Yuan Wang, Graham Herzig, Cassandra Molano, Aimin Liu
{"title":"Differential expression of the Tmem132 family genes in the developing mouse nervous system.","authors":"Yuan Wang, Graham Herzig, Cassandra Molano, Aimin Liu","doi":"10.2139/ssrn.4100200","DOIUrl":"https://doi.org/10.2139/ssrn.4100200","url":null,"abstract":"The family of novel transmembrane proteins (TMEM) 132 have been associated with multiple neurological disorders and cancers in humans, but have hardly been studied in vivo. Here we report the expression patterns of the five Tmem132 genes (a, b, c, d and e) in developing mouse nervous system with RNA in situ hybridization in wholemount embryos and tissue sections. Our results reveal differential and partially overlapping expression of multiple Tmem132 family members in both the central and peripheral nervous system, suggesting potential partial redundancy among them.","PeriodicalId":55598,"journal":{"name":"Gene Expression Patterns","volume":"46 1","pages":"119257"},"PeriodicalIF":1.2,"publicationDate":"2022-06-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"91220202","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}
{"title":"Embryonic expression patterns of Wnt genes in the RTA-clade spider Cupiennius salei","authors":"Ralf Janssen , Bo Joakim Eriksson","doi":"10.1016/j.gep.2022.119247","DOIUrl":"10.1016/j.gep.2022.119247","url":null,"abstract":"<div><p>Spiders represent widely used model organisms for chelicerate and even arthropod development and evolution. Wnt genes are important and evolutionary conserved factors that control and regulate numerous developmental processes. Recent studies comprehensively investigated the complement and expression of spider Wnt genes revealing conserved as well as diverged aspects of their expression and thus (likely) function among different groups of spiders representing Mygalomorphae (tarantulas), and both main groups of Araneae (true spiders) (Haplogynae/Synspermiata and Entelegynae). The allegedly most modern/derived group of entelegyne spiders is represented by the RTA-clade of which no comprehensive data on Wnt expression were available prior to this study. Here, we investigated the embryonic expression of all Wnt genes of the RTA-clade spider <em>Cupiennius salei</em>. We found that most of the Wnt expression patterns are conserved between <em>Cupiennius</em> and other spiders, especially more basally branching species. Surprisingly, most differences in Wnt gene expression are seen in the common model spider <em>Parasteatoda tepidariorum</em> (a non-RTA clade entelegyne species). These results show that data and conclusions drawn from research on one member of a group of animals (or any other organism) cannot necessarily be extrapolated to the group as a whole, and instead highlight the need for comprehensive taxon sampling.</p></div>","PeriodicalId":55598,"journal":{"name":"Gene Expression Patterns","volume":"44 ","pages":"Article 119247"},"PeriodicalIF":1.2,"publicationDate":"2022-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S1567133X22000175/pdfft?md5=52ae1e5367b3f207f7d69559f8d29499&pid=1-s2.0-S1567133X22000175-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"88382672","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Xiaogang An , Ye Wang , Bang Han , Liu Hong , Dingjun Zha , Yu Han
{"title":"Expression and distribution of Nob1 in the developing rat cochleae","authors":"Xiaogang An , Ye Wang , Bang Han , Liu Hong , Dingjun Zha , Yu Han","doi":"10.1016/j.gep.2022.119235","DOIUrl":"10.1016/j.gep.2022.119235","url":null,"abstract":"<div><h3>Background</h3><p>Mammalian inner ear cells are produced during embryonic development<span>. NIN1/RPN12 binding protein 1 homolog (Nob1), a ribosome assembly factor, is believed to be involved in transcriptional regulation and may play an important role in mediating certain physiological and pathological functions.