yuan ,&nbsp;Xuanzeng Liu ,&nbsp;Huihui Chang ,&nbsp;Xuan Jing ,&nbsp;Yimeng Nie ,&nbsp;Yuan Huang","doi":"10.1016/j.ygeno.2024.110971","DOIUrl":"10.1016/j.ygeno.2024.110971","url":null,"abstract":"<div><div>It is widely accepted that repetitive elements (REs) represent the primary mechanism driving genome size variation across eukaryotes. The observed genome sizes and REs of 59 species within the Acrididae were obtained and characterized. The genome sizes observed ranged from 6.60 pg to 19.35 pg, while the proportion of REs varied from 57.92 % to 83.58 %. The primary contributors were identified as LTR (2.34 % ∼ 20.98 %) and LINEs (6.70 % ∼ 16.33 %). The results of ancestral reconstruction indicated that the proportion of REs in ancestral nodes was 69.53 %, which suggests that they have undergone extensive genome expansion or contraction. A significant positive correlation was identified between the proportion of REs and genome size. Transposable elements were found to account for approximately 41 % of the observed variation in genome size. Moreover, the LTR was identified as the most significant RE type in relation to genome size expansion within the Acrididae.</div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"117 1","pages":"Article 110971"},"PeriodicalIF":3.4,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142791568","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Rapid sequencing and identification for 18-STRs long amplicon panel using portable devices and nanopore sequencer","authors":"Jiarong Zhang ,&nbsp;Tingting Yang ,&nbsp;Zihan Xie ,&nbsp;Zilin Ren ,&nbsp;Linyu Shi ,&nbsp;Jiang-wei Yan ,&nbsp;Ming Ni","doi":"10.1016/j.ygeno.2024.110970","DOIUrl":"10.1016/j.ygeno.2024.110970","url":null,"abstract":"<div><div>STRs are the most commonly used forensic genetic markers for human identification. Nanopore sequencing has shown the advantages of high portability and large data throughput. Previous studies indicate it has great potential for profiling STRs based on the ligation library preparation method. However, this method, which requires more library preparation time and operations, is unsuitable for rapid STR profiling, particularly for field forensic applications. The transposase-based rapid library preparation method offers the possibility to perform human identification using portable instruments. However, the amplicons of conventional STR panels are too small and would be cut into scraps with rapid methods, making them impractical for genotyping. In this study, we developed an 18-STRs multiplex amplification panel with amplicons of ∼1.4 Kbp. The PCR conditions were optimized to be finished within 2 h and 12 min, and the PCR products could undergo rapid methods that involved random fragmentation. We found that, on average, 29.16 % of reads from the long-amplicon panel and rapid library kit covered the whole STR region, sufficient for downstream STR profiling analysis. We conducted a small validation experiment on 24 samples using portable instruments powered by a 1.5 kW‧h portable power source. The entire process took 10.5 h and we obtained enough data from 24 samples to perform trustworthy pairwise identification analysis using the STR profiles. The overall accuracy of the analysis was 95.36 %. In sum, the study evaluated and demonstrated the viability and potential of nanopore sequencing for forensic application in the field.</div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"117 1","pages":"Article 110970"},"PeriodicalIF":3.4,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142750463","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Transcriptome and metabolome revealed the effects of hypoxic environment on ovarian development of Tibetan sheep","authors":"Dan Zhang ,&nbsp;Chao Yuan ,&nbsp;Xuejiao An ,&nbsp;Tingting Guo ,&nbsp;Zengkui Lu ,&nbsp;Jianbin Liu","doi":"10.1016/j.ygeno.2024.110973","DOIUrl":"10.1016/j.ygeno.2024.110973","url":null,"abstract":"<div><div>Many studies on the adaptability of Tibetan sheep to hypoxia have been reported, but little attention has been paid to the reproduction of Tibetan sheep living at an altitude of more than 4000 m. In this study, the ovaries of Alpine Merino sheep (AM) living in middle-high altitude areas (2500 m) and the ovaries of Gangba Tibetan sheep (GB) and Huoba Tibetan sheep (HB) living in ultra-high altitude areas (4400 m or more) were collected. Through morphological, transcriptomics and metabolomics, the effects of ultra-high altitude areas on Tibetan sheep ovarian development and the molecular mechanism of sheep's adaptability to ultra-high altitude environment were explored. The results showed that the number of granulosa cells in AM was significantly higher than that in GB and