Gene Expression Patterns最新文献

A great diversity of ROBO4 expression and regulations identified by data mining and transgene mice 通过数据挖掘和转基因小鼠确定了 ROBO4 表达和调控的多样性。

IF 1 4区生物学

Gene Expression Patterns Pub Date : 2024-09-01 DOI: 10.1016/j.gep.2024.119375

{"title":"A great diversity of ROBO4 expression and regulations identified by data mining and transgene mice","authors":"","doi":"10.1016/j.gep.2024.119375","DOIUrl":"10.1016/j.gep.2024.119375","url":null,"abstract":"<div>ROBO4 involves in the stabilization of blood vessel and mediates the migration of hematopoietic stem cell and newborn neuron. However, the patterns of expression and regulation are not quite clear. To resolve this, we analyzed the single cell sequence data, and confirmed that Robo4 mainly expresses in various endothelial cells, but also in epithelial cells, pericytes, and stem or progenitor cells of bone marrow, fibroblast cells/mesenchymal stem cell of adipose tissues, muscle cells and neuron. Robo4 expressions in endothelial cells derived from capillary vessel, tip/stalk/activated endothelial cells were higher than that in artery and large vein (matured endothelial cells). On the other hand, via mining the gene expression data deposited in the NCBI Gene Expression Omnibus database as well as National Genomics Data Center (NGDC), we uncovered that the expression of Robo4 were regulated by different stimulus and variable in diseases’ condition.Moreover, we constructed enhanced GFP (eGFP) transgene mouse controlled by Robo4 promoter using CRISPR/CAS9 system. We found GFP signals in many cell types from the embryonic section, confirming a widely expression of Robo4. Together, Robo4 widely and dynamically express in multiple cell types, and can be regulated by diverse factors.</div>","PeriodicalId":55598,"journal":{"name":"Gene Expression Patterns","volume":null,"pages":null},"PeriodicalIF":1.0,"publicationDate":"2024-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142057377","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

The expression pattern of Wnt6, Wnt10A, and HOXA13 during regenerating tails of Gekko Japonicus 日本壁虎再生尾部过程中 Wnt6 和 HOXA13 的表达模式。

IF 1 4区生物学

Gene Expression Patterns Pub Date : 2024-08-10 DOI: 10.1016/j.gep.2024.119374

引用次数: 0

Unveiling the dynamics of embryogenesis and immune genes expression pattern in the amur common carp (Cyprinus carpio haematopterus) 揭示阿穆尔鲤鱼（Cyprinus carpio haematopterus）胚胎发生动态和免疫基因表达模式。

IF 1.2 4区生物学

Gene Expression Patterns Pub Date : 2024-05-15 DOI: 10.1016/j.gep.2024.119367

Smruti Mahapatra , Bristy Ganguly , Saswati Pani , Manas Kumar Sinha , Ashis Saha , Mrinal Samanta

{"title":"Unveiling the dynamics of embryogenesis and immune genes expression pattern in the amur common carp (Cyprinus carpio haematopterus)","authors":"Smruti Mahapatra , Bristy Ganguly , Saswati Pani , Manas Kumar Sinha , Ashis Saha , Mrinal Samanta","doi":"10.1016/j.gep.2024.119367","DOIUrl":"10.1016/j.gep.2024.119367","url":null,"abstract":"<div>Amur common carp (Cyprinus carpio haematopterus), is a commercially important fish species that has been genetically improved over the years through selective breeding. Despite its significance in aquaculture, limited knowledge exists regarding its embryogenesis and immune genes associated with its early stages of life. This article represents a detailed study of the embryogenesis and innate immune gene expression analysis of the Amur common carp during its ontogenic developments. The entire embryonic developmental process of ∼44 h could be divided into eight periods, beginning with the formation of the zygote, followed by cleavage, morula, blastula, segmentation, pharyngula, and hatching. The segmentation period, which lasted for ∼ 6 h, exhibited the most significant changes, such as muscle contraction, rudimentary heart formation, increased somites number, and the initiation of blood circulation throughout the yolk. The expression of immune-related genes, namely toll-like receptor (TLR)4, nucleotide-binding oligomerization domain (NOD)1, NOD2 and interleukin (IL)-8 showed stage-specific patterns with varying levels of expression across the developmental stages. The TLR4 gene exhibited the highest expression during the neurella stage, while NOD1 and NOD2 peaked during hatching and IL-8 reached its maximum level during the gastrula stage. This is the first report of the innate immune gene expression during the embryogenesis of Amur common carp.</div>","PeriodicalId":55598,"journal":{"name":"Gene Expression Patterns","volume":null,"pages":null},"PeriodicalIF":1.2,"publicationDate":"2024-05-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140961023","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Comparative analysis of the expression patterns of TM9SF family members in mice 小鼠体内 TM9SF 家族成员表达模式的比较分析