</span></p></div><div><h3>Methods</h3><p>We investigated the expression levels and distribution patterns of Nob1 in rat cochlea at different developmental stages using reverse transcription-polymerase chain reaction (RT-PCR), Western blot analysis, and immunofluorescence microscopy (P0, P3, P7, P14, and P30, n = 11 per age group).</p></div><div><h3>Results</h3><p>The expression of Nob1 was gradually upregulated from Postnatal day (P) 0 to P14 and stabilized at P30. Our results analyzing Nob1 expression at P0 and P3 in the rat cochleae revealed expression in the greater epithelial ridge cells, lesser epithelial ridge cells, and spiral ganglion neurons (SGNs), whereas low levels of Nob1 expression were observed in the stria vascularis cells. During the development of the cochlea, the organ of Corti undergoes dramatic architectural remodeling. Nob1 expression was stably detected in supporting cells and hair cells from P7 to P30, and its expression gradually increased in the SGNs.</p></div><div><h3>Conclusions</h3><p>Thus, the present study revealed that upregulation of Nob1 might explain the maturation of the cytoarchitecture<span> in the cochlea during the postnatal period, and a complete understanding of its function in the mammalian inner ear may help to develop strategies to resolve auditory hair cell loss.</span></p></div>","PeriodicalId":55598,"journal":{"name":"Gene Expression Patterns","volume":"44 ","pages":"Article 119235"},"PeriodicalIF":1.2,"publicationDate":"2022-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"85223221","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}
Judith Habicher , Remy Manuel , Andrea Pedroni , Charles Ferebee , Konstantinos Ampatzis , Henrik Boije
{"title":"A new transgenic reporter line reveals expression of protocadherin 9 at a cellular level within the zebrafish central nervous system","authors":"Judith Habicher , Remy Manuel , Andrea Pedroni , Charles Ferebee , Konstantinos Ampatzis , Henrik Boije","doi":"10.1016/j.gep.2022.119246","DOIUrl":"10.1016/j.gep.2022.119246","url":null,"abstract":"<div><p>The wiring of neuronal networks is far from understood. One outstanding question is how neurons of different types link up to form subnetworks within the greater context. Cadherins have been suggested to create an inclusion code where interconnected neurons express the same subtypes. Here, we have used a CRISPR/Cas9 knock-in approach to generate a transgenic zebrafish reporter line for protocadherin 9 (<em>pcdh9</em>), which is predominantly expressed within the central nervous system. Expression of eGFP was detected in subsets of neurons in the cerebellum, retina and spinal cord, in both larvae and juveniles. A closer characterization of the spinal locomotor network revealed that a portion of distinct classes of both excitatory and inhibitory interneurons, as well as motor neurons, expressed <em>pcdh9</em>. This transgenic line could thus be used to test the cadherin network hypothesis, through electrophysiological characterization of eGFP positive cells, to show if these are synaptically connected and form a discrete network within the spinal cord.</p></div>","PeriodicalId":55598,"journal":{"name":"Gene Expression Patterns","volume":"44 ","pages":"Article 119246"},"PeriodicalIF":1.2,"publicationDate":"2022-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S1567133X22000163/pdfft?md5=c4c251f4174dc8361615278519c3ea5a&pid=1-s2.0-S1567133X22000163-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"82023473","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Juan-Juan Sun , Zhi-Hui Sun , Jin-Liang Wei, Jun Ding, Jian Song, Ya-Qing Chang