HB. The transcriptome revealed several genes related to follicular development, such as <em>DAPL1</em>, <em>IGFBP1</em>, <em>C5</em>, <em>GPR12</em>, <em>STRA6</em>, <em>BMPER</em>, etc., which were mainly enriched in related pathways such as cell growth and development. Through metabolomics analysis, it was found that the differential metabolites between the three groups of sheep were mainly lipids and lipid-like small molecules, such as Glycerol 3-Phosphate, PC (16: 0 / 18: 3 (9Z, 12Z, 15Z)), mainly enriched in lipid metabolism and other related pathways. The results of combined analysis showed that Tryptophan metabolism and Steroid hormone biosynthesis may have a significant effect on Tibetan sheep follicular development. Some genes (including <em>HSD17B7</em>, <em>CYP11A1</em>, <em>CYP19</em>, <em>HSD3B1</em>, <em>CYP17</em>, etc.) and some metabolites (including Cortisone, 2-Methoxyestrone, etc.) are enriched in these pathways, regulating ovarian and follicular development by affecting estrogen, progesterone, etc.. The results further revealed the molecular mechanism of Tibetan sheep to adapt to the ultra-high altitude environment and maintain normal ovarian and follicular development through the regulation of genes and metabolites.</div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"117 1","pages":"Article 110973"},"PeriodicalIF":3.4,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142779877","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"SlAN2 overexpression improves cold resistance in tomato (Solanum lycopersicum L.) by regulating glycolysis and ascorbic acid metabolism","authors":"Minghui Ye ,&nbsp;Deying Wang ,&nbsp;Ruixin Li ,&nbsp;Kunyang Zhuang ,&nbsp;Hongjiao Wang ,&nbsp;Xinyin Cao ,&nbsp;Tengfei Qin ,&nbsp;Hengjia Zhang ,&nbsp;Shangjing Guo ,&nbsp;Bingjie Wu","doi":"10.1016/j.ygeno.2024.110978","DOIUrl":"10.1016/j.ygeno.2024.110978","url":null,"abstract":"<div><div>Chilling stress seriously affects the growth and yield of tomato. Anthocyanin is a typical chilling-induced metabolite with strong antioxidant activity and photoprotective capacity. Here, we found that anthocyanin was also involved in ascorbic acid biosynthesis and glycolysis under chilling stress. <em>SlAN2</em> is an important positive gene in anthocyanin biosynthesis. The results of physiological indicators showed that <em>SlAN2</em> overexpression lines (A189) had a greater ability to tolerate cold stress than wild-type (WT) plants. Conjoint analysis of transcriptomics and metabonomics of A189 lines and WT plants was used to analyze the metabolic difference and the cold resistance mechanisms caused by anthocyanin under chilling stress. The anthocyanin accumulated more in A189 than that in WT under chilling stress at 4 °C for 24 h, which led to hexoses and ascorbic acid increased significantly. Results indicate that <em>SlAN2</em> overexpression reduces the expression of key enzyme genes in glycolytic pathway such as phosphofructokinase (PFK) and pyruvate kinase (PK) genes, weakens glycolysis ability, and promotes accumulation of hexoses in A189 lines at 4 °C for 24 h compared with wild lines. Additionally, ascorbic acid content is increased by up-regulated the genes of ascorbate peroxidase (APX) and dehydroascorbate reductase (DHAR). The increased hexose content can reduce cell osmotic potential, freezing point and synthesize more ascorbic acid, while the increased ascorbic acid content can enhance the ability to scavenge reactive oxygen species, so improves the cold resistance of tomato. The glycolysis and ascorbic acid metabolism pathway mediated by <em>SlAN2</em> provides a new insight for the molecular mechanism of anthocyanins in improving the cold resistance of tomato and provides a new theoretical basis for cultivating new cold-tolerant tomato varieties.</div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"117 1","pages":"Article 110978"},"PeriodicalIF":3.4,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142823539","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Single-cell RNA sequencing reveals the heterogeneity of myofibroblasts in wound repair","authors":"Miaonan Liu ,&nbsp;Xiaoxuan Liu ,&nbsp;Jingchi Zhang ,&nbsp;Shaocong Liang ,&nbsp;Yan Gong ,&nbsp;Shengjun Shi ,&nbsp;Xiaopeng Yuan","doi":"10.1016/j.ygeno.2024.110982","DOIUrl":"10.1016/j.ygeno.2024.110982","url":null,"abstract":"<div><div>Skin wound repair involves myofibroblasts crucial for tissue integrity. This study utilized single-cell RNA sequencing to explore myofibroblast diversity in various wound healing scenarios. Analysis of 89,148 cells from skin ulcers, keloids, and normal scars identified 13 cell clusters. Myofibroblast subcluster analysis unveiled 11 subsets, with subclusters 1 and 9 predominant in ulcers. Subcluster 1 exhibited heightened matrix metalloproteinase expression and involvement in bacterial response and angiogenesis, crucial in inflammation. Tissue validation confirmed subcluster 1 significance., while animal models supported upregulated <em>CA12</em>, <em>TDO2</em>, and <em>IL-7R</em> in chronic ulcers. These findings illuminate myofibroblast heterogeneity and their impact on wound healing, offering insights into potential therapeutic targets.