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Salignon J, Millan-Ariño L, Garcia M, Riedel CG. Cactus: A user-friendly and reproducible ATAC-Seq and mRNA-Seq analysis pipeline for data preprocessing, differential analysis, and enrichment analysis. Genomics 2024:110858. [PMID: 38735595 DOI: 10.1016/j.ygeno.2024.110858] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2024] [Revised: 05/06/2024] [Accepted: 05/09/2024] [Indexed: 05/14/2024]
Abstract
The ever decreasing cost of Next-Generation Sequencing coupled with the emergence of efficient and reproducible analysis pipelines has rendered genomic methods more accessible. However, downstream analyses are basic or missing in most workflows, creating a significant barrier for non-bioinformaticians. To help close this gap, we developed Cactus, an end-to-end pipeline for analyzing ATAC-Seq and mRNA-Seq data, either separately or jointly. Its Nextflow-, container-, and virtual environment-based architecture ensures efficient and reproducible analyses. Cactus preprocesses raw reads, conducts differential analyses between conditions, and performs enrichment analyses in various databases, including DNA-binding motifs, ChIP-Seq binding sites, chromatin states, and ontologies. We demonstrate the utility of Cactus in a multi-modal and multi-species case study as well as by showcasing its unique capabilities as compared to other ATAC-Seq pipelines. In conclusion, Cactus can assist researchers in gaining comprehensive insights from chromatin accessibility and gene expression data in a quick, user-friendly, and reproducible manner.
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Affiliation(s)
- Jérôme Salignon
- Department of Bioscience and Nutrition, Karolinska Institute, Blickagången 16, Huddinge SE-141 83, Sweden.
| | - Lluís Millan-Ariño
- Department of Bioscience and Nutrition, Karolinska Institute, Blickagången 16, Huddinge SE-141 83, Sweden
| | - Maxime Garcia
- National Genomics Infrastructure, Science for Life Laboratory, Tomtebodavägen 23A, Solna SE-171 65, Sweden; Department of Oncology-Pathology, Karolinska Institute, Visionsgatan 4, Solna SE-171 64, Sweden
| | - Christian G Riedel
- Department of Bioscience and Nutrition, Karolinska Institute, Blickagången 16, Huddinge SE-141 83, Sweden
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Zhao B, Zhang H, Liu Y, Zu G, Zhang Y, Hu J, Liu S, You L. Forebrain excitatory neuron-specific loss of Brpf1 attenuates excitatory synaptic transmission and impairs spatial and fear memory. Neural Regen Res 2024; 19:1133-1141. [PMID: 37862219 PMCID: PMC10749587 DOI: 10.4103/1673-5374.385307] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Revised: 06/10/2023] [Accepted: 07/19/2023] [Indexed: 10/22/2023] Open
Abstract
Bromodomain and plant homeodomain (PHD) finger containing protein 1 (Brpf1) is an activator and scaffold protein of a multiunit complex that includes other components involving lysine acetyltransferase (KAT) 6A/6B/7. Brpf1, KAT6A, and KAT6B mutations were identified as the causal genes of neurodevelopmental disorders leading to intellectual disability. Our previous work revealed strong and specific expression of Brpf1 in both the postnatal and adult forebrain, especially the hippocampus, which has essential roles in learning and memory. Here, we hypothesized that Brpf1 plays critical roles in the function of forebrain excitatory neurons, and that its deficiency leads to learning and memory deficits. To test this, we knocked out Brpf1 in forebrain excitatory neurons using CaMKIIa-Cre. We found that Brpf1 deficiency reduced the frequency of miniature excitatory postsynaptic currents and downregulated the expression of genes Pcdhgb1, Slc16a7, Robo3, and Rho, which are related to neural development, synapse function, and memory, thereby damaging spatial and fear memory in mice. These findings help explain the mechanisms of intellectual impairment in patients with BRPF1 mutation.
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Affiliation(s)
- Baicheng Zhao
- Department of Human Anatomy & Histoembryology, School of Basic Medical Sciences, Fudan University, Shanghai, China
| | - Hang Zhang
- Department of Human Anatomy & Histoembryology, School of Basic Medical Sciences, Fudan University, Shanghai, China
| | - Ying Liu
- Department of Human Anatomy & Histoembryology, School of Basic Medical Sciences, Fudan University, Shanghai, China
| | - Gaoyu Zu
- Department of Human Anatomy & Histoembryology, School of Basic Medical Sciences, Fudan University, Shanghai, China
| | - Yuxiao Zhang
- Shanghai Key Laboratory of Brain Functional Genomics (Ministry of Education), Affiliated Mental Health Center (ECNU), School of Psychology and Cognitive Science, East China Normal University, Shanghai, China
- Shanghai Changning Mental Health Center, Shanghai, China
- NYU-ECNU Institute of Brain and Cognitive Science at NYU Shanghai, Shanghai, China
| | - Jiayi Hu
- Department of Human Anatomy & Histoembryology, School of Basic Medical Sciences, Fudan University, Shanghai, China
| | - Shuai Liu
- Shanghai Key Laboratory of Brain Functional Genomics (Ministry of Education), Affiliated Mental Health Center (ECNU), School of Psychology and Cognitive Science, East China Normal University, Shanghai, China
- Shanghai Changning Mental Health Center, Shanghai, China
- NYU-ECNU Institute of Brain and Cognitive Science at NYU Shanghai, Shanghai, China
| | - Linya You
- Department of Human Anatomy & Histoembryology, School of Basic Medical Sciences, Fudan University, Shanghai, China
- Key Laboratory of Medical Imaging Computing and Computer Assisted Intervention of Shanghai, Shanghai, China
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Li X, Li S, Bai S, Tang Y, Jia Z, Yin J, Xu X, Zhang J, Irwin DM, Zhang S, Wang Z. Research Note: SOCS2 contributes to reduction of the third digit during development of the chicken forelimb. Poult Sci 2024; 103:103672. [PMID: 38564834 PMCID: PMC10999695 DOI: 10.1016/j.psj.2024.103672] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2024] [Revised: 03/08/2024] [Accepted: 03/14/2024] [Indexed: 04/04/2024] Open
Abstract
The development of the avian wing pattern has been the subject of heated debate due to its special shape. The Suppressor of cytokine signaling 2 (SOCS2) gene encodes a negative regulator of growth hormone (GH) signaling and bone growth and is known to be strongly expressed in the third digit of chicken forelimbs. These observations suggest that SOCS2 might regulate the morphology of the avian wing, however, the function of SOCS2 in avian limb development remains unknown. Here, we reexamined SOCS2 expression in successive developmental stages of chicken limb development by in situ hybridization (ISH) and describe extended expression from the posterior of the stypolod to the third digit of the forelimbs. We used the RCAS avian retrovirus to overexpress SOCS2 in the developing chicken limb buds, which resulted in reduced or malformed chicken wings while hindlimbs developed normally. Transcriptome sequencing (mRNA-Seq) revealed changes in expression of genes known to be associated with growth and development in forelimbs with overexpressed SOCS2. This study highlights a pivotal role for SOCS2 during the development of the wing in the chicken and provides new insight into molecular mechanisms regulating avian limb development.
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Affiliation(s)
- Xiaoping Li
- College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang 110866, PR China
| | - Shanshan Li
- College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang 110866, PR China
| | - Shibin Bai
- College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang 110866, PR China
| | - Yining Tang
- College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang 110866, PR China
| | - Ziqiu Jia
- College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang 110866, PR China
| | - Jialong Yin
- College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang 110866, PR China
| | - Xiaona Xu
- College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang 110866, PR China
| | - Junpeng Zhang
- College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang 110866, PR China
| | - David M Irwin
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Shuyi Zhang
- College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang 110866, PR China
| | - Zhe Wang
- College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang 110866, PR China.
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Seok HY, Lee SY, Sarker S, Bayzid M, Moon YH. Genome-Wide Analysis of Stress-Responsive Genes and Alternative Splice Variants in Arabidopsis Roots under Osmotic Stresses. Int J Mol Sci 2023; 24:14580. [PMID: 37834024 PMCID: PMC10573044 DOI: 10.3390/ijms241914580] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2023] [Revised: 09/05/2023] [Accepted: 09/25/2023] [Indexed: 10/15/2023] Open
Abstract
Plant roots show distinct gene-expression profiles from those of shoots under abiotic stress conditions. In this study, we performed mRNA sequencing (mRNA-Seq) to analyze the transcriptional profiling of Arabidopsis roots under osmotic stress conditions-high salinity (NaCl) and drought (mannitol). The roots demonstrated significantly distinct gene-expression changes from those of the aerial parts under both the NaCl and the mannitol treatment. We identified 68 closely connected transcription-factor genes involved in osmotic stress-signal transduction in roots. Well-known abscisic acid (ABA)-dependent and/or ABA-independent osmotic stress-responsive genes were not considerably upregulated in the roots compared to those in the aerial parts, indicating that the osmotic stress response in the roots may be regulated by other uncharacterized stress pathways. Moreover, we identified 26 osmotic-stress-responsive genes with distinct expressions of alternative splice variants in the roots. The quantitative reverse-transcription polymerase chain reaction further confirmed that alternative splice variants, such as those for ANNAT4, MAGL6, TRM19, and CAD9, were differentially expressed in the roots, suggesting that alternative splicing is an important regulatory mechanism in the osmotic stress response in roots. Altogether, our results suggest that tightly connected transcription-factor families, as well as alternative splicing and the resulting splice variants, are involved in the osmotic stress response in roots.
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Affiliation(s)
- Hye-Yeon Seok
- Korea Nanobiotechnology Center, Pusan National University, Busan 46241, Republic of Korea; (H.-Y.S.); (S.-Y.L.)
| | - Sun-Young Lee
- Korea Nanobiotechnology Center, Pusan National University, Busan 46241, Republic of Korea; (H.-Y.S.); (S.-Y.L.)
| | - Swarnali Sarker
- Department of Integrated Biological Science, Pusan National University, Busan 46241, Republic of Korea; (S.S.); (M.B.)
| | - Md Bayzid
- Department of Integrated Biological Science, Pusan National University, Busan 46241, Republic of Korea; (S.S.); (M.B.)
| | - Yong-Hwan Moon
- Department of Integrated Biological Science, Pusan National University, Busan 46241, Republic of Korea; (S.S.); (M.B.)
- Department of Molecular Biology, Pusan National University, Busan 46241, Republic of Korea
- Institute of Systems Biology, Pusan National University, Busan 46241, Republic of Korea
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Hasegawa Y, Watanabe T, Otsuka R, Toné S, Kubota S, Hirakawa H. Genome assembly and transcriptomic analyses of the repeatedly rejuvenating jellyfish Turritopsis dohrnii. DNA Res 2022; 30:6909006. [PMID: 36519838 PMCID: PMC9835754 DOI: 10.1093/dnares/dsac047] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2022] [Revised: 11/16/2022] [Accepted: 11/24/2022] [Indexed: 12/23/2022] Open
Abstract
Only two hydromedusan species, Turritopsis dohrnii and T. sp., have exhibited experimental multiple-repeat life cycle reversion in the laboratory, which can be artificially induced by various means such as incubation with CsCl, heat shock, and mechanical damage with needles. In the present study, we constructed a genome assembly of T. dohrnii using Pacific Biosciences long-reads and Illumina short-reads, for which the genome DNA was extracted from 1,500 young medusae originated from a single clone. The total length of the draft genome sequence of T. dohrnii was 435.9 Mb (N50 length 747.2 kb). We identified 23,314 high-confidence genes and found the characteristics of RNA expression amongst developmental stages. Our genome assembly and transcriptome data provide a key model system resource that will be useful for understanding cyclical rejuvenation.
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Affiliation(s)
- Yoshinori Hasegawa
- To whom correspondence should be addressed. Tel: +81 438 52 3944. Fax: +81 438 52 3921. (Y.H); Tel: +81 438 52 3906. Fax: +81 438 52 3924. (H.H)
| | - Takashi Watanabe
- Department of Applied Genomics, Kazusa DNA Research Institute, Kisarazu, Chiba 292-0818, Japan
| | - Reo Otsuka
- Graduate School of Science and Engineering, Tokyo Denki University, Hatoyama, Saitama 350-0394, Japan
| | - Shigenobu Toné
- Graduate School of Science and Engineering, Tokyo Denki University, Hatoyama, Saitama 350-0394, Japan
| | - Shin Kubota
- Turritopsis Immortal Jellyfish Regenerative Biological Research/Experience Laboratory, Arita, Wakayama 643-0002, Japan
| | - Hideki Hirakawa
- To whom correspondence should be addressed. Tel: +81 438 52 3944. Fax: +81 438 52 3921. (Y.H); Tel: +81 438 52 3906. Fax: +81 438 52 3924. (H.H)
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Wang Z, Cai D, Li K, Ju X, Nie Q. Transcriptome analysis of the inhibitory effect of cycloleucine on myogenesis. Poult Sci 2022; 101:102219. [PMID: 36308813 PMCID: PMC9618838 DOI: 10.1016/j.psj.2022.102219] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Revised: 09/28/2022] [Accepted: 09/29/2022] [Indexed: 11/07/2022] Open
Abstract
N6-Methyladenosine (m6A) has been reported to involve and play an important role in various biological activities but seldom in poultry myogenesis. Cycloleucine usually functions as a nucleic acid methylation inhibitor, the inhibition efficiency of cycloleucine at the m6A level and corresponding dynamic changes of poultry muscle cells remain unknown. In this study, we aim to find out the effect of cycloleucine on the total N6-Methyladenosine level and its molecular mechanism for regulating myogenesis. A total of 745 differentially expressed genes (DEGs) were obtained by 10 mM, 20 mM, and 30 mM of cycloleucine treatment compared with 0 mM treatment. DEGs in 10 mM cycloleucine were significantly enriched in the biological process of skeletal muscle and satellite cell proliferation and differentiation, DEGs in 20 and 30 mM cycloleucine were enriched in some metabolic and biosynthetic processes. The trend analysis showed that 85% of all DEGs were significantly clustered into 4 files, among them 59% DEGs were dose-dependent and 26% were dose-independent, 52% DEGs were in downtrend and 33% DEGs were in uptrend. Also, the cycloleucine treatment could trigger cell cycle arrest in the G1 phase and depress myoblast cell proliferation and inhibit myotube formation. In conclusion, cycloleucine could continuously reduce the m6A level of myoblast cells, depress myoblast cell proliferation and inhibit myotube formation.