{"title":"Identification and functional analysis of foxl2 and nodal in sea cucumber, Apostichopus japonicus","authors":"Juan-Juan Sun , Zhi-Hui Sun , Jin-Liang Wei, Jun Ding, Jian Song, Ya-Qing Chang","doi":"10.1016/j.gep.2022.119245","DOIUrl":"10.1016/j.gep.2022.119245","url":null,"abstract":"<div><p>Sea cucumber (<span><em>Apostichopus japonicus</em></span><span>) is an important mariculture species in China. To date, the mechanisms of sex determination and differentiation in sea cucumber remain unclear. Identifying sex-specific molecular markers<span> is an effective method for revealing the genetic basis of sex determination and sex differentiation. In this study, </span></span><em>foxl2</em> and <em>nodal</em> homologous genes were identified in <em>A. japonicus</em>. <em>Foxl2</em> exhibited dynamic and sexually dimorphic expression patterns in the gonads, with prominent expression in the ovaries and minimal expression in the testis according to real-time quantitative PCR (RT-qPCR) study. As <em>nodal</em> was specifically expressed in the ovary, it could serve as an ovary-specific marker in sea cucumber. Additionally, knockdown of <em>foxl2</em> or <em>nodal</em> using RNA interference (RNAi) led to the down-regulation of <span><em>piwi</em></span>, <em>germ cell-less</em>, and <em>dmrt1</em>, suggesting that <em>foxl2</em> and <em>nodal</em> may play important roles in gonad maintenance of sea cucumber. Overall, this study adds to our understanding of the roles of <em>foxl2</em> and <em>nodal</em><span> in the gonadal development of </span><em>A. japonicus</em>, which provides further insight into the mechanisms of sea cucumber sex determination and differentiation.</p></div>","PeriodicalId":55598,"journal":{"name":"Gene Expression Patterns","volume":"44 ","pages":"Article 119245"},"PeriodicalIF":1.2,"publicationDate":"2022-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"77734907","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}
Sol Torruella-Gonzalez , Paula G. Slater , Dasfne Lee-Liu , Juan Larraín
{"title":"Cornifelin expression during Xenopus laevis metamorphosis and in response to spinal cord injury","authors":"Sol Torruella-Gonzalez , Paula G. Slater , Dasfne Lee-Liu , Juan Larraín","doi":"10.1016/j.gep.2022.119234","DOIUrl":"10.1016/j.gep.2022.119234","url":null,"abstract":"<div><h3>Background</h3><p><span>In a high-throughput RNA sequencing analysis, comparing the transcriptional response between </span><span><em>Xenopus laevis</em></span><span> regenerative and non-regenerative stages to spinal cord injury, cornifelin was found among the most highly differentially expressed genes. Cornifelin is mainly expressed in stratified squamous epithelia, but its expression in the spinal cord and other central nervous structures has only been described during early development.</span></p></div><div><h3>Results</h3><p><span>Here, we report cornifelin expression in the spinal cord, retina, and cornea throughout metamorphosis and in the spinal cord after injury. Cornifelin was detected in the grey matter and meninges of the spinal cord from NF-50 to NF-66, with decreased expression in the grey matter during metamorphosis. In the retina, cornifelin was expressed in the </span>ganglion cell<span><span> layer, the inner and outer nuclear layer, and the outer segment from NF-50 to NF-66. After spinal cord injury, we only observed cornifelin upregulation in NF-66 but no significant changes in NF-50. However, we found cornifelin positive cells in NF-50 meninges closing the spinal cord stumps 1 day after injury and delineating the borders of the spinal cord following the continuity of tissue regeneration in the following days after injury. Instead, in NF-66, cornifelin positive cells were distributed to the ventral side of the spinal cord at 6 days after injury, and at the injury gap </span>at 10 days after injury.</span></p></div><div><h3>Conclusions</h3><p>Cornifelin is expressed in the <em>Xenopus laevis</em> spinal cord and eye during metamorphosis and plays a role in the meningeal response to spinal cord injury.</p></div>","PeriodicalId":55598,"journal":{"name":"Gene Expression Patterns","volume":"43 ","pages":"Article 119234"},"PeriodicalIF":1.2,"publicationDate":"2022-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39789291","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}
Dashzeveg Bayarsaihan , Badam Enkhmandakh , Anushree Vijaykumar , Paul Robson , Mina Mina