IF 1.2 4区生物学

Gene Expression Patterns Pub Date : 2024-05-06 DOI: 10.1016/j.gep.2024.119366

Rui Zhao , Wenxiong Liao , Duo Tan , Haiyou Huang , Chun Hu , Meilan Chen

{"title":"Comparative analysis of the expression patterns of TM9SF family members in mice","authors":"Rui Zhao , Wenxiong Liao , Duo Tan , Haiyou Huang , Chun Hu , Meilan Chen","doi":"10.1016/j.gep.2024.119366","DOIUrl":"10.1016/j.gep.2024.119366","url":null,"abstract":"<div>Transmembrane 9 superfamily proteins (TM9SFs) define a highly conserved protein family, each member of which is characterized by a variable extracellular domain and presumably nine transmembrane domains. Although previous studies have delineated the potential cytological roles of TM9SFs like autophagy and secretory pathway, their functions during development are largely unknown. To establish the basis for dissecting the functions of TM9SFs in vivo, we employed the open-source database, structure prediction, immunofluorescence and Western blot to describe the gene and protein expression patterns of TM9SFs in human and mouse. While TM9SFs are ubiquitously and homogeneously expressed in all tissues in human with RNA sequencing and proteomics analysis, we found that all mice Tm9sf proteins are preferentially expressed in lung except Tm9sf1 which is enriched in brain although they all distributed in various tissues we examined. In addition, we further explored their expression patterns in the mice central nervous system (CNS) and its extension tissue retina. Interestingly, we could show that Tm9sf1is developmentally up-regulated in brain. In addition, we also detected all Tm9sf proteins are located in neurons and microglia instead of astrocytes. Importantly, Tm9sf3 is localized in the nuclei which is distinct from the other members that are dominantly targeted to the plasma membrane/cytoplasm as expected. Finally, we also found that Tm9sf family members are broadly expressed in the layers of INL, OPL, and GCL of retina and likely targeted to the plasma membrane of retinal cells. Thus, our data provided a comprehensive overview of TM9SFs expression patterns, illustrating their ubiquitous roles in different organs, implying the possible roles of Tm9sf2/3/4 in lung functions and Tm9sf1 in neurodevelopment, and highlighting a unique cell biological functions of TM9SF3 in neuronal and microglia.</div>","PeriodicalId":55598,"journal":{"name":"Gene Expression Patterns","volume":null,"pages":null},"PeriodicalIF":1.2,"publicationDate":"2024-05-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140893108","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Ontogeny and tissue specific expression profiles of recombination activating genes (RAGs) during development in Nile tilapia, Oreochromis niloticus 尼罗罗非鱼（Oreochromisniloticus）发育过程中重组激活基因（RAGs）的本体和组织特异性表达谱。

IF 1.2 4区生物学

Gene Expression Patterns Pub Date : 2024-03-07 DOI: 10.1016/j.gep.2024.119358

Ravikumar M. Chovatia , Arpit Acharya , Kiran D. Rasal , Megha Kadam Bedekar , Kezhedath Jeena , R. Bharathi Rathinam , Chandana Dinakaran , Gayatri Tripathi

{"title":"Ontogeny and tissue specific expression profiles of recombination activating genes (RAGs) during development in Nile tilapia, Oreochromis niloticus","authors":"Ravikumar M. Chovatia , Arpit Acharya , Kiran D. Rasal , Megha Kadam Bedekar , Kezhedath Jeena , R. Bharathi Rathinam , Chandana Dinakaran , Gayatri Tripathi","doi":"10.1016/j.gep.2024.119358","DOIUrl":"10.1016/j.gep.2024.119358","url":null,"abstract":"<div>Recombination activating genes (RAGs) mediates the process of rearrangement and somatic recombination (V(D)J) to generate different antibody repertoire. Studies on the expression pattern of adaptive immune genes during ontogenic development are crucial for the formulation of fish immunization strategy. In the present study, Nile tilapia was taken to explore the relative expression profile of RAG genes during their developmental stages. The developmental stages of Nile tilapia, i.e., unfertilized egg, 0, 2, 4, 6, 8, 10, 12, 14, 16, 18, 20, 22, 24, 26, 28 and 30 days post-hatch (dph) and kidney, blood, gill, liver and spleen tissues from adult fish were collected and the cDNA synthesis was carried out. Gene specific primers for RAG-1 and RAG-2 of Nile tilapia were designed and their annealing temperature (Tm) was optimized by gradient PCR. Consequently, PCR was performed to confirm the specific amplification of RAG-1 and RAG-2 genes. Quantitative real-time PCR (qRT-PCR) gene expression of RAG-1 and RAG-2 were noticed in all the developmental stages; however, a significant increase was observed after 12 dph and peaked at 24 dph, followed by a gradual decrease until 30 dph. Tissue-specific gene expression profiling revealed that the highest expression of RAG-1 and RAG-2 was observed in the kidney, followed by spleen, gill, liver and blood. The findings of the study explored the suitable timing of lymphoid maturation that could be technically used for the adoption of strategies to improve disease resistance of fish larvae for mitigating larval mortality.</div>","PeriodicalId":55598,"journal":{"name":"Gene Expression Patterns","volume":null,"pages":null},"PeriodicalIF":1.2,"publicationDate":"2024-03-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140068933","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Transcriptional regulation of the alternative sex hormone-binding globulin promoter by KLF4. KLF4 对替代性荷尔蒙结合球蛋白启动子的转录调控。