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Affiliation(s)
- Zhijun Wang
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou 510642, China,National-Local Joint Engineering Research Center for Livestock Breeding, Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, and Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou 510642, China
| | - Danfeng Cai
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou 510642, China,National-Local Joint Engineering Research Center for Livestock Breeding, Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, and Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou 510642, China
| | - Kan Li
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou 510642, China,National-Local Joint Engineering Research Center for Livestock Breeding, Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, and Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou 510642, China
| | - Xing Ju
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou 510642, China,National-Local Joint Engineering Research Center for Livestock Breeding, Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, and Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou 510642, China
| | - Qinghua Nie
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou 510642, China,National-Local Joint Engineering Research Center for Livestock Breeding, Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, and Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou 510642, China,Corresponding author:
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Jiang H, Jing Q, Yang Q, Qiao C, Liao Y, Liu W, Xing Y. Efficient Simultaneous Introduction of Premature Stop Codons in Three Tumor Suppressor Genes in PFFs via a Cytosine Base Editor. Genes (Basel) 2022; 13:genes13050835. [PMID: 35627220 PMCID: PMC9140995 DOI: 10.3390/genes13050835] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Revised: 04/29/2022] [Accepted: 05/05/2022] [Indexed: 12/04/2022] Open
Abstract
Base editing is an efficient and precise gene-editing technique, by which a single base can be changed without introducing double-strand breaks, and it is currently widely used in studies of various species. In this study, we used hA3A-BE3-Y130F to simultaneously introduce premature stop codons (TAG, TGA, and TAA) into three tumor suppressor genes, TP53, PTEN, and APC, in large white porcine fetal fibroblasts (PFFs). Among the isolated 290 single-cell colonies, 232 (80%) had premature stop codons in all the three genes. C−to−T conversion was found in 98.6%, 92.8%, and 87.2% of these cell colonies for TP53, PTEN, and APC, respectively. High frequencies of bystander C−to−T edits were observed within the editing window (positions 3−8), and there were nine (3.01%) clones with the designed simultaneous three-gene C−to−T conversion without bystander conversion. C−to−T conversion outside the editing window was found in 9.0%, 14.1%, and 26.2% of the 290 cell colonies for TP53, PTEN, and APC, respectively. Low-frequency C−to−G or C−to−A transversion occurred in APC. The mRNA levels of the three genes showed significant declines in triple-gene-mutant (Tri-Mut) cells as expected. No PTEN and a significantly lower (p < 0.05) APC protein expression were detected in Tri-Mut cells. Interestingly, the premature stop codon introduced into the TP53 gene did not eliminate the expression of its full-length protein in the Tri-Mut cells, suggesting that stop codon read-through occurred. Tri-Mut cells showed a significantly higher (p < 0.05) proliferation rate than WT cells. Furthermore, we identified 1418 differentially expressed genes (DEGs) between the Tri-Mut and WT groups, which were mainly involved in functions such as tumor progression, cell cycle, and DNA repair. This study indicates that hA3A-BE3-Y130F can be a powerful tool to create diverse knockout cell models without double-strand breaks (DSBs), with further possibilities to produce porcine models with various purposes.
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An Q, Chen S, Zhang L, Zhang Z, Cheng Y, Wu H, Liu A, Chen Z, Li B, Chen J, Zheng Y, Man C, Wang F, Chen Q, Du L. The mRNA and miRNA profiles of goat bronchial epithelial cells stimulated by Pasteurella multocida strains of serotype A and D. PeerJ 2022; 10:e13047. [PMID: 35321408 PMCID: PMC8935994 DOI: 10.7717/peerj.13047] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Accepted: 02/11/2022] [Indexed: 01/11/2023] Open
Abstract
Pasteurella multocida (P. multocida) is a zoonotic bacterium that predominantly colonizes the respiratory tract and lungs of a variety of farmed and wild animals, and causes severe respiratory disease. To investigate the characteristics of the host immune response induced by P. multocida strains of serotype A and D, high-throughput mRNA-Seq and miRNA-Seq were performed to analyze the changes in goat bronchial epithelial cells stimulated by these two serotypes of P. multocida for 4 h. Quantitative RT-PCR was used to validate the randomly selected genes and miRNAs. The results revealed 204 and 117 differentially expressed mRNAs (|log2(Fold-change)| ≥ 1, p-value < 0.05) in the P. multocida serotype A and D stimulated groups, respectively. Meanwhile, the number of differentially expressed miRNAs (|log2(Fold-change)| > 0.1, p-value < 0.05) were 269 and 290, respectively. GO and KEGG enrichment analyses revealed 13 GO terms (p-value < 0.05) and four KEGG pathways (p-value < 0.05) associated with immunity. In the serotype A-stimulated group, the immune-related pathways were the GABAergic synapse and Toll-like receptor signaling pathways, while in the serotype D-stimulated group, the immune-related pathways were the phagosome and B cell receptor signaling pathways. Based on the predicted results of TargetScan and miRanda, the differentially expressed mRNA-miRNA network of immune-related GO terms and KEGG pathways was constructed. According to the cell morphological changes and the significant immune-related KEGG pathways, it was speculated that the P. multocida serotype D strain-stimulated goat bronchial epithelial cells may induce a cellular immune response earlier than serotype A-stimulated cells. Our study provides valuable insight into the host immune response mechanism induced by P. multocida strains of serotype A and D.
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Affiliation(s)
- Qi An
- Hainan Key Lab of Tropical Animal Reproduction, Breeding and Epidemic Disease Research, Animal Genetic Engineering Key Lab of Haikou, College of Animal Science and Technology, Hainan University, Haikou, Hainan, China
| | - Si Chen
- Hainan Key Lab of Tropical Animal Reproduction, Breeding and Epidemic Disease Research, Animal Genetic Engineering Key Lab of Haikou, College of Animal Science and Technology, Hainan University, Haikou, Hainan, China
| | - Luyin Zhang
- Hainan Key Lab of Tropical Animal Reproduction, Breeding and Epidemic Disease Research, Animal Genetic Engineering Key Lab of Haikou, College of Animal Science and Technology, Hainan University, Haikou, Hainan, China
| | - Zhenxing Zhang
- Hainan Key Lab of Tropical Animal Reproduction, Breeding and Epidemic Disease Research, Animal Genetic Engineering Key Lab of Haikou, College of Animal Science and Technology, Hainan University, Haikou, Hainan, China
| | - Yiwen Cheng
- Hainan Key Lab of Tropical Animal Reproduction, Breeding and Epidemic Disease Research, Animal Genetic Engineering Key Lab of Haikou, College of Animal Science and Technology, Hainan University, Haikou, Hainan, China
| | - Haotian Wu
- Hainan Key Lab of Tropical Animal Reproduction, Breeding and Epidemic Disease Research, Animal Genetic Engineering Key Lab of Haikou, College of Animal Science and Technology, Hainan University, Haikou, Hainan, China
| | - Ang Liu
- Hainan Key Lab of Tropical Animal Reproduction, Breeding and Epidemic Disease Research, Animal Genetic Engineering Key Lab of Haikou, College of Animal Science and Technology, Hainan University, Haikou, Hainan, China
| | - Zhen Chen
- Hainan Key Lab of Tropical Animal Reproduction, Breeding and Epidemic Disease Research, Animal Genetic Engineering Key Lab of Haikou, College of Animal Science and Technology, Hainan University, Haikou, Hainan, China
| | - Bin Li
- Hainan Key Lab of Tropical Animal Reproduction, Breeding and Epidemic Disease Research, Animal Genetic Engineering Key Lab of Haikou, College of Animal Science and Technology, Hainan University, Haikou, Hainan, China
| | - Jie Chen
- Hainan Key Lab of Tropical Animal Reproduction, Breeding and Epidemic Disease Research, Animal Genetic Engineering Key Lab of Haikou, College of Animal Science and Technology, Hainan University, Haikou, Hainan, China
| | - Yiying Zheng
- Hainan Key Lab of Tropical Animal Reproduction, Breeding and Epidemic Disease Research, Animal Genetic Engineering Key Lab of Haikou, College of Animal Science and Technology, Hainan University, Haikou, Hainan, China
| | - Churiga Man
- Hainan Key Lab of Tropical Animal Reproduction, Breeding and Epidemic Disease Research, Animal Genetic Engineering Key Lab of Haikou, College of Animal Science and Technology, Hainan University, Haikou, Hainan, China
| | - Fengyang Wang
- Hainan Key Lab of Tropical Animal Reproduction, Breeding and Epidemic Disease Research, Animal Genetic Engineering Key Lab of Haikou, College of Animal Science and Technology, Hainan University, Haikou, Hainan, China
| | - Qiaoling Chen
- Hainan Key Lab of Tropical Animal Reproduction, Breeding and Epidemic Disease Research, Animal Genetic Engineering Key Lab of Haikou, College of Animal Science and Technology, Hainan University, Haikou, Hainan, China
| | - Li Du
- Hainan Key Lab of Tropical Animal Reproduction, Breeding and Epidemic Disease Research, Animal Genetic Engineering Key Lab of Haikou, College of Animal Science and Technology, Hainan University, Haikou, Hainan, China
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Liu C, Yu H, Li X, Gong Y, Wu P, Feng QS. Anti-hepatocellular carcinoma efficacy of Fuzheng Xiaozheng prescription and its interventional mechanism studies. J Ethnopharmacol 2022; 285:114913. [PMID: 34910953 DOI: 10.1016/j.jep.2021.114913] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Revised: 12/03/2021] [Accepted: 12/09/2021] [Indexed: 06/14/2023]
Abstract
ETHNOPHARMACOLOGICAL RELEVANCE Fuzheng Xiaozheng prescription (FZXZP), a traditional Chinese medicine, which was derived from the famous decoction, Sanjiasan, in the book of "Wenyilun" in Ming dynasty. Due to its function of invigorating the circulation of blood in Chinese medicine, it was usually used for treating the liver cirrhosis, hepatocellular carcinoma (HCC), etc. Clinical application found that FZXZP exhibited satisfactory therapeutic effects in HCC treatments. However, we still know little about the underlying mechanisms. AIM OF STUDY In this study, we aim to gain a deeper insight into the inhibiting effects of FZXZP on HCC rats and preliminarily elucidate the underlying intervention effects. MATERIALS AND METHODS Two doses of FZXZP were adopted to evaluate the therapeutic effects on rat HCC, and then the intervention effects were evaluated from different aspects. High performance liquid chromatography (HPLC) was used for the active compounds prediction in FZXZP. Finally, the mRNA-Seq was conducted to reveal the intervention mechanisms and the mechanisms were further validated by quantitative Real-time PCR (qRT-PCR) and lipid contents analyses. RESULTS The results showed that FZXZP significantly alleviated the serum biochemical indicators and improved the pathological characteristics of HCC rats. Mechanistically, FZXZP could regulate some lipid related metabolisms, including arachidonic acid, linoleic acid and retinol, as well as improving the steroid hormone biosynthesis, to improve the inflammatory statuses and restoring ability of HCC livers, and these were further confirmed by our following analyses on serum lipid contents and cytokine expressions. In addition, FZXZP could also negatively regulate four extracellular growth factors which could result in the blocking of two cancer-related signaling pathways, Ras/MAPK and Ras/PI3K-Akt. CONCLUSION Our results suggested that FZXZP demonstrated significant inhibiting effects on rat HCC progresses, and these may be realized by improving the inflammatory statuses and blocking the Ras/MAPK and Ras/PI3K-Akt signaling pathways.
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MESH Headings
- Animals
- Rats
- Antineoplastic Agents, Phytogenic/chemistry
- Antineoplastic Agents, Phytogenic/pharmacology
- Carcinoma, Hepatocellular/chemically induced
- Carcinoma, Hepatocellular/drug therapy
- Diethylnitrosamine/toxicity
- Dose-Response Relationship, Drug
- Drugs, Chinese Herbal/chemistry
- Drugs, Chinese Herbal/pharmacology
- Gene Expression Regulation, Neoplastic/drug effects
- Liver/drug effects
- Liver/pathology
- Liver Neoplasms/chemically induced
- Liver Neoplasms/drug therapy
- Random Allocation
- Rats, Sprague-Dawley
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
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Affiliation(s)
- Chao Liu
- College of Basic Medical Sciences, Chengdu University of Traditional Chinese Medicine, Chengdu, 610075, China
| | - Han Yu
- College of Basic Medical Sciences, Chengdu University of Traditional Chinese Medicine, Chengdu, 610075, China
| | - Xia Li
- College of Basic Medical Sciences, Chengdu University of Traditional Chinese Medicine, Chengdu, 610075, China
| | - Yanju Gong
- College of Basic Medical Sciences, Chengdu University of Traditional Chinese Medicine, Chengdu, 610075, China
| | - Peijie Wu
- College of Basic Medical Sciences, Chengdu University of Traditional Chinese Medicine, Chengdu, 610075, China
| | - Quan-Sheng Feng
- College of Basic Medical Sciences, Chengdu University of Traditional Chinese Medicine, Chengdu, 610075, China.