{"title":"Single-cell transcriptome analysis defines mesenchymal stromal cells in the mouse incisor dental pulp","authors":"Dashzeveg Bayarsaihan , Badam Enkhmandakh , Anushree Vijaykumar , Paul Robson , Mina Mina","doi":"10.1016/j.gep.2021.119228","DOIUrl":"10.1016/j.gep.2021.119228","url":null,"abstract":"<div><p><span>The dental pulp is known to be highly heterogenous, comprising distinct cell types including mesenchymal stromal cells<span> (MSCs), which represent neural-crest-derived cells with the ability to differentiate into multiple cell lineages<span><span><span>. However, the cellular heterogeneity and the transcriptome signature of different cell clusters within the dental pulp remain to be established. To better understand discrete cell types, we applied a single-cell </span>RNA sequencing<span> strategy to establish the RNA<span> expression profiles of individual dental pulp cells from 5- to 6-day-old mouse incisors. Our study revealed distinct subclasses of cells representing osteoblast, odontoblast, endothelial, pancreatic, neuronal, immune, pericyte and </span></span></span>ameloblast lineages. Collectively, our research demonstrates the complexity and diversity of cell subclasses within the incisor dental pulp, thus providing a foundation for uncovering the </span></span></span>molecular processes that govern cell fate decisions and lineage commitment in dental pulp-derived MSCs.</p></div>","PeriodicalId":55598,"journal":{"name":"Gene Expression Patterns","volume":"43 ","pages":"Article 119228"},"PeriodicalIF":1.2,"publicationDate":"2022-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39819790","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}
{"title":"CCCTC-binding factor is an upstream regulator of the pluripotency factor Oct4 and functions in active transcription of linc1253 and linc1356 genes in pluripotent cells","authors":"Feng Wang, Baiquan Ci, Yangzi Wang","doi":"10.1016/j.gep.2021.119230","DOIUrl":"10.1016/j.gep.2021.119230","url":null,"abstract":"<div><p>The embryonic stem cell- (ESC) specific transcription factor Oct4<span><span> is a well-known master regulator of pluripotency. The aim of this study was to identify upstream regulators of Oct4 and explore their functional link in regulating lincRNA expression in ESCs. By quantitative real-time PCR (RT-qPCR) analysis upon CCCTC-binding factor (CTCF) or Oct4 knockdown, here, we found that the chromatin insulator </span>CTCF transcriptionally controls Oct4 gene expression in mouse ES cells. Furthermore, co-immunoprecipitation assays showed that CTCF physically interacts with Oct4. By analyzing CTCF and Oct4 ChIP-seq datasets in mouse ES cells and investigating their genomic occupancies, we demonstrated that CTCF and Oct4 share overlapping regulatory functions and are required for active transcription of long intergenic non-coding RNAs (lincRNAs) linc1253 and linc1356, which were reported to repress cellular lineage programs and maintain a pluripotent state. In summary, we propose an integrated model of transcriptional control mediated by CTCF, the master weaver of the genome, for the upstream regulation of Oct4-and ESC-associated genes. These results connect the chromatin insulator CTCF and the pluripotency factor Oct4 in the regulation of lincRNAs in pluripotent cells.</span></p></div>","PeriodicalId":55598,"journal":{"name":"Gene Expression Patterns","volume":"43 ","pages":"Article 119230"},"PeriodicalIF":1.2,"publicationDate":"2022-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39819791","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}