IF 1.2 4区生物学

Gene Expression Patterns Pub Date : 2024-03-07 DOI: 10.1016/j.gep.2024.119357

Warren M Meyers

{"title":"Transcriptional regulation of the alternative sex hormone-binding globulin promoter by KLF4.","authors":"Warren M Meyers","doi":"10.1016/j.gep.2024.119357","DOIUrl":"https://doi.org/10.1016/j.gep.2024.119357","url":null,"abstract":"In most mammals the major site of sex hormone-binding globulin (SHBG) synthesis is the liver wherefrom it is secreted into the bloodstream and is the primary determinant of sex steroid access to target tissues. The minor site of SHBG synthesis is the testis and in lower mammals testicular SHBG has long been known to be synthesized and secreted by Sertoli cells. However, human testicular SHBG is expressed in developing germ cells from an upstream alternative promoter (altP-SHBG). Transcripts arising from this region comprise an alternative first exon (1A) with the resultant protein confined to the acrosomal compartment of the mature spermatozoa. I have dissected the regulatory components of the alternative SHBG promoter and identified motifs that are required for optimal transcriptional activity from this region. Transcriptional activity is driven by two CACCC elements that appear to be functionally redundant. The transcription factor KLF4 interacts with promoter the region spanning these elements in vivo. Knockdown of Klf4 results in decreased altP-SHBG activity, while Klf4 overexpression relieves the effects of knockdown. Based on their shared patterns of expression in vivo, I conclude that KLF4 is a transcriptional regulator of SHBG in male germ cells.","PeriodicalId":55598,"journal":{"name":"Gene Expression Patterns","volume":null,"pages":null},"PeriodicalIF":1.2,"publicationDate":"2024-03-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140068934","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Gene expression analysis of oxidative stress-related genes in the apical, middle, and basal turns of the cochlea 耳蜗顶端、中部和基底转折处氧化应激相关基因的基因表达分析

IF 1.2 4区生物学

Gene Expression Patterns Pub Date : 2024-03-01 DOI: 10.1016/j.gep.2024.119356

Yang Yang, Xin Chen, Chaoyong Tian, Bei Fan, Xiaogang An, Zhenzhen Liu, Qiong Li, Wenjuan Mi, Ying Lin, Dingjun Zha

{"title":"Gene expression analysis of oxidative stress-related genes in the apical, middle, and basal turns of the cochlea","authors":"Yang Yang, Xin Chen, Chaoyong Tian, Bei Fan, Xiaogang An, Zhenzhen Liu, Qiong Li, Wenjuan Mi, Ying Lin, Dingjun Zha","doi":"10.1016/j.gep.2024.119356","DOIUrl":"https://doi.org/10.1016/j.gep.2024.119356","url":null,"abstract":"<div>It can be observed from aminoglycoside-induced hair cell damage that the cochlea basal turn is more susceptible to trauma than the apex. Drug-induced hearing loss is closely related to oxidative damage. The basilar membrane directly exposed to these ototoxic drugs exhibits differences in damage, indicating that there is an inherent difference in the sensitivity to oxidative damage from the apex to the base of the cochlea. It has been reported that the morphology and characteristics of the cochlea vary from the apex to the base. Therefore, we investigated oxidative stress-related gene expression profiles in the apical, middle, and basal turns of the cochlea. The Oxidative Stress RT2 Profiler™ PCR Array revealed that three of the 84 genes (Mb, Mpo, and Ncf1) were upregulated in the middle turn compared to their level in the apical turn. Moreover, eight genes (Mb, Duox1, Ncf1, Ngb, Fmo2, Gpx3, Mpo, and Gstk1) were upregulated in the basal turn compared to their level in the apical turn. The qPCR verification data were similar to that of the PCR Array. We found that MPO was expressed in the rat cochlea and protected against gentamicin-induced hair cell death. This study summarized the data for the gradient of expression of oxidative stress-related genes in the cochlea and found potential candidate targets for prevention of ototoxic deafness, which may provide new insights for cochlear pathology.</div>","PeriodicalId":55598,"journal":{"name":"Gene Expression Patterns","volume":null,"pages":null},"PeriodicalIF":1.2,"publicationDate":"2024-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140013922","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Embryonic expression patterns of TBL1 family in zebrafish TBL1 家族在斑马鱼胚胎期的表达模式