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10
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Chen K, Iwasaki N, Qiu X, Xu H, Takai Y, Tashiro K, Shimasaki Y, Oshima Y. Obesogenic and developmental effects of TBT on the gene expression of juvenile Japanese medaka (Oryzias latipes). Aquat Toxicol 2021; 237:105907. [PMID: 34274867 DOI: 10.1016/j.aquatox.2021.105907] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Revised: 06/17/2021] [Accepted: 06/28/2021] [Indexed: 06/13/2023]
Abstract
The widely used antifoulant tributyltin chloride (TBT) is highly toxic to aquatic organisms. In the present study, four-week-old Japanese medaka (Oryzias latipes) juveniles were orally exposed to TBT at 1 and 10 ng/g bw/d for 1, 2, and 4 weeks, respectively. Half of the tested medaka juveniles showed bone morphology alterations in both 1 and 10 ng/g bw/d TBT 4-week exposure groups. Nile Red (NR) staining showed that the juveniles exposed to 1 ng/g bw/d TBT for 2 and 4 weeks had significantly enlarged adipocyte areas. The mRNA-Seq analysis indicated that 1 ng/g bw/d TBT exposure for 2 weeks affected bone morphology through developmental processes. The GO and KEGG analyses suggested that the adipogenic effect of TBT observed in this study may be induced by metabolic processes, oxidative phosphorylation, and fatty acid degradation and metabolism pathways. Therefore, both morphological observation and mRNA-Seq analysis showed obesogenic effects and developmental toxicity of TBT to juvenile Japanese medaka.
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Affiliation(s)
- Kun Chen
- Institute of Environmental Health and Ecological Security, School of Environment and Safety Engineering, Jiangsu University, Zhenjiang 212013, China; Laboratory of Marine Environmental Science, Department of Bioscience and Biotechnology, Faculty of Agriculture, Kyushu University, Fukuoka 819-0395, Japan
| | - Naoto Iwasaki
- Laboratory of Marine Environmental Science, Department of Bioscience and Biotechnology, Faculty of Agriculture, Kyushu University, Fukuoka 819-0395, Japan
| | - Xuchun Qiu
- Institute of Environmental Health and Ecological Security, School of Environment and Safety Engineering, Jiangsu University, Zhenjiang 212013, China; Laboratory of Marine Environmental Science, Department of Bioscience and Biotechnology, Faculty of Agriculture, Kyushu University, Fukuoka 819-0395, Japan.
| | - Hai Xu
- Institute of Environmental Health and Ecological Security, School of Environment and Safety Engineering, Jiangsu University, Zhenjiang 212013, China
| | - Yuki Takai
- Laboratory of Marine Environmental Science, Department of Bioscience and Biotechnology, Faculty of Agriculture, Kyushu University, Fukuoka 819-0395, Japan
| | - Kosuke Tashiro
- Laboratory of Molecular Gene Technology, Faculty of Agriculture, Kyushu University, Fukuoka 819-0395, Japan
| | - Yohei Shimasaki
- Laboratory of Marine Environmental Science, Department of Bioscience and Biotechnology, Faculty of Agriculture, Kyushu University, Fukuoka 819-0395, Japan
| | - Yuji Oshima
- Laboratory of Marine Environmental Science, Department of Bioscience and Biotechnology, Faculty of Agriculture, Kyushu University, Fukuoka 819-0395, Japan; Institute of Nature and Environmental Technology, Kanazawa University, Kanazawa 920-1192, Japan.
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11
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Hong M, Chen D, Hong Z, Tang K, Yao Y, Chen L, Ye T, Qian J, Du Y, Sun R. Ex vivo and in vivo chemoprotective activity and potential mechanism of Martynoside against 5-fluorouracil-induced bone marrow cytotoxicity. Biomed Pharmacother 2021; 138:111501. [PMID: 33765584 DOI: 10.1016/j.biopha.2021.111501] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Revised: 03/03/2021] [Accepted: 03/09/2021] [Indexed: 12/12/2022] Open
Abstract
Martynoside (MAR) is a bioactive glycoside of Rehmannia glutinosa, a traditional Chinese herb frequently prescribed for treating chemotherapy-induced pancytopenia. Despite its clinical usage in China for thousands of years, the mechanism of MAR's hematopoietic activity and its impact on chemotherapy-induced antitumor activity are still unclear. Here, we showed that MAR protected ex vivo bone marrow cells from 5-fluorouracil (5-FU)-induced cell death and inflammation response by down-regulating the TNF signaling pathway, in which II1b was the most regulatory gene. Besides, using mouse models with melanoma and colon cancer, we further demonstrated that MAR had protective effects against 5-FU-induced myelosuppression in mice without compromising its antitumor activity. Our results showed that MAR increased the number of bone marrow nucleated cells (BMNCs) and the percentage of leukocyte and granulocytic populations in 5-FU-induced myelosuppressive mice, accompanied by an increase in numbers of circulating white blood cells and platelets. The transcriptome profile of BMNCs further showed that the mode of action of MAR might be associated with the increased survival of BMNCs and the improvement of the bone marrow microenvironment. In summary, we revealed the potential molecular mechanism of MAR to counteract 5-FU-induced bone marrow cytotoxicity both ex vivo and in vivo, and highlighted its potential clinical usage in cancer patients experiencing chemotherapy-induced multi-lineage myelosuppression.
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Affiliation(s)
- Mengying Hong
- Cancer Institute, The Second Affiliated Hospital, ZJU-UCLA Joint Center for Medical Education and Research, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310009, China
| | - Dongdong Chen
- Cancer Institute, The Second Affiliated Hospital, ZJU-UCLA Joint Center for Medical Education and Research, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310009, China
| | - Zhuping Hong
- Pharmaceutical Informatics Institute, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, Zhejiang Province, China
| | - Kejun Tang
- Cancer Institute, The Second Affiliated Hospital, ZJU-UCLA Joint Center for Medical Education and Research, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310009, China
| | - Yuanyuan Yao
- Department of Colorectal Surgery, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310003, Zhejiang Province, China
| | - Liubo Chen
- Cancer Institute, The Second Affiliated Hospital, ZJU-UCLA Joint Center for Medical Education and Research, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310009, China
| | - Tingting Ye
- Pharmaceutical Informatics Institute, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, Zhejiang Province, China
| | - Jing Qian
- Pharmaceutical Informatics Institute, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, Zhejiang Province, China
| | - Yushen Du
- Cancer Institute, The Second Affiliated Hospital, ZJU-UCLA Joint Center for Medical Education and Research, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310009, China; Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, CA 90095, USA.
| | - Ren Sun
- Cancer Institute, The Second Affiliated Hospital, ZJU-UCLA Joint Center for Medical Education and Research, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310009, China; Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, CA 90095, USA; School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China.
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12
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Cao J, Xian W, Palihati M, Zhu Y, Wang G, Xie Y, Zhou G, You L. Deficiency of intellectual disability-related gene Brpf1 reduced inhibitory neurotransmission in MGE-derived GABAergic interneurons. G3 (Bethesda) 2021; 11:6179329. [PMID: 33744924 PMCID: PMC8496217 DOI: 10.1093/g3journal/jkab090] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Accepted: 03/09/2021] [Indexed: 12/13/2022]
Abstract
Intellectual disability is closely related to impaired GABA neurotransmission. Brpf1 was specifically expressed in medial ganglionic eminence (MGE), a developmental niche of GABAergic interneurons, and patients with BRPF1 mutations showed intellectual disability. To test its role in the development and function of MGE-derived GABAergic interneurons, we performed immunofluorescence staining, whole-cell patch-clamp, MGE transplantation, and mRNA-Seq to understand its effect on neuronal differentiation, dendritic morphology, electrophysiology, migration, and gene regulation, using mouse MGE-derived GABAergic interneurons infected with AAV-shBrpf1. The results showed that Brpf1 knockdown had a decreasing trend, although not significant, on the differentiation of GABAergic interneurons into parvalbumin+ interneurons. Moreover, increased firing threshold, decreased number of evoked action potentials, and a reduced amplitude of miniature inhibitory postsynaptic currents were observed before any significant change of MAP2+ dendritic morphology and in vivo migration ability appeared. Finally, mRNA-Seq analysis revealed that genes related to neurodevelopment and synaptic transmission such as Map2k7 were dysregulated. Our results demonstrated a key role of Brpf1 in inhibitory neurotransmission and related gene expression of GABAergic interneurons.
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Affiliation(s)
- Jingli Cao
- Department of Human Anatomy & Histoembryology, School of Basic Medical Sciences, Fudan University, Shanghai 200032, China
| | - Weiwei Xian
- Department of Human Anatomy & Histoembryology, School of Basic Medical Sciences, Fudan University, Shanghai 200032, China
| | - Maierdan Palihati
- Department of Human Anatomy & Histoembryology, School of Basic Medical Sciences, Fudan University, Shanghai 200032, China
| | - Yu Zhu
- Department of Human Anatomy & Histoembryology, School of Basic Medical Sciences, Fudan University, Shanghai 200032, China
| | - Guoxiang Wang
- Institutes of Brain Sciences, Fudan University, Shanghai 200032, China
| | - Yunli Xie
- Institutes of Brain Sciences, Fudan University, Shanghai 200032, China
| | - Guomin Zhou
- Department of Human Anatomy & Histoembryology, School of Basic Medical Sciences, Fudan University, Shanghai 200032, China.,Key Laboratory of Medical Imaging Computing and Computer Assisted Intervention of Shanghai, Shanghai 200032, China
| | - Linya You
- Department of Human Anatomy & Histoembryology, School of Basic Medical Sciences, Fudan University, Shanghai 200032, China.,Key Laboratory of Medical Imaging Computing and Computer Assisted Intervention of Shanghai, Shanghai 200032, China
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13
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Chen K, Guo B, Yu C, Chen P, Chen J, Gao G, Wang X, Zhu A. Comparative Transcriptome Analysis Provides New Insights into the Molecular Regulatory Mechanism of Adventitious Root Formation in Ramie ( Boehmeria nivea L.). Plants (Basel) 2021; 10:plants10010160. [PMID: 33467608 PMCID: PMC7830346 DOI: 10.3390/plants10010160] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Revised: 12/18/2020] [Accepted: 01/05/2021] [Indexed: 11/16/2022]
Abstract
The occurrence of adventitious roots is necessary for the survival of cuttings. In this study, comparative transcriptome analysis between two ramie (Boehmeria nivea L.) varieties with different adventitious root (AR) patterns was performed by mRNA-Seq before rooting (control, CK) and 10 days water-induced adventitious rooting (treatment, T) to reveal the regulatory mechanism of rooting. Characterization of the two ramie cultivars, Zhongzhu No 2 (Z2) and Huazhu No 4 (H4), indicated that Z2 had a high adventitious rooting rate but H4 had a low rooting rate. Twelve cDNA libraries of the two varieties were constructed, and a total of 26,723 genes were expressed. In the non-water culture condition, the number of the distinctive genes in H4 was 2.7 times of that in Z2, while in the water culture condition, the number of the distinctive genes in Z2 was nearly 2 times of that in H4. A total of 4411 and 5195 differentially expressed genes (DEGs) were identified in the comparison of H4CK vs. H4T and Z2CK vs. Z2T, respectively. After the water culture, more DEGs were upregulated in Z2, but more DEGs were downregulated in H4. Gene ontology (GO) functional analysis of the DEGs indicated that the polysaccharide metabolic process, carbohydrate metabolic process, cellular carbohydrate metabolic process, cell wall macromolecule metabolic process, and photosystem GO terms were distinctively significantly enriched in H4. Simultaneously, Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis showed that photosynthesis, photosynthesis antenna proteins, and starch and sucrose metabolism pathways were distinctively significantly enriched in H4. Moreover, KEGG analysis showed that jasmonic acid (JA) could interact with ethylene to regulate the occurrence and number of AR in Z2. This study reveals the transcriptomic divergence of two ramie varieties with high and low adventitious rooting rates, and provides insights into the molecular regulatory mechanism of AR formation in ramie.
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14
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Jang JS, Berg B, Holicky E, Eckloff B, Mutawe M, Carrasquillo MM, Ertekin-Taner N, Cuninngham JM. Comparative evaluation for the globin gene depletion methods for mRNA sequencing using the whole blood-derived total RNAs. BMC Genomics 2020; 21:890. [PMID: 33308163 PMCID: PMC7733259 DOI: 10.1186/s12864-020-07304-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Accepted: 12/06/2020] [Indexed: 01/12/2023] Open
Abstract
Background There are challenges in generating mRNA-Seq data from whole-blood derived RNA as globin gene and rRNA are frequent contaminants. Given the abundance of erythrocytes in whole blood, globin genes comprise some 80% or more of the total RNA. Therefore, depletion of globin gene RNA and rRNA are critical steps required to have adequate coverage of reads mapping to the reference transcripts and thus reduce the total cost of sequencing. In this study, we directly compared the performance of probe hybridization (GLOBINClear Kit and Globin-Zero Gold rRNA Removal Kit) and RNAse-H enzymatic depletion (NEBNext® Globin & rRNA Depletion Kit and Ribo-Zero Plus rRNA Depletion Kit) methods from 1 μg of whole blood-derived RNA on mRNA-Seq profiling. All RNA samples were treated with DNaseI for additional cleanup before the depletion step and were processed for poly-A selection for library generation. Results Probe hybridization revealed a better overall performance than the RNAse-H enzymatic depletion method, detecting a higher number of genes and transcripts without 3′ region bias. After depletion, samples treated with probe hybridization showed globin genes at 0.5% (±0.6%) of the total mapped reads; the RNAse-H enzymatic depletion had 3.2% (±3.8%). Probe hybridization showed more junction reads and transcripts compared with RNAse-H enzymatic depletion and also had a higher correlation (R > 0.9) than RNAse-H enzymatic depletion (R > 0.85). Conclusion In this study, our results showed that 1 μg of high-quality RNA from whole blood could be routinely used for transcriptional profiling analysis studies with globin gene and rRNA depletion pre-processing. We also demonstrated that the probe hybridization depletion method is better suited to mRNA sequencing analysis with minimal effect on RNA quality during depletion procedures.