{"title":"Identification and validation of stage-specific reference genes for gene expression analysis in Callosobruchus maculatus (Coleoptera: Bruchidae)","authors":"Gagandeep Singh Brar , Gurmeet Kaur , Satnam Singh , Jayendra Nath Shukla , Suneet Pandher","doi":"10.1016/j.gep.2022.119233","DOIUrl":"10.1016/j.gep.2022.119233","url":null,"abstract":"<div><p>In light of a number of recent studies highlighting the increasing research interest in bruchids, it is crucial to validate suitable reference genes that could be used in quantitative gene expression studies. <span><em>Callosobruchus maculatus</em></span> is a serious pest of stored grains and field legumes in which reference genes have not been assessed and validated to date. The present study aimed to identify and validate reference genes in different developmental stages of <em>C. maculatus</em> shortlisted from commonly used reference genes such as <span><span><span><em>VATPase</em><em>, TRIP12, </em></span><em>TBP</em><em>, TF11D, ACTIN, </em></span><em>GST</em><span><em>, ANNEXIN, PTCD3, </em><em>RPL32</em><em>,</em></span></span> and <em>β -Tub</em> in various insects. Dedicated algorithms like GeNorm, NormFinder, and BestKeeper were used to analyze the stability of these candidate genes, which revealed <em>GST</em> for third instar, <em>ANNEXIN</em> and <em>PTCD3</em> for the fourth instar, <em>TF11D</em> and <em>VATPase</em> for male pupa, <em>RPL32</em> and <em>β-tub</em> for female pupa, <em>β-tub</em> and <em>TBP</em> for adult male and <em>VATPase</em> and <em>GST</em> for adult females as suitable reference genes for expression studies in <em>C. maculatus.</em> The final comprehensive ranking using RefFinder identified <em>GST</em> and <em>TBP</em> as the best reference genes for all the developmental stages of <em>C. maculatus</em>. To the best of our knowledge, this is the first report which evaluates and validates stable reference genes in <em>C. maculatus</em>. The information of stage-specific gene expression, generated in this study will be useful for future molecular, physiological, and biochemical studies on <em>C. maculatus</em> and other closely related bruchids.</p></div>","PeriodicalId":55598,"journal":{"name":"Gene Expression Patterns","volume":"43 ","pages":"Article 119233"},"PeriodicalIF":1.2,"publicationDate":"2022-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39892410","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}
Ji-Seong Kim , Minjeong Jang , Hualin Nie , Jeongeun Lee , Eunhye Hong , Su-Jung Kim , Sun Hyung Kim
{"title":"Differential expression pattern of novel MADS-box genes in early root formation and differentiation of sweet potato","authors":"Ji-Seong Kim , Minjeong Jang , Hualin Nie , Jeongeun Lee , Eunhye Hong , Su-Jung Kim , Sun Hyung Kim","doi":"10.1016/j.gep.2021.119216","DOIUrl":"10.1016/j.gep.2021.119216","url":null,"abstract":"<div><p>MADS-box genes are important transcription factors affecting overall development, but their role in sweet potato [<span><em>Ipomoea</em><em> batata</em></span>s (L.) Lam.] has not been fully studied. This study isolated six novel MADS-box genes (<em>IbSOC1</em>, <em>IbFUL1</em>, <em>IbAGL6</em>, <em>IbSVP1</em>, <em>IbSVP2</em>, and <em>IbSVP3</em>) from sweet potato [<em>Ipomoea batata</em>s (L.) Lam. cv. Annouimo] during the early root differentiation stage using the <em>de novo</em><span> transcriptome assembly sequencing method. At the early root differentiation (between 0 and 3 days after transplanting), the </span><em>IbSOC1</em>, <em>IbFUL1</em>, and <em>IbSVP2</em> genes decreased rapidly, whereas the <em>IbSVP3</em> gene decreased gradually. In the early stages of root formation (0–30 days), the levels of <em>IbSVP1</em> and <em>IbSVP3</em> expression were steady, but the levels of <em>IbSOC1</em> expression decreased gradually. The expression of six novel genes was also conducted in the tuberous root formation stage (30–90 days), and the <em>IbSVP3</em><span> gene increased significantly according to the formation of the tuberous root. Six novel MADS-box genes that were believed to influence the entire root formation of sweet potato were isolated from the sweet potato. This study provides a genetic basis for further research on sweet potato root formation and development.</span></p></div>","PeriodicalId":55598,"journal":{"name":"Gene Expression Patterns","volume":"43 ","pages":"Article 119216"},"PeriodicalIF":1.2,"publicationDate":"2022-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39727970","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}