IF 1.2 4区生物学

Gene Expression Patterns Pub Date : 2024-01-23 DOI: 10.1016/j.gep.2024.119355

Yuanqi Jia , Qiu Jiang , Shuna Sun

{"title":"Embryonic expression patterns of TBL1 family in zebrafish","authors":"Yuanqi Jia , Qiu Jiang , Shuna Sun","doi":"10.1016/j.gep.2024.119355","DOIUrl":"10.1016/j.gep.2024.119355","url":null,"abstract":"<div>Except the addition of TBL1Y in human, transducing beta like 1 (TBL1) family mainly consists of two members TBL1X and TBL1XR1, taking part in multiple intracellular signaling pathways such as Wnt/β-catenin and NF-κB in cancer progression. However, the gene expression patterns of this family during embryonic development remain largely unknown. Here we took advantage of zebrafish model to characterize the spatial and temporal expression patterns of TBL1 family genes including tbl1x, tbl1xr1a and tbl1xr1b. The in situ hybridization studies of gene expression showed robust expressions of tbl1x and tbl1xr1b as maternal transcripts except tbl1xr1a. As the embryo develops, zygotic expressions of all TBL1 family members occur and have a redundant and broad pattern including in brain, neural retina, pharyngeal arches, otic vesicles, and pectoral fins. Ubiquitous expression of all family members were ranked from the strongest to the weakest: tbl1xr1a, tbl1x, and tbl1xr1b. In addition, one tbl1xr1a transcript tbl1xr1a202 showed unique and rich expression in the developing heart and lateral line neuromasts. Overall, all members of zebrafish TBL1 family shared numerous similarities and exhibited certain distinctions in the expression patterns, indicating that they might have redundant and exclusive functions to be further explored.</div>","PeriodicalId":55598,"journal":{"name":"Gene Expression Patterns","volume":null,"pages":null},"PeriodicalIF":1.2,"publicationDate":"2024-01-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139558299","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Exosome complex components 1 and 2 are vital for early mammalian development 外泌体复合物组分1和2对哺乳动物的早期发育至关重要。

IF 1.2 4区生物学

Gene Expression Patterns Pub Date : 2023-11-07 DOI: 10.1016/j.gep.2023.119346

Sanjana Srinivasan, Xinjian He, Sarah Mirza, Jesse Mager

{"title":"Exosome complex components 1 and 2 are vital for early mammalian development","authors":"Sanjana Srinivasan, Xinjian He, Sarah Mirza, Jesse Mager","doi":"10.1016/j.gep.2023.119346","DOIUrl":"10.1016/j.gep.2023.119346","url":null,"abstract":"<div>Exosome Complex Components 1 and 2 (EXOSC1 and 2) are two proteins in the RNA Exosome complex whose main function is 5’ → 3’ RNA degradation and processing. The RNA exosome complex is comprised of nine subunits that form two separate components: the S1/KH cap and the PH-core. EXOSC1 and 2 are both part of the S1/KH cap and are involved in binding nascent RNA. As part of a systemic characterization of early lethal alleles produced by the Knockout Mouse Project, we have examined Exosc1 and Exosc2 homozygous null (mutant) embryos to determine developmental and molecular phenotypes of embryos lacking their functions. Our studies reveal that Exosc1 null embryos implant and form an egg cylinder but are developmentally delayed and fail to initiate gastrulation by embryonic day 7.5. In contrast, Exosc2 null embryos are lethal during peri-implantation stages, and while they do form a morphologically normal blastocyst at E3.5, they cannot be recovered at post-implantation stages. We show the absence of stage-specific developmental and altered lineage-specification in both Exosc1 and Exosc2 mutant embryos and conclude that these genes are essential for the successful progression through early mammalian development.</div>","PeriodicalId":55598,"journal":{"name":"Gene Expression Patterns","volume":null,"pages":null},"PeriodicalIF":1.2,"publicationDate":"2023-11-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"71523485","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Developmental expression of peroxiredoxin gene family in early embryonic development of Xenopus tropicalis 热带爪蟾早期胚胎发育过程中过氧氧化还原素基因家族的发育表达。

IF 1.2 4区生物学

Gene Expression Patterns Pub Date : 2023-10-14 DOI: 10.1016/j.gep.2023.119345

Linke Zhong , Tingting Fu , Chengdong Wang , Xufeng Qi , Wai-Yee Chan , Dongqing Cai , Hui Zhao

引用次数: 1