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Affiliation(s)
- Jin Sung Jang
- Medical Genome Facility, Center for Individualized Medicine, Mayo Clinic, Rochester, MN, USA. .,Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA.
| | - Brianna Berg
- Medical Genome Facility, Center for Individualized Medicine, Mayo Clinic, Rochester, MN, USA
| | - Eileen Holicky
- Medical Genome Facility, Center for Individualized Medicine, Mayo Clinic, Rochester, MN, USA
| | - Bruce Eckloff
- Medical Genome Facility, Center for Individualized Medicine, Mayo Clinic, Rochester, MN, USA
| | - Mark Mutawe
- Medical Genome Facility, Center for Individualized Medicine, Mayo Clinic, Rochester, MN, USA
| | | | - Nilüfer Ertekin-Taner
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA.,Department of Neurology, Mayo Clinic, Jacksonville, FL, USA
| | - Julie M Cuninngham
- Medical Genome Facility, Center for Individualized Medicine, Mayo Clinic, Rochester, MN, USA. .,Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA.
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15
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Takai Y, Mizoguchi N, Kinoshita M, Qiu X, Shimasaki Y, Oshima Y. Establishment of a Japanese medaka (Oryzias latipes) transgenic line expressing Takifugu rubripes pufferfish saxitoxin and tetrodotoxin binding protein 1, and evaluation of tributyltin toxicity via in ovo nanoinjection. Comp Biochem Physiol C Toxicol Pharmacol 2020; 234:108785. [PMID: 32376496 DOI: 10.1016/j.cbpc.2020.108785] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/19/2020] [Revised: 04/25/2020] [Accepted: 04/28/2020] [Indexed: 12/27/2022]
Abstract
Pufferfish saxitoxin and tetrodotoxin binding proteins (PSTBPs) play an important role in the toxification of certain species of pufferfish. Recombinant Takifugu rubripes PSTBP1 (rTrub.PSTBP1) is reported to bind to tributyltin, and so it has been suggested that rTrub.PSTBP1 may reduce the toxicity of tributyltin. However, the role of PSTBP1 in vivo remains to be elucidated. Here, we established a transgenic medaka line showing whole-body Renilla reniformis green fluorescent protein and Trub.PSTBP1 expression, as confirmed by real-time polymerase chain reaction and mRNA-Seq analysis. mRNA-Seq analysis also showed that cytochrome P450 superfamily genes and the gene encoding ATP-binding cassette sub-family G member 2 were highly expressed in the transgenic medaka. Using embryos of the transgenic medaka line, we conducted an in ovo nanoinjection test to examine the effect of Trub.PSTBP1 in vivo, and obtained data suggesting that Trub.PSTBP1 expression may have reduced the toxicity of tributyltin in our transgenic medaka line. Our findings will be useful for future functional analyses of Trub.PSTBP1.
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Affiliation(s)
- Yuki Takai
- Laboratory of Marine Environmental Science, Department of Bioscience and Biotechnology, Faculty of Agriculture, Kyushu University, Fukuoka 819-0395, Japan
| | - Naohiro Mizoguchi
- Laboratory of Marine Environmental Science, Department of Bioscience and Biotechnology, Faculty of Agriculture, Kyushu University, Fukuoka 819-0395, Japan
| | - Masato Kinoshita
- Department of Applied Biosciences, Graduate School of Agriculture, Kyoto University, Kyoto 606-8502, Japan
| | - Xuchun Qiu
- Institute of Environmental Health and Ecological Security, School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang, Jiangsu 212013, PR China
| | - Yohei Shimasaki
- Laboratory of Marine Environmental Science, Department of Bioscience and Biotechnology, Faculty of Agriculture, Kyushu University, Fukuoka 819-0395, Japan
| | - Yuji Oshima
- Laboratory of Marine Environmental Science, Department of Bioscience and Biotechnology, Faculty of Agriculture, Kyushu University, Fukuoka 819-0395, Japan; Institute of Nature and Environmental Technology, Kanazawa University, Kanazawa 920-1192, Japan.
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16
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Chi Y, Youn DY, Xiaoli AM, Liu L, Pessin JB, Yang F, Pessin JE. Regulation of gene expression during the fasting-feeding cycle of the liver displays mouse strain specificity. J Biol Chem 2020; 295:4809-4821. [PMID: 32075912 DOI: 10.1074/jbc.ra119.012349] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Revised: 02/12/2020] [Indexed: 11/06/2022] Open
Abstract
The liver maintains metabolic homeostasis by integrating the regulation of nutrient status with both hormonal and neural signals. Many studies on hepatic signaling in response to nutrients have been conducted in mice. However, no in-depth study is currently available that has investigated genome-wide changes in gene expression during the normal physiological fasting-feeding cycle in nutrient-sensitive and -insensitive mice. Using two strains of mice, C57BL/6J and BALB/cJ, and deploying deep RNA-Seq complemented with quantitative RT-PCR, we found that feeding causes substantial and transient changes in gene expression in the livers of both mouse strains. The majority of significantly changed transcripts fell within the areas of biological regulation and cellular and metabolic processes. Among the metabolisms of three major types of macronutrients (i.e. carbohydrates, proteins, and lipids), feeding affected lipid metabolism the most. We also noted that the C57BL/6J and BALB/cJ mice significantly differed in gene expression and in changes in gene expression in response to feeding. In both fasted and fed states, both mouse strains shared common expression patterns for about 10,200 genes, and an additional 400-600 genes were differentially regulated in one strain but not the other. Among the shared genes, more lipogenic genes were induced upon feeding in BABL/cJ than in C57BL/6J mice. In contrast, in the population of differentially enriched genes, C57BL/6J mice expressed more genes involved in lipid metabolism than BALB/cJ mice. In summary, these results reveal that the two mouse strains used here exhibit several differences in feeding-induced hepatic responses in gene expression, especially in lipogenic genes.
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Affiliation(s)
- Yuling Chi
- Department of Medicine, Albert Einstein College of Medicine, Bronx, New York 10461 .,Fleischer Institute of Diabetes and Metabolism, Albert Einstein College of Medicine, Bronx, New York 10461
| | - Dou Yeon Youn
- Department of Medicine, Albert Einstein College of Medicine, Bronx, New York 10461.,Fleischer Institute of Diabetes and Metabolism, Albert Einstein College of Medicine, Bronx, New York 10461
| | - Alus M Xiaoli
- Department of Medicine, Albert Einstein College of Medicine, Bronx, New York 10461.,Fleischer Institute of Diabetes and Metabolism, Albert Einstein College of Medicine, Bronx, New York 10461.,Department of Developmental and Molecular Biology, Albert Einstein College of Medicine, Bronx, New York 10461
| | - Li Liu
- Department of Medicine, Albert Einstein College of Medicine, Bronx, New York 10461.,Fleischer Institute of Diabetes and Metabolism, Albert Einstein College of Medicine, Bronx, New York 10461
| | - Jacob B Pessin
- Department of Medicine, Albert Einstein College of Medicine, Bronx, New York 10461.,Fleischer Institute of Diabetes and Metabolism, Albert Einstein College of Medicine, Bronx, New York 10461
| | - Fajun Yang
- Department of Medicine, Albert Einstein College of Medicine, Bronx, New York 10461.,Fleischer Institute of Diabetes and Metabolism, Albert Einstein College of Medicine, Bronx, New York 10461.,Department of Developmental and Molecular Biology, Albert Einstein College of Medicine, Bronx, New York 10461
| | - Jeffrey E Pessin
- Department of Medicine, Albert Einstein College of Medicine, Bronx, New York 10461 .,Fleischer Institute of Diabetes and Metabolism, Albert Einstein College of Medicine, Bronx, New York 10461.,Department of Molecular Pharmacology, Albert Einstein College of Medicine, Bronx, New York 10461
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17
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Bell OH, Copland DA, Ward A, Nicholson LB, Lange CAK, Chu CJ, Dick AD. Single Eye mRNA-Seq Reveals Normalisation of the Retinal Microglial Transcriptome Following Acute Inflammation. Front Immunol 2020; 10:3033. [PMID: 31993055 PMCID: PMC6964706 DOI: 10.3389/fimmu.2019.03033] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Accepted: 12/10/2019] [Indexed: 01/07/2023] Open
Abstract
Background: Whether retinal microglia can maintain or restore immune homeostasis during and after inflammation is unclear. We performed single-eye mRNA-sequencing on microglia at different timepoints following a single inflammatory stimulus to characterise their transcriptome during and after resolution of endotoxin-induced uveitis (EIU). Experimental Approach: Cx3cr1 CreER :R26-tdTomato (C57BL/6) male heterozygotes were administered tamoxifen via different regimes at 4-5 weeks of age. Four weeks post-tamoxifen, mice were injected intravitreally with 10 ng lipopolysaccharide (endotoxin induced uveitis, EIU). Six-hundred retinal microglia were obtained by FACS from individual naïve retinas and at 4 h, 18 h, and 2 weeks following EIU induction. Samples were sequenced to a depth of up to 16.7 million reads using the SMART-Seq v4 Ultra Low Input RNA kit. The data was analysed using Partek software and Ingenuity Pathway Analysis. Genes were considered differentially-expressed (DEG) if the FDR step-up p-value was ≤0.05 and the fold-change was ≥±2. Results: Flow cytometric analysis indicates that the Cx3cr1 CreER :R26-tdTomato strain is both sensitive (>95% tagging) and specific (>95% specificity) for microglia when tamoxifen is administered topically to the eye for 3 days. During "early" activation, 613 DEGs were identified. In contrast, 537 DEGs were observed during peak cellular infiltrate and none at 2 weeks, compared to baseline controls (1,069 total unique DEGs). Key marker changes were validated by qPCR, flow cytometry, and fluorescence microscopy. C5AR1 was identified and validated as a robust marker of differentiating microglial subsets during an LPS response. Conclusion: Using EIU to provide a single defined inflammatory stimulus, mRNA-Seq identified acute transcriptional changes in retinal microglia which returned to their original transcriptome after 2 weeks. Yolk-sac derived microglia are capable of restoring their homeostatic state after acute inflammation.
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Affiliation(s)
- Oliver H Bell
- Academic Unit of Ophthalmology, Translational Health Sciences, University of Bristol, Bristol, United Kingdom
| | - David A Copland
- Academic Unit of Ophthalmology, Translational Health Sciences, University of Bristol, Bristol, United Kingdom
| | - Amy Ward
- Academic Unit of Ophthalmology, Translational Health Sciences, University of Bristol, Bristol, United Kingdom
| | - Lindsay B Nicholson
- Academic Unit of Ophthalmology, Translational Health Sciences, University of Bristol, Bristol, United Kingdom
| | - Clemens A K Lange
- Eye Clinic, Medical Centre, University of Freiburg, Freiburg, Germany.,Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Colin J Chu
- Academic Unit of Ophthalmology, Translational Health Sciences, University of Bristol, Bristol, United Kingdom
| | - Andrew D Dick
- Academic Unit of Ophthalmology, Translational Health Sciences, University of Bristol, Bristol, United Kingdom.,Institute of Ophthalmology and the National Institute for Health Research Biomedical Research Centre, Moorfields Eye Hospital and University College London, London, United Kingdom
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18
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Wang X, Zhang D, Ma S, Li P, Zhou W, Zhang C, Jia W. Predicting the likelihood of early recurrence based on mRNA sequencing of pituitary adenomas. Gland Surg 2019; 8:648-656. [PMID: 32042672 DOI: 10.21037/gs.2019.11.02] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Background There is no comprehensive and objective method existing for predicting early recurrence of pituitary adenomas (PAs). The most advanced gene sequencing technology can be applied to build a prognostic model that can effectively predict early recurrence of PAs. Methods In this study, using mRNA-Seq data, the corresponding postoperative early recurrence status, and other clinical features of 107 PA samples were obtained and randomly divided into the training and validation groups. Cox regression and receiver operating characteristic (ROC) analysis accompanied by the risk score method was used to build a seven-gene prediction model. Results Area under curve values was 0.857 in the training group, 0.936 in the validation group, and 0.848 in all patients. Patients with low-risk scores had a significantly lower probability of early postoperative recurrence compared to those acquiring high-risk scores in the training group, validation group, and all patient (P<0.0001) groups. In addition, 6 out of these 7 significant genes were highly correlated to the early recurrence of PAs. Conclusions This prediction model derived from mRNA-Seq data may help in identifying the early recurrence of PAs, consequently aiding in the classification of patients with PAs and the administration of the appropriate therapeutic and follow-up strategy for these patients.
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Affiliation(s)
- Xi Wang
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing 100070, China
| | - Dainan Zhang
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing 100070, China.,Beijing Neurosurgical Institute, Capital Medical University, Beijing 100070, China
| | - Shunchang Ma
- Beijing Neurosurgical Institute, Capital Medical University, Beijing 100070, China
| | - Peiliang Li
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing 100070, China.,Department of Neurosurgery, Ditan Hospital, Capital Medical University, Beijing 100070, China
| | - Wenjianlong Zhou
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing 100070, China
| | - Chuanbao Zhang
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing 100070, China.,Beijing Neurosurgical Institute, Capital Medical University, Beijing 100070, China
| | - Wang Jia
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing 100070, China.,Beijing Neurosurgical Institute, Capital Medical University, Beijing 100070, China
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Ke X, Lin J, Li P, Wu Z, Xu R, Ci Z, Yang M, Han L, Zhang D. Transcriptional profiling of genes in tongue epithelial tissue from immature and adult rats by the RNA-Seq technique. J Cell Physiol 2019; 235:3069-3078. [PMID: 31549403 DOI: 10.1002/jcp.29211] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2019] [Accepted: 09/03/2019] [Indexed: 12/29/2022]
Abstract
Children are more sensitive than adults to bitterness and thus dislike bitter tastes more than adults do. However, why children are more sensitive to bitterness has never been revealed. To elucidate the effects of age on taste perception, a double-bottle preference test was first performed with immature and adult rats. Then, RNA-Seq analysis was performed on tongues obtained from rats of the same ages as those in the double-bottle test. The immature rats exhibited a lower consumption rate of bitter solution than the adult rats. Bioinformatics analysis yielded 1,347 differentially expressed genes (DEGs) between male adult rats (MARs, 80 days old) and male immature rats (MIRs, 20 days old) and 380 DEGs between female adult rats (FARs, 80 days old) and female immature rats (FIRs, 20 days old). These DEGs were mainly associated with growth, development, differentiation, and extracellular processes, among other mechanisms. According to Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis, the DEGs were enriched for bitter taste transduction. Specifically, the Gnb3 and TRPM5 genes were downregulated in FARs compared with FIRs and in MARs compared with MIRs, and the protein expression of TRPM5 was significantly downregulated in MARs compared with MIRs. The data presented herein suggest that transcriptional regulation of taste-associated signal transduction occurs differently in tongue epithelial tissue of rats at different ages, although additional analyses are needed to confirm this conclusion.
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Affiliation(s)
- Xiumei Ke
- State Key Laboratory Breeding Base of Systematic Research, Development and Utilization of Chinese Medicine Resources, School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, China.,School of Basic Medical Sciences, Jiujiang University, Jiujiang, China
| | - Junzhi Lin
- Central Laboratory, The Teaching Hospital of Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Pan Li
- State Key Laboratory Breeding Base of Systematic Research, Development and Utilization of Chinese Medicine Resources, School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Zhenfeng Wu
- School of pharmacy, Jiangxi University of Traditional Chinese Medicine, Nanchang, China
| | - Runchun Xu
- State Key Laboratory Breeding Base of Systematic Research, Development and Utilization of Chinese Medicine Resources, School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Zhimin Ci
- State Key Laboratory Breeding Base of Systematic Research, Development and Utilization of Chinese Medicine Resources, School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Ming Yang
- School of pharmacy, Jiangxi University of Traditional Chinese Medicine, Nanchang, China
| | - Li Han
- State Key Laboratory Breeding Base of Systematic Research, Development and Utilization of Chinese Medicine Resources, School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Dingkun Zhang
- State Key Laboratory Breeding Base of Systematic Research, Development and Utilization of Chinese Medicine Resources, School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, China
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20
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Kazakiewicz D, Claesen J, Górczak K, Plewczynski D, Burzykowski T. A Multivariate Negative-Binomial Model with Random Effects for Differential Gene-Expression Analysis of Correlated mRNA Sequencing Data. J Comput Biol 2019; 26:1339-1348. [PMID: 31314581 DOI: 10.1089/cmb.2019.0168] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Experimental designs such as matched-pair or longitudinal studies yield mRNA sequencing (mRNA-Seq) counts that are correlated across samples. Most of the approaches for the analysis of correlated mRNA-Seq data are restricted to a specific design and/or balanced data only (with the same number of samples in each group). We propose a model that is applicable to the analysis of correlated mRNA-Seq data of different types: paired, clustered, longitudinal, or others. Any combination of explanatory variables, as well as unbalanced data, can be processed within the proposed modeling framework. The model assumes that exon counts of a particular gene of an individual sample jointly follow a multivariate negative-binomial distribution. Additional correlation between exon counts obtained for, for example, individual samples within the same pair or cluster, is taken into account by including into the model a cluster-level normally distributed random effect. An interesting feature of the model is that it provides explicit expression for marginal correlation between exon counts at different levels. The performance of the model is evaluated by using a simulation study and an analysis of two real-life data sets: a paired mRNA-Seq experiment for 24 patients with clear-cell renal-cell carcinoma and a longitudinal mRNA-Seq experiment for 29 patients with Lyme disease.
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Affiliation(s)
- Denis Kazakiewicz
- Interuniversity Institute for Biostatistics and statistical Bioinformatics, Hasselt University, Diepenbeek, Belgium.,Center for Innovative Research, Medical University of Białystok, Białystok, Poland
| | - Jürgen Claesen
- Interuniversity Institute for Biostatistics and statistical Bioinformatics, Hasselt University, Diepenbeek, Belgium
| | - Katarzyna Górczak
- Interuniversity Institute for Biostatistics and statistical Bioinformatics, Hasselt University, Diepenbeek, Belgium.,Department of Mathematical and Statistical Methods, Poznań University of Life Sciences, Poznań, Poland
| | - Dariusz Plewczynski
- Center for Innovative Research, Medical University of Białystok, Białystok, Poland.,Centre of New Technologies, University of Warsaw, Warsaw, Poland.,Faculty of Mathematics and Information Science, Warsaw University of Technology, Warsaw, Poland
| | - Tomasz Burzykowski
- Interuniversity Institute for Biostatistics and statistical Bioinformatics, Hasselt University, Diepenbeek, Belgium.,Center for Innovative Research, Medical University of Białystok, Białystok, Poland
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21
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Davey PA, Rodrigues M, Clarke JL, Aldred N. Transcriptional characterisation of the Exaiptasia pallida pedal disc. BMC Genomics 2019; 20:581. [PMID: 31299887 DOI: 10.1186/s12864-019-5917-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2019] [Accepted: 06/20/2019] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND Biological adhesion (bioadhesion), enables organisms to attach to surfaces as well as to a range of other targets. Bioadhesion evolved numerous times independently and is ubiquitous throughout the kingdoms of life. To date, investigations have focussed on various taxa of animals, plants and bacteria, but the fundamental processes underlying bioadhesion and the degree of conservation in different biological systems remain poorly understood. This study had two aims: 1) To characterise tissue-specific gene regulation in the pedal disc of the model cnidarian Exaiptasia pallida, and 2) to elucidate putative genes involved in pedal disc adhesion. RESULTS Five hundred and forty-seven genes were differentially expressed in the pedal disc compared to the rest of the animal. Four hundred and twenty-seven genes were significantly upregulated and 120 genes were significantly downregulated. Forty-one condensed gene ontology terms and 19 protein superfamily classifications were enriched in the pedal disc. Eight condensed gene ontology terms and 11 protein superfamily classifications were depleted. Enriched superfamilies were consistent with classifications identified previously as important for the bioadhesion of unrelated marine invertebrates. A host of genes involved in regulation of extracellular matrix generation and degradation were identified, as well as others related to development and immunity. Ab initio prediction identified 173 upregulated genes that putatively code for extracellularly secreted proteins. CONCLUSION The analytical workflow facilitated identification of genes putatively involved in adhesion, immunity, defence and development of the E. pallida pedal disc. When defence, immunity and development-related genes were identified, those remaining corresponded most closely to formation of the extracellular matrix (ECM), implicating ECM in the adhesion of anemones to surfaces. This study therefore provides a valuable high-throughput resource for the bioadhesion community and lays a foundation for further targeted research to elucidate bioadhesion in the Cnidaria.
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Abstract
The recent technological developments in the field of single-cell RNA-Seq enable us to assay the transcriptome of up to a million single cells in parallel. However, the analyses of such big datasets present a major challenge. During the last decade, a wide variety of strategies have been proposed covering different steps of the analysis. Here, we introduce a selection of computational tools to provide an overview of a generic analysis pipeline.The first step of every scRNA-Seq experiment is proper study design, which does not require sophisticated experimental or informatics skills but is nonetheless presumably the most important step. The quality of the resulting data strictly depends on the proper planning of the experiment, including the selection of the most suitable technology for the biological question of interest as well as an elaborated study design to minimize the influence of confounding factors. Once the experiment has been conducted, the raw sequencing data needs to be processed to extract the gene expression information for each cell. This task comprises quality assessment of the sequenced reads, alignment against a reference genome, demultiplexing of the cell barcodes, and quantification of the reads/transcripts per gene. As any other transcriptomics technology, single-cell mRNA-Seq requires data normalization to assure sample-to-sample, here cell-to-cell, comparability and the consideration of confounding factors.Once gene expression values have been extracted from the reads and normalized, the researcher has the agony of choosing between a plethora of analysis approaches to investigate diverse aspects of the single-cell transcriptomes, such as dimensionality reduction and clustering to explore cellular heterogeneity or trajectory analysis to model differentiation processes.In this chapter, we present a wrap-up of the abovementioned steps to conduct single-cell RNA-Seq analyses and present a selection of existing tools.
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23
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Xiao Z, Cheng G, Jiao Y, Pan C, Li R, Jia D, Zhu J, Wu C, Zheng M, Jia J. Holo-Seq: single-cell sequencing of holo-transcriptome. Genome Biol 2018; 19:163. [PMID: 30333049 PMCID: PMC6193298 DOI: 10.1186/s13059-018-1553-7] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Accepted: 09/28/2018] [Indexed: 02/02/2023] Open
Abstract
Current single-cell RNA-seq approaches are hindered by preamplification bias, loss of strand of origin information, and the inability to observe small-RNA and mRNA dual transcriptomes. Here, we introduce a single-cell holo-transcriptome sequencing (Holo-Seq) that overcomes all three hurdles. Holo-Seq has the same quantitative accuracy and uniform coverage with a complete strand of origin information as bulk RNA-seq. Most importantly, Holo-Seq can simultaneously observe small RNAs and mRNAs in a single cell. Furthermore, we acquire small RNA and mRNA dual transcriptomes of 32 human hepatocellular carcinoma single cells, which display the genome-wide super-enhancer activity and hepatic neoplasm kinetics of these cells.
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Affiliation(s)
- Zhengyun Xiao
- Life Sciences Institute and Innovation Center for Cell Signaling Network, Zhejiang University, Hangzhou, 310058, Zhejiang, People's Republic of China
| | - Guo Cheng
- Life Sciences Institute and Innovation Center for Cell Signaling Network, Zhejiang University, Hangzhou, 310058, Zhejiang, People's Republic of China
| | - Yang Jiao
- Life Sciences Institute and Innovation Center for Cell Signaling Network, Zhejiang University, Hangzhou, 310058, Zhejiang, People's Republic of China
| | - Chen Pan
- Life Sciences Institute and Innovation Center for Cell Signaling Network, Zhejiang University, Hangzhou, 310058, Zhejiang, People's Republic of China
| | - Ran Li
- Life Sciences Institute and Innovation Center for Cell Signaling Network, Zhejiang University, Hangzhou, 310058, Zhejiang, People's Republic of China
| | - Danmei Jia
- Life Sciences Institute and Innovation Center for Cell Signaling Network, Zhejiang University, Hangzhou, 310058, Zhejiang, People's Republic of China
| | - Jing Zhu
- Beijing Ming-tian Genetics Ltd., Beijing, 100070, People's Republic of China
| | - Chao Wu
- Life Sciences Institute and Innovation Center for Cell Signaling Network, Zhejiang University, Hangzhou, 310058, Zhejiang, People's Republic of China.
| | - Min Zheng
- Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Zhejiang University, Hangzhou, 310003, Zhejiang, People's Republic of China.
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University, Hangzhou, 310003, Zhejiang, People's Republic of China.
| | - Junling Jia
- Life Sciences Institute and Innovation Center for Cell Signaling Network, Zhejiang University, Hangzhou, 310058, Zhejiang, People's Republic of China.
- Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Zhejiang University, Hangzhou, 310003, Zhejiang, People's Republic of China.
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24
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Hudson J, Gardiner M, Deshpande N, Egan S. Transcriptional response of Nautella italica R11 towards its macroalgal host uncovers new mechanisms of host-pathogen interaction. Mol Ecol 2017; 27:1820-1832. [PMID: 29215165 DOI: 10.1111/mec.14448] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2017] [Revised: 11/21/2017] [Accepted: 11/24/2017] [Indexed: 12/14/2022]
Abstract
Macroalgae (seaweeds) are essential for the functioning of temperate marine ecosystems, but there is increasing evidence to suggest that their survival is under threat from anthropogenic stressors and disease. Nautella italica R11 is recognized as an aetiological agent of bleaching disease in the red alga, Delisea pulchra. Yet, there is a lack of knowledge surrounding the molecular mechanisms involved in this model host-pathogen interaction. Here we report that mutations in the gene encoding for a LuxR-type quorum sensing transcriptional regulator, RaiR, render N. italica R11 avirulent, suggesting this gene is important for regulating the expression of virulence phenotypes. Using an RNA sequencing approach, we observed a strong transcriptional response of N. italica R11 towards the presence of D. pulchra. In particular, genes involved in oxidative stress resistance, carbohydrate and central metabolism were upregulated in the presence of the host, suggesting a role for these functions in the opportunistic pathogenicity of N. italica R11. Furthermore, we show that RaiR regulates a subset of genes in N. italica R11, including those involved in metabolism and the expression of phage-related proteins. The outcome of this research reveals new functions important for virulence of N. italica R11 and contributes to our greater understanding of the complex factors mitigating microbial diseases in macroalgae.
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Affiliation(s)
- Jennifer Hudson
- School of Biological, Earth and Environmental Sciences, Centre for Marine Bio-Innovation, UNSW Sydney, Sydney, NSW, Australia
| | - Melissa Gardiner
- School of Biological, Earth and Environmental Sciences, Centre for Marine Bio-Innovation, UNSW Sydney, Sydney, NSW, Australia
| | - Nandan Deshpande
- School of Biotechnology and Biomolecular Sciences, UNSW Sydney, Sydney, NSW, Australia
| | - Suhelen Egan
- School of Biological, Earth and Environmental Sciences, Centre for Marine Bio-Innovation, UNSW Sydney, Sydney, NSW, Australia
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25
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Zhang S, Zhang Y, Yu P, Hu Y, Zhou H, Guo L, Xu X, Zhu X, Waqas M, Qi J, Zhang X, Liu Y, Chen F, Tang M, Qian X, Shi H, Gao X, Chai R. Characterization of Lgr5+ Progenitor Cell Transcriptomes after Neomycin Injury in the Neonatal Mouse Cochlea. Front Mol Neurosci 2017; 10:213. [PMID: 28725177 PMCID: PMC5496572 DOI: 10.3389/fnmol.2017.00213] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2017] [Accepted: 06/16/2017] [Indexed: 12/17/2022] Open
Abstract
Lgr5+ supporting cells (SCs) are enriched hair cell (HC) progenitors in the cochlea. Both in vitro and in vivo studies have shown that HC injury can spontaneously activate Lgr5+ progenitors to regenerate HCs in the neonatal mouse cochlea. Promoting HC regeneration requires the understanding of the mechanism of HC regeneration, and this requires knowledge of the key genes involved in HC injury-induced self-repair responses that promote the proliferation and differentiation of Lgr5+ progenitors. Here, as expected, we found that neomycin-treated Lgr5+ progenitors (NLPs) had significantly greater HC regeneration ability, and greater but not significant proliferation ability compared to untreated Lgr5+ progenitors (ULPs) in response to neomycin exposure. Next, we used RNA-seq analysis to determine the differences in the gene-expression profiles between the transcriptomes of NLPs and ULPs from the neonatal mouse cochlea. We first analyzed the genes that were enriched and differentially expressed in NLPs and ULPs and then analyzed the cell cycle genes, the transcription factors, and the signaling pathway genes that might regulate the proliferation and differentiation of Lgr5+ progenitors. We found 9 cell cycle genes, 88 transcription factors, 8 microRNAs, and 16 cell-signaling pathway genes that were significantly upregulated or downregulated after neomycin injury in NLPs. Lastly, we constructed a protein-protein interaction network to show the interaction and connections of genes that are differentially expressed in NLPs and ULPs. This study has identified the genes that might regulate the proliferation and HC regeneration of Lgr5+ progenitors after neomycin injury, and investigations into the roles and mechanisms of these genes in the cochlea should be performed in the future to identify potential therapeutic targets for HC regeneration.
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Affiliation(s)
- Shasha Zhang
- Key Laboratory for Developmental Genes and Human Disease, Ministry of Education, Institute of Life Sciences, Southeast UniversityNanjing, China.,Research Institute of OtolaryngologyNanjing, China.,Co-innovation Center of Neuroregeneration, Nantong UniversityNantong, China
| | - Yuan Zhang
- Key Laboratory for Developmental Genes and Human Disease, Ministry of Education, Institute of Life Sciences, Southeast UniversityNanjing, China
| | - Pengfei Yu
- Bioinformatics Department, Admera Health LLCSouth Plainfield, NJ, United States
| | - Yao Hu
- School of Pharmacy, Institute for Stem Cell and Neural Regeneration, Nanjing Medical UniversityNanjing, China
| | - Han Zhou
- Jiangsu Provincial Key Medical Discipline (Laboratory), Department of Otolaryngology Head and Neck Surgery, Affiliated Drum Tower Hospital of Nanjing University Medical SchoolNanjing, China
| | - Lingna Guo
- Key Laboratory for Developmental Genes and Human Disease, Ministry of Education, Institute of Life Sciences, Southeast UniversityNanjing, China
| | - Xiaochen Xu
- Key Laboratory for Developmental Genes and Human Disease, Ministry of Education, Institute of Life Sciences, Southeast UniversityNanjing, China
| | - Xiaocheng Zhu
- Jiangsu Provincial Key Medical Discipline (Laboratory), Department of Otolaryngology Head and Neck Surgery, Affiliated Drum Tower Hospital of Nanjing University Medical SchoolNanjing, China
| | - Muhammad Waqas
- Key Laboratory for Developmental Genes and Human Disease, Ministry of Education, Institute of Life Sciences, Southeast UniversityNanjing, China.,Department of Biotechnology, Federal Urdu University of Arts, Science and TechnologyKarachi, Pakistan
| | - Jieyu Qi
- Key Laboratory for Developmental Genes and Human Disease, Ministry of Education, Institute of Life Sciences, Southeast UniversityNanjing, China
| | - Xiaoli Zhang
- Jiangsu Provincial Key Medical Discipline (Laboratory), Department of Otolaryngology Head and Neck Surgery, Affiliated Drum Tower Hospital of Nanjing University Medical SchoolNanjing, China
| | - Yan Liu
- School of Pharmacy, Institute for Stem Cell and Neural Regeneration, Nanjing Medical UniversityNanjing, China
| | - Fangyi Chen
- Department of Biomedical Engineering, Southern University of Science and TechnologyShenzhen, China
| | - Mingliang Tang
- Key Laboratory for Developmental Genes and Human Disease, Ministry of Education, Institute of Life Sciences, Southeast UniversityNanjing, China
| | - Xiaoyun Qian
- Jiangsu Provincial Key Medical Discipline (Laboratory), Department of Otolaryngology Head and Neck Surgery, Affiliated Drum Tower Hospital of Nanjing University Medical SchoolNanjing, China
| | - Haibo Shi
- Department of Otorhinolaryngology Head and Neck Surgery, The Sixth People's Hospital Affiliated to Shanghai Jiao Tong UniversityShanghai, China
| | - Xia Gao
- Research Institute of OtolaryngologyNanjing, China.,Jiangsu Provincial Key Medical Discipline (Laboratory), Department of Otolaryngology Head and Neck Surgery, Affiliated Drum Tower Hospital of Nanjing University Medical SchoolNanjing, China
| | - Renjie Chai
- Key Laboratory for Developmental Genes and Human Disease, Ministry of Education, Institute of Life Sciences, Southeast UniversityNanjing, China.,Research Institute of OtolaryngologyNanjing, China.,Co-innovation Center of Neuroregeneration, Nantong UniversityNantong, China
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26
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Wei L, Cao L, Miao Y, Wu S, Xu S, Wang R, Du J, Liang A, Fu Y. Transcriptome analysis of Spodoptera frugiperda 9 (Sf9) cells infected with baculovirus, AcMNPV or AcMNPV-BmK IT. Biotechnol Lett 2017; 39:1129-1139. [PMID: 28527118 DOI: 10.1007/s10529-017-2356-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2017] [Accepted: 05/11/2017] [Indexed: 10/19/2022]
Abstract
OBJECTIVES To analyze the transcriptome of Spodoptera frugiperda 9 (Sf9) cells infected with AcMNPV or AcMNPV-BmK IT. RESULTS A comprehensive transcriptome profile for Sf9 cells infected with AcMNPV or AcMNPV-BmK IT is shown. 43127572, 46529744 and 47235310 RNA-Seq profiles permitted the quantification of expression levels for control (C), AcMNPV-BmK IT treatment (ABT) and AcMNPV treatment (AT) groups. There were 997 up-regulated or down-regulated candidate genes with significant different expression level in these treatment groups. CONCLUSION These results provide a broad spectrum of candidate genes that are critically involved in the molecular regulation mechanism of Sf9 cells infected with AcMNPV-BmK IT.
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Affiliation(s)
- Lili Wei
- Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Institute of Biotechnology, Shanxi University, Taiyuan, 030006, China
| | - Leixi Cao
- Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Institute of Biotechnology, Shanxi University, Taiyuan, 030006, China
| | - Yanyan Miao
- Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Institute of Biotechnology, Shanxi University, Taiyuan, 030006, China
| | - Shuju Wu
- School of Life Science and Technology, Harbin Normal University, Harbin, 150025, China
| | - Shumei Xu
- Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Institute of Biotechnology, Shanxi University, Taiyuan, 030006, China
| | - Ruisheng Wang
- Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Institute of Biotechnology, Shanxi University, Taiyuan, 030006, China
| | - Jun Du
- Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Institute of Biotechnology, Shanxi University, Taiyuan, 030006, China
| | - Aihua Liang
- Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Institute of Biotechnology, Shanxi University, Taiyuan, 030006, China
| | - Yuejun Fu
- Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Institute of Biotechnology, Shanxi University, Taiyuan, 030006, China.
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27
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Johnson M, Purdom E. Clustering of mRNA-Seq data based on alternative splicing patterns. Biostatistics 2017; 18:295-307. [PMID: 27780810 PMCID: PMC6415726 DOI: 10.1093/biostatistics/kxw044] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2016] [Revised: 05/16/2016] [Accepted: 08/12/2016] [Indexed: 01/18/2023] Open
Abstract
Sequencing of messenger RNA (mRNA) can provide estimates of the levels of individual isoforms within the cell. It remains to adapt many standard statistical methods commonly used for analyzing gene expression levels to take advantage of this additional information. One novel question is whether we can find clusters of samples that are distinguished not by their gene expression but by their isoform usage. We propose a novel approach for clustering mRNA-Seq data that identifies such clusters. We show via simulation that our methods are more sensitive to finding clusters based on isoform usage than standard clustering techniques. We demonstrate its performance by finding a technical artifact that resulted in different batches having different isoform usage patterns, and illustrate its usage on several The Cancer Genome Atlas datasets.
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28
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Kumar A, Castellano I, Patti FP, Delledonne M, Abdelgawad H, Beemster GTS, Asard H, Palumbo A, Buia MC. Molecular response of Sargassum vulgare to acidification at volcanic CO 2 vents: insights from de novo transcriptomic analysis. Mol Ecol 2017; 26:2276-2290. [PMID: 28133853 DOI: 10.1111/mec.14034] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2016] [Revised: 01/03/2017] [Accepted: 01/11/2017] [Indexed: 12/20/2022]
Abstract
Ocean acidification is an emerging problem that is expected to impact ocean species to varying degrees. Currently, little is known about its effect on molecular mechanisms induced in fleshy macroalgae. To elucidate genome wide responses to acidification, a transcriptome analysis was carried out on Sargassum vulgare populations growing under acidified conditions at volcanic CO2 vents and compared with populations in a control site. Several transcripts involved in a wide range of cellular and metabolic processes were differentially expressed. No drastic changes were observed in the carbon acquisition processes and RuBisCO level. Moreover, relatively few stress genes, including those for antioxidant enzymes and heat-shock proteins, were affected. Instead, increased expression of transcripts involved in energy metabolism, photosynthetic processes and ion homeostasis suggested that algae increased energy production to maintain ion homeostasis and other cellular processes. Also, an increased allocation of carbon to cell wall and carbon storage was observed. A number of genes encoding proteins involved in cellular signalling, information storage and processing and transposition were differentially expressed between the two conditions. The transcriptional changes of key enzymes were largely confirmed by enzymatic activity measurements. Altogether, the changes induced by acidification indicate an adaptation of growth and development of S. vulgare at the volcanic CO2 vents, suggesting that this fleshy alga exhibits a high plasticity to low pH and can adopt molecular strategies to grow also in future more acidified waters.
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Affiliation(s)
- Amit Kumar
- Department of Integrative Marine Ecology, Center of Villa Dohrn - Benthic Ecology, Stazione Zoologica Anton Dohrn, Ischia, Naples, Italy
| | - Immacolata Castellano
- Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, Naples, Italy
| | - Francesco Paolo Patti
- Department of Integrative Marine Ecology, Center of Villa Dohrn - Benthic Ecology, Stazione Zoologica Anton Dohrn, Ischia, Naples, Italy
| | | | - Hamada Abdelgawad
- Department of Biology, Integrated Molecular Plant Physiology Research Group (IMPRES), University of Antwerp, Antwerp, Belgium
| | - Gerrit T S Beemster
- Department of Biology, Integrated Molecular Plant Physiology Research Group (IMPRES), University of Antwerp, Antwerp, Belgium
| | - Han Asard
- Department of Biology, Integrated Molecular Plant Physiology Research Group (IMPRES), University of Antwerp, Antwerp, Belgium
| | - Anna Palumbo
- Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, Naples, Italy
| | - Maria Cristina Buia
- Department of Integrative Marine Ecology, Center of Villa Dohrn - Benthic Ecology, Stazione Zoologica Anton Dohrn, Ischia, Naples, Italy
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29
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Arms EM, Yan Z, St.Clair DA. Differential Transcriptional Regulation in Roots of Tomato Near-Isogenic Lines in Response to Rapid-Onset Water Stress. Front Plant Sci 2017; 8:166. [PMID: 28270818 PMCID: PMC5318454 DOI: 10.3389/fpls.2017.00166] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/21/2016] [Accepted: 01/26/2017] [Indexed: 06/06/2023]
Abstract
Cultivated tomato (Solanum lycopersicum L.) is susceptible to abiotic stresses, including drought and chilling stress, while its wild relative (Solanum habrochaites) exhibits tolerance to many abiotic stresses. Chilling roots to 6°C induces rapid-onset water stress by impeding water movement from roots to shoots. Wild S. habrochaites responds to root chilling by closing stomata and maintaining shoot turgor, while cultivated tomato fails to close stomata and wilts. This phenotypic response (shoot turgor maintenance under root chilling) is controlled by a major QTL stm9 on chromosome 9 from S. habrochaites that was previously high-resolution mapped to a 0.32 cM region, but its effects on transcriptional regulation were unknown. Here we used paired near isogenic lines (NILs) differing only for the presence or absence of the S. habrochaites introgression containing stm9 in an otherwise S. lycopersicum background to investigate global transcriptional regulation in response to rapid-onset water stress induced by root chilling. NIL175 contains the S. habrochaites introgression and exhibits tolerance to root chilling stress, while NIL163 does not contain the introgression and is susceptible. RNA from roots of the two NILs was obtained at five time points during exposure to root chilling and mRNA-Seq performed. Differential expression analysis and hierarchical clustering of transcript levels were used to determine patterns of and changes in mRNA levels. Our results show that the transcriptional response of roots exposed to chilling stress is complex, with both overlapping and unique responses in tolerant and susceptible lines. In general, susceptible NIL 163 had a more complex transcriptional response to root chilling, while NIL175 exhibited a more targeted response to the imposed stress. Our evidence suggests that both the tolerant and susceptible NILs may be primed for response to root-chilling, with many of these response genes located on chromosome 9. Furthermore, serine/threonine kinase activity likely has an important role in the root chilling response of tolerant NIL175.
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Affiliation(s)
- Erin M. Arms
- St. Clair Lab, Plant Sciences Department, University of California DavisDavis, CA, USA
| | - Zhanghang Yan
- Korf Lab, Genome Center, University of California DavisDavis, CA, USA
| | - Dina A. St.Clair
- St. Clair Lab, Plant Sciences Department, University of California DavisDavis, CA, USA
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Vannozzi A, Donnini S, Vigani G, Corso M, Valle G, Vitulo N, Bonghi C, Zocchi G, Lucchin M. Transcriptional Characterization of a Widely-Used Grapevine Rootstock Genotype under Different Iron-Limited Conditions. Front Plant Sci 2017; 7:1994. [PMID: 28105035 PMCID: PMC5214570 DOI: 10.3389/fpls.2016.01994] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2016] [Accepted: 12/16/2016] [Indexed: 05/06/2023]
Abstract
Iron chlorosis is a serious deficiency that affects orchards and vineyards reducing quality and yield production. Chlorotic plants show abnormal photosynthesis and yellowing shoots. In grapevine iron uptake and homeostasis are most likely controlled by a mechanism known as "Strategy I," characteristic of non-graminaceous plants and based on a system of soil acidification, iron reduction and transporter-mediated uptake. Nowadays, grafting of varieties of economic interest on tolerant rootstocks is widely used practice against many biotic and abiotic stresses. Nevertheless, many interspecific rootstocks, and in particular those obtained by crossing exclusively non-vinifera genotypes, can show limited nutrient uptake and transport, in particular for what concerns iron. In the present study, 101.14, a commonly used rootstock characterized by susceptibility to iron chlorosis was subjected to both Fe-absence and Fe-limiting conditions. Grapevine plantlets were grown in control, Fe-deprived, and bicarbonate-supplemented hydroponic solutions. Whole transcriptome analyses, via mRNA-Seq, were performed on root apices of stressed and unstressed plants. Analysis of differentially expressed genes (DEGs) confirmed that Strategy I is the mechanism responsible for iron uptake in grapevine, since many orthologs genes to the Arabidopsis "ferrome" were differentially regulated in stressed plant. Molecular differences in the plant responses to Fe absence and presence of bicarbonate were also identified indicating the two treatments are able to induce response-mechanisms only partially overlapping. Finally, we measured the expression of a subset of genes differentially expressed in 101.14 (such as IRT1, FERRITIN1, bHLH38/39) or known to be fundamental in the "strategy I" mechanism (AHA2 and FRO2) also in a tolerant rootstock (M1) finding important differences which could be responsible for the different degrees of tolerance observed.
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Affiliation(s)
- Alessandro Vannozzi
- Dipartimento di Agronomia Animali Alimenti Risorse Naturali e Ambiente, Università di PadovaLegnaro, Italy
- Centro Interdipartimentale per la Ricerca in Viticoltura ed EnologiaConegliano, Italy
| | - Silvia Donnini
- Dipartimento di Scienze Agrarie e Ambientali, Università di MilanoMilano, Italy
| | - Gianpiero Vigani
- Dipartimento di Scienze Agrarie e Ambientali, Università di MilanoMilano, Italy
| | - Massimiliano Corso
- Dipartimento di Agronomia Animali Alimenti Risorse Naturali e Ambiente, Università di PadovaLegnaro, Italy
- Centro Interdipartimentale per la Ricerca in Viticoltura ed EnologiaConegliano, Italy
| | - Giorgio Valle
- Centro di Ricerca Interdipartimentale per le Biotecnologie InnovativePadova, Italy
| | - Nicola Vitulo
- Centro di Ricerca Interdipartimentale per le Biotecnologie InnovativePadova, Italy
| | - Claudio Bonghi
- Dipartimento di Agronomia Animali Alimenti Risorse Naturali e Ambiente, Università di PadovaLegnaro, Italy
- Centro Interdipartimentale per la Ricerca in Viticoltura ed EnologiaConegliano, Italy
| | - Graziano Zocchi
- Dipartimento di Scienze Agrarie e Ambientali, Università di MilanoMilano, Italy
| | - Margherita Lucchin
- Dipartimento di Agronomia Animali Alimenti Risorse Naturali e Ambiente, Università di PadovaLegnaro, Italy
- Centro Interdipartimentale per la Ricerca in Viticoltura ed EnologiaConegliano, Italy
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Chen K, Tsutsumi Y, Yoshitake S, Qiu X, Xu H, Hashiguchi Y, Honda M, Tashiro K, Nakayama K, Hano T, Suzuki N, Hayakawa K, Shimasaki Y, Oshima Y. Alteration of development and gene expression induced by in ovo-nanoinjection of 3-hydroxybenzo[c]phenanthrene into Japanese medaka (Oryzias latipes) embryos. Aquat Toxicol 2017; 182:194-204. [PMID: 27930992 DOI: 10.1016/j.aquatox.2016.11.020] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2016] [Revised: 11/04/2016] [Accepted: 11/24/2016] [Indexed: 06/06/2023]
Abstract
Benzo[c]phenanthrene (BcP) is a highly toxic polycyclic aromatic hydrocarbon (PAHs) found throughout the environment. In fish, it is metabolized to 3-hydroxybenzo[c]phenanthrene (3-OHBcP). In the present study, we observed the effects of 1nM 3-OHBcP on the development and gene expression of Japanese medaka (Oryzias latipes) embryos. Embryos were nanoinjected with the chemical after fertilization. Survival, developmental stage, and heart rate of the embryos were observed, and gene expression differences were quantified by messenger RNA sequencing (mRNA-Seq). The exposure to 1nM 3-OHBcP accelerated the development of medaka embryos on the 1st, 4th, and 6th days post fertilization (dpf), and increased heart rates significantly on the 5th dpf. Physical development differences of exposed medaka embryos were consistent with the gene expression profiles of the mRNA-Seq results for the 3rd dpf, which show that the expression of 780 genes differed significantly between the solvent control and 1nM 3-OHBcP exposure groups. The obvious expression changes in the exposure group were found for genes involved in organ formation (eye, muscle, heart), energy supply (ATPase and ATP synthase), and stress-response (heat shock protein genes). The acceleration of development and increased heart rate, which were consistent with the changes in mRNA expression, suggested that 3-OHBcP affects the development of medaka embryos. The observation on the developmental stages and heart beat, in ovo-nanoinjection and mRNA-Seq may be efficient tools to evaluate the effects of chemicals on embryos.
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Affiliation(s)
- Kun Chen
- Laboratory of Marine Environmental Science, Faculty of Agriculture, Kyushu University, Fukuoka 812-8581, Japan
| | - Yuki Tsutsumi
- Laboratory of Marine Environmental Science, Faculty of Agriculture, Kyushu University, Fukuoka 812-8581, Japan
| | - Shuhei Yoshitake
- Laboratory of Marine Environmental Science, Faculty of Agriculture, Kyushu University, Fukuoka 812-8581, Japan
| | - Xuchun Qiu
- Laboratory of Marine Environmental Science, Faculty of Agriculture, Kyushu University, Fukuoka 812-8581, Japan
| | - Hai Xu
- Laboratory of Marine Environmental Science, Faculty of Agriculture, Kyushu University, Fukuoka 812-8581, Japan; School of Environment and Safety Engineering, Jiangsu University, Zhenjiang 212013, PR China
| | | | - Masato Honda
- Laboratory of Marine Environmental Science, Faculty of Agriculture, Kyushu University, Fukuoka 812-8581, Japan
| | - Kosuke Tashiro
- Laboratory of Molecular Gene Technology, Faculty of Agriculture, Kyushu University, Fukuoka 812-8581, Japan
| | - Kei Nakayama
- Center for Marine Environmental Studies, Ehime University, 2-5 Bunkyo-cho, Matsuyama 790-8577, Japan
| | - Takeshi Hano
- National Research Institute of Fisheries and Environment of Inland Sea, Japan Fisheries Research and Education Agency, Maruishi 2-17-5, Hatsukaichi-shi, Hiroshima 739-0452, Japan
| | - Nobuo Suzuki
- Institute of Nature and Environmental Technology, Kanazawa University, Kakuma-machi, Kanazawa 920-1192, Japan
| | - Kazuichi Hayakawa
- Institute of Nature and Environmental Technology, Kanazawa University, Kakuma-machi, Kanazawa 920-1192, Japan
| | - Yohei Shimasaki
- Laboratory of Marine Environmental Science, Faculty of Agriculture, Kyushu University, Fukuoka 812-8581, Japan
| | - Yuji Oshima
- Laboratory of Marine Environmental Science, Faculty of Agriculture, Kyushu University, Fukuoka 812-8581, Japan.
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Abstract
MicroRNAs (miRNAs) are endogenously expressed small noncoding RNAs. The genomic locations of animal miRNAs are significantly clustered in discrete loci. We found duplication and de novo formation were important mechanisms to create miRNA clusters and the clustered miRNAs tend to be evolutionarily conserved. We proposed a "functional co-adaptation" model to explain how clustering helps newly emerged miRNAs survive and develop functions. We presented evidence that abundance of miRNAs in the same clusters were highly correlated and those miRNAs exerted cooperative repressive effects on target genes in human tissues. By transfecting miRNAs into human and fly cells and extensively profiling the transcriptome alteration with deep-sequencing, we further demonstrated the functional co-adaptation between new and old miRNAs in the miR-17-92 cluster. Our population genomic analysis suggest that positive Darwinian selection might be the driving force underlying the formation and evolution of miRNA clustering. Our model provided novel insights into mechanisms and evolutionary significance of miRNA clustering.
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Affiliation(s)
- Yirong Wang
- State Key Laboratory of Protein and Plant Gene Research, Center for Bioinformatics, School of Life Sciences and Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
| | - Junjie Luo
- State Key Laboratory of Protein and Plant Gene Research, Center for Bioinformatics, School of Life Sciences and Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China
| | - Hong Zhang
- State Key Laboratory of Protein and Plant Gene Research, Center for Bioinformatics, School of Life Sciences and Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China
| | - Jian Lu
- State Key Laboratory of Protein and Plant Gene Research, Center for Bioinformatics, School of Life Sciences and Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China
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Volkova OA, Kondrakhin YV, Yevshin IS, Valeev TF, Sharipov RN. Assessment of translational importance of mammalian mRNA sequence features based on Ribo-Seq and mRNA-Seq data. J Bioinform Comput Biol 2016; 14:1641006. [PMID: 27122318 DOI: 10.1142/s0219720016410067] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Ribosome profiling technology (Ribo-Seq) allowed to highlight more details of mRNA translation in cell and get additional information on importance of mRNA sequence features for this process. Application of translation inhibitors like harringtonine and cycloheximide along with mRNA-Seq technique helped to assess such important characteristic as translation efficiency. We assessed the translational importance of features of mRNA sequences with the help of statistical analysis of Ribo-Seq and mRNA-Seq data. Translationally important features known from literature as well as proposed by the authors were used in analysis. Such comparisons as protein coding versus non-coding RNAs and high- versus low-translated mRNAs were performed. We revealed a set of features that allowed to discriminate the compared categories of RNA. Significant relationships between mRNA features and efficiency of translation were also established.