</div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"117 1","pages":"Article 110982"},"PeriodicalIF":3.4,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142871887","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Genomic regions associated with Holstein heifer times bred to artificial insemination and embryo transfer services","authors":"Victoria Kelson ,&nbsp;Jennifer Kiser ,&nbsp;Kimberly Davenport ,&nbsp;Emaly Suarez ,&nbsp;Brenda Murdoch ,&nbsp;Holly Neibergs","doi":"10.1016/j.ygeno.2024.110972","DOIUrl":"10.1016/j.ygeno.2024.110972","url":null,"abstract":"<div><div>This study aimed to identify loci (<em>p</em> &lt; 1 × 10⁻⁵) and gene sets (normalized enrichment score (NES) ≥ 3.0) associated with the number of times a heifer is bred to attain a successful pregnancy (TBRD) for Holstein heifers bred by artificial insemination (AI, <em>n</em> = 2754) or that were embryo transfer (ET, <em>n</em> = 1566) recipients. Eight loci were associated (p &lt; 1 × 10⁻⁵) with TBRD in AI bred heifers and four loci were associated with TBRD in ET recipients. The gene set enrichment analysis with SNP data identified one gene set enriched (NES ≥ 3.0) with TBRD in AI bred heifers and two gene sets that were enriched with TBRD in ET recipients. The estimated pseudo-heritability for times bred to AI was 0.063 and 0.043 for ET. The identification of loci associated with embryonic loss aids in the selection of Holstein heifers with higher reproductive efficiencies that are AI bred or that are ET recipients.</div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"117 1","pages":"Article 110972"},"PeriodicalIF":3.4,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142779876","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Single-cell RNA sequencing unveils dynamic transcriptional profiles during the process of donkey spermatogenesis and maturation","authors":"Yadan Jin,&nbsp;Fangdi Zhang,&nbsp;Ruixue Ma,&nbsp;Jingya Xing,&nbsp;Min Wang,&nbsp;Yujiang Sun,&nbsp;Guoliang Zhang","doi":"10.1016/j.ygeno.2024.110974","DOIUrl":"10.1016/j.ygeno.2024.110974","url":null,"abstract":"<div><h3>Introduction</h3><div>With the increasing demand for donkey production, there has been a growing focus on the breeding of donkeys. However, our current understanding of the mechanisms underlying spermatogenesis and maturation in donkeys during reproduction remains limited.</div></div><div><h3>Objectives</h3><div>This study is to provide a comprehensive single-cell landscape analysis of spermatogenesis and maturation in donkeys.</div></div><div><h3>Methods</h3><div>In this study, we employed single-cell RNA sequencing to investigate cell composition, gene expression patterns, and regulatory roles during spermatogenesis and maturation in donkeys.</div></div><div><h3>Results</h3><div>The expression patterns of CDK1, CETN3, and UBE2J1 were found to be indicative of specific germ cells during donkey spermatogenesis. Additionally, the DEFB121, ELSPBP1, and NPC2 genes were specifically identified in the principal cells of the donkey epididymis.</div></div><div><h3>Conclusions</h3><div>We performed single-cell RNA sequencing to analyze the cellular composition and spatial distribution of donkey testis and epididymis, thereby generating comprehensive transcriptional atlases at the single-cell resolution.</div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"117 1","pages":"Article 110974"},"PeriodicalIF":3.4,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142853480","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Retraction notice to “LncRNA HOTAIR regulates the expression of E-cadherin to affect nasopharyngeal carcinoma progression by recruiting histone methylase EZH2 to mediate H3K27 trimethylation” [Genomics Volume 113, Issue 4, July 2021, Pages 2276–2289]","authors":"Feng-lian Yang ,&nbsp;Yu-xia Wei ,&nbsp;Bi-yun Liao ,&nbsp;Gui-jiang Wei ,&nbsp;Hai-mei Qin ,&nbsp;Xiao-xia Pang ,&nbsp;Jun-li Wang","doi":"10.1016/j.ygeno.2024.110939","DOIUrl":"10.1016/j.ygeno.2024.110939","url":null,"abstract":"","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"117 1","pages":"Article 110939"},"PeriodicalIF":3.4,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142692859","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}