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Affiliation(s)
- Oxana A Volkova
- * Laboratory of Gene Engineering, The Federal Research Center Institute of Cytology and Genetics, The Siberian Branch of the Russian Academy of Sciences, prosp. acad. Lavrentyeva, 10, Novosibirsk 630090, Russia
| | - Yury V Kondrakhin
- † Laboratory of Bioinformatics, Design Technological Institute of Digital Techniques, The Siberian Branch of the Russian Academy of Sciences, ul. acad. Rzhanova, 6, Novosibirsk 630090, Russia.,‡ Institute of Systems Biology, Ltd, ul. Krasina, 54, Novosibirsk 630112, Russia
| | - Ivan S Yevshin
- † Laboratory of Bioinformatics, Design Technological Institute of Digital Techniques, The Siberian Branch of the Russian Academy of Sciences, ul. acad. Rzhanova, 6, Novosibirsk 630090, Russia.,‡ Institute of Systems Biology, Ltd, ul. Krasina, 54, Novosibirsk 630112, Russia
| | - Tagir F Valeev
- ‡ Institute of Systems Biology, Ltd, ul. Krasina, 54, Novosibirsk 630112, Russia.,§ Laboratory of Complex Systems Simulation, A.P. Ershov Institute of Informatics Systems, The Siberian Branch of the Russian Academy of Sciences, prosp. acad. Lavrentyeva, 6, Novosibirsk 630090, Russia
| | - Ruslan N Sharipov
- † Laboratory of Bioinformatics, Design Technological Institute of Digital Techniques, The Siberian Branch of the Russian Academy of Sciences, ul. acad. Rzhanova, 6, Novosibirsk 630090, Russia.,‡ Institute of Systems Biology, Ltd, ul. Krasina, 54, Novosibirsk 630112, Russia.,¶ Specialized Educational Scientific Center, Novosibirsk State University, ul. Pirogova, 2, Novosibirsk 630090, Russia
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Casimiro-Soriguer I, Narbona E, Buide ML, del Valle JC, Whittall JB. Transcriptome and Biochemical Analysis of a Flower Color Polymorphism in Silene littorea (Caryophyllaceae). Front Plant Sci 2016; 7:204. [PMID: 26973662 PMCID: PMC4770042 DOI: 10.3389/fpls.2016.00204] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2015] [Accepted: 02/06/2016] [Indexed: 05/23/2023]
Abstract
Flower color polymorphisms are widely used as model traits from genetics to ecology, yet determining the biochemical and molecular basis can be challenging. Anthocyanin-based flower color variations can be caused by at least 12 structural and three regulatory genes in the anthocyanin biosynthetic pathway (ABP). We use mRNA-Seq to simultaneously sequence and estimate expression of these candidate genes in nine samples of Silene littorea representing three color morphs (dark pink, light pink and white) across three developmental stages in hopes of identifying the cause of flower color variation. We identified 29 putative paralogs for the 15 candidate genes in the ABP. We assembled complete coding sequences for 16 structural loci and nine of ten regulatory loci. Among these 29 putative paralogs, we identified 622 SNPs, yet only nine synonymous SNPs in Ans had allele frequencies that differentiated pigmented petals (dark pink and light pink) from white petals. These Ans allele frequency differences were further investigated with an expanded sequencing survey of 38 individuals, yet no SNPs consistently differentiated the color morphs. We also found one locus, F3h1, with strong differential expression between pigmented and white samples (>42x). This may be caused by decreased expression of Myb1a in white petal buds. Myb1a in S. littorea is a regulatory locus closely related to Subgroup 7 Mybs known to regulate F3h and other loci in the first half of the ABP in model species. We then compare the mRNA-Seq results with petal biochemistry which revealed cyanidin as the primary anthocyanin and five flavonoid intermediates. Concentrations of three of the flavonoid intermediates were significantly lower in white petals than in pigmented petals (rutin, quercetin and isovitexin). The biochemistry results for rutin, quercetin, luteolin and apigenin are consistent with the transcriptome results suggesting a blockage at F3h, possibly caused by downregulation of Myb1a.
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Affiliation(s)
- Inés Casimiro-Soriguer
- Department of Molecular Biology and Biochemical Engineering, Pablo de Olavide UniversitySeville, Spain
- Department of Plant Biology and Ecology, University of SevilleSeville, Spain
| | - Eduardo Narbona
- Department of Molecular Biology and Biochemical Engineering, Pablo de Olavide UniversitySeville, Spain
| | - M. L. Buide
- Department of Molecular Biology and Biochemical Engineering, Pablo de Olavide UniversitySeville, Spain
| | - José C. del Valle
- Department of Molecular Biology and Biochemical Engineering, Pablo de Olavide UniversitySeville, Spain
| | - Justen B. Whittall
- Department of Biology, Santa Clara University, College of Arts and SciencesSanta Clara, CA, USA
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Kawahara Y, Oono Y, Wakimoto H, Ogata J, Kanamori H, Sasaki H, Mori S, Matsumoto T, Itoh T. TENOR: Database for Comprehensive mRNA-Seq Experiments in Rice. Plant Cell Physiol 2016; 57:e7. [PMID: 26578693 DOI: 10.1093/pcp/pcv179] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2015] [Accepted: 11/06/2015] [Indexed: 05/18/2023]
Abstract
Here we present TENOR (Transcriptome ENcyclopedia Of Rice, http://tenor.dna.affrc.go.jp), a database that encompasses large-scale mRNA sequencing (mRNA-Seq) data obtained from rice under a wide variety of conditions. Since the elucidation of the ability of plants to adapt to various growing conditions is a key issue in plant sciences, it is of great interest to understand the regulatory networks of genes responsible for environmental changes. We used mRNA-Seq and performed a time-course transcriptome analysis of rice, Oryza sativa L. (cv. Nipponbare), under 10 abiotic stress conditions (high salinity; high and low phosphate; high, low and extremely low cadmium; drought; osmotic; cold; and flood) and two plant hormone treatment conditions (ABA and jasmonic acid). A large number of genes that were responsive to abiotic stresses and plant hormones were detected by differential expression analysis. Furthermore, several responsive genes were found to encode transcription factors that could control the transcriptional network of stress responses, but the timing of the induction of these genes was not uniform across conditions. A significant number of cis-regulatory elements were enriched in the promoter regions of the responsive genes and were shared among conditions. These data suggest that some key components of gene regulation networks are shared between different stress signaling pathways. All the resources (novel genes identified from mRNA-Seq data, expression profiles, co-expressed genes and cis-regulatory elements) can be searched for and are available in TENOR.
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Affiliation(s)
- Yoshihiro Kawahara
- Agrogenomics Research Center, National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki, 305-8602 Japan
| | - Youko Oono
- Agrogenomics Research Center, National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki, 305-8602 Japan
| | - Hironobu Wakimoto
- Agrogenomics Research Center, National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki, 305-8602 Japan Life Science Research Center, BITS. Co., Ltd., 5-201 Kandamatsunaga-cho, Chiyoda-ku, Tokyo, 101-0023 Japan
| | - Jun Ogata
- Agrogenomics Research Center, National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki, 305-8602 Japan
| | - Hiroyuki Kanamori
- Agrogenomics Research Center, National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki, 305-8602 Japan
| | - Harumi Sasaki
- Agrogenomics Research Center, National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki, 305-8602 Japan
| | - Satomi Mori
- Agrogenomics Research Center, National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki, 305-8602 Japan
| | - Takashi Matsumoto
- Agrogenomics Research Center, National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki, 305-8602 Japan
| | - Takeshi Itoh
- Agrogenomics Research Center, National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki, 305-8602 Japan
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Shen T, Sanchez HN, Zan H, Casali P. Genome-Wide Analysis Reveals Selective Modulation of microRNAs and mRNAs by Histone Deacetylase Inhibitor in B Cells Induced to Undergo Class-Switch DNA Recombination and Plasma Cell Differentiation. Front Immunol 2015; 6:627. [PMID: 26697020 PMCID: PMC4677488 DOI: 10.3389/fimmu.2015.00627] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2015] [Accepted: 11/30/2015] [Indexed: 01/27/2023] Open
Abstract
As we have suggested, epigenetic factors, such as microRNAs (miRNAs), can interact with genetic programs to regulate B cell functions, thereby informing antibody and autoantibody responses. We have shown that histone deacetylase (HDAC) inhibitors (HDI) inhibit the differentiation events critical to the maturation of the antibody response: class-switch DNA recombination (CSR), somatic hypermutation (SHM), and plasma cell differentiation, by modulating intrinsic B cell mechanisms. HDI repress the expression of AID and Blimp-1, which are critical for CSR/SHM and plasma cell differentiation, respectively, in mouse and human B cells by upregulating selected miRNAs that silenced AICDA/Aicda and PRDM1/Prdm1 mRNAs, as demonstrated by multiple qRT-PCRs (J Immunol 193:5933-5950, 2014). To further define the selectivity of HDI-mediated modulation of miRNA and gene expression, we performed genome-wide miRNA-Seq and mRNA-Seq analysis in B cells stimulated by LPS plus IL-4 and treated with HDI or nil. Consistent with what we have shown using qRT-PCR, these HDI-treated B cells displayed reduced expression of Aicda and Prdm1, and increased expression of miR-155, miR-181b, and miR-361, which target Aicda, and miR-23b, miR-30a, and miR-125b, which target Prdm1. In B cells induced to undergo CSR and plasma cell differentiation, about 23% of over 22,000 mRNAs analyzed were expressed at a significantly high copy number (more than 20 copies/cell). Only 18 (0.36%) of these highly expressed mRNAs, including Aicda, Prdm1, and Xbp1, were downregulated by HDI by 50% or more. Further, only 16 (0.30%) of the highly expressed mRNAs were upregulated (more than twofold) by HDI. The selectivity of HDI-mediated modulation of gene expression was emphasized by unchanged expression of the genes that are involved in regulation, targeting, or DNA repair processes of CSR, as well as unchanged expression of the genes encoding epigenetic regulators and factors that are important for cell signaling or apoptosis. Our findings indicate that, in B cells induced to undergo CSR and plasma cell differentiation, HDI modulate selected miRNAs and mRNAs, possibly as a result of HDACs existing in unique contexts of HDAC/cofactor complexes, as occurring in B lymphocytes, particularly when in an activated state.
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Affiliation(s)
- Tian Shen
- Department of Microbiology and Immunology, University of Texas School of Medicine, UT Health Science Center , San Antonio, TX , USA
| | - Helia N Sanchez
- Department of Microbiology and Immunology, University of Texas School of Medicine, UT Health Science Center , San Antonio, TX , USA
| | - Hong Zan
- Department of Microbiology and Immunology, University of Texas School of Medicine, UT Health Science Center , San Antonio, TX , USA
| | - Paolo Casali
- Department of Microbiology and Immunology, University of Texas School of Medicine, UT Health Science Center , San Antonio, TX , USA
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Corso M, Vannozzi A, Maza E, Vitulo N, Meggio F, Pitacco A, Telatin A, D'Angelo M, Feltrin E, Negri AS, Prinsi B, Valle G, Ramina A, Bouzayen M, Bonghi C, Lucchin M. Comprehensive transcript profiling of two grapevine rootstock genotypes contrasting in drought susceptibility links the phenylpropanoid pathway to enhanced tolerance. J Exp Bot 2015; 66:5739-52. [PMID: 26038306 PMCID: PMC4566973 DOI: 10.1093/jxb/erv274] [Citation(s) in RCA: 77] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
In light of ongoing climate changes in wine-growing regions, the selection of drought-tolerant rootstocks is becoming a crucial factor for developing a sustainable viticulture. In this study, M4, a new rootstock genotype that shows tolerance to drought, was compared from a genomic and transcriptomic point of view with the less drought-tolerant genotype 101.14. The root and leaf transcriptome of both 101.14 and the M4 rootstock genotype was analysed, following exposure to progressive drought conditions. Multifactorial analyses indicated that stress treatment represents the main factor driving differential gene expression in roots, whereas in leaves the genotype is the prominent factor. Upon stress, M4 roots and leaves showed a higher induction of resveratrol and flavonoid biosynthetic genes, respectively. The higher expression of VvSTS genes in M4, confirmed by the accumulation of higher levels of resveratrol in M4 roots compared with 101.14, was coupled to an up-regulation of several VvWRKY transcription factors. Interestingly, VvSTS promoter analyses performed on both the resequenced genomes highlighted a significantly higher number of W-BOX elements in the tolerant genotype. It is proposed that the elevated synthesis of resveratrol in M4 roots upon water stress could enhance the plant's ability to cope with the oxidative stress usually associated with water deficit.
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Affiliation(s)
- Massimiliano Corso
- Department of Agronomy, Food, Natural resources, Animals and Environment (DAFNAE), University of Padova Agripolis, 35020 Legnaro, Italy Centro Interdipartimentale per la Ricerca in Viticoltura ed Enologia (CIRVE), Via XXVIII Aprile, 14-31015 Conegliano (TV), Italy
| | - Alessandro Vannozzi
- Department of Agronomy, Food, Natural resources, Animals and Environment (DAFNAE), University of Padova Agripolis, 35020 Legnaro, Italy Centro Interdipartimentale per la Ricerca in Viticoltura ed Enologia (CIRVE), Via XXVIII Aprile, 14-31015 Conegliano (TV), Italy
| | - Elie Maza
- Genomics and Biotechnology of Fruit (GBF) Laboratory, Institut National Polytechnique de Toulouse, Avenue de l'Agrobiopole, F-31326 Castanet-Tolosan Cedex (Toulouse), France
| | - Nicola Vitulo
- CRIBI, University of Padova, viale G. Colombo 3, 35121 Padova, Italy
| | - Franco Meggio
- Department of Agronomy, Food, Natural resources, Animals and Environment (DAFNAE), University of Padova Agripolis, 35020 Legnaro, Italy Centro Interdipartimentale per la Ricerca in Viticoltura ed Enologia (CIRVE), Via XXVIII Aprile, 14-31015 Conegliano (TV), Italy
| | - Andrea Pitacco
- Department of Agronomy, Food, Natural resources, Animals and Environment (DAFNAE), University of Padova Agripolis, 35020 Legnaro, Italy Centro Interdipartimentale per la Ricerca in Viticoltura ed Enologia (CIRVE), Via XXVIII Aprile, 14-31015 Conegliano (TV), Italy
| | - Andrea Telatin
- CRIBI, University of Padova, viale G. Colombo 3, 35121 Padova, Italy
| | - Michela D'Angelo
- CRIBI, University of Padova, viale G. Colombo 3, 35121 Padova, Italy
| | - Erika Feltrin
- CRIBI, University of Padova, viale G. Colombo 3, 35121 Padova, Italy
| | - Alfredo Simone Negri
- Department of Agricultural and Environmental Sciences-Production, Landscape, Agroenergy (DiSAA), University of Milano, Milano 20133, Italy
| | - Bhakti Prinsi
- Department of Agricultural and Environmental Sciences-Production, Landscape, Agroenergy (DiSAA), University of Milano, Milano 20133, Italy
| | - Giorgio Valle
- CRIBI, University of Padova, viale G. Colombo 3, 35121 Padova, Italy
| | - Angelo Ramina
- Department of Agronomy, Food, Natural resources, Animals and Environment (DAFNAE), University of Padova Agripolis, 35020 Legnaro, Italy Centro Interdipartimentale per la Ricerca in Viticoltura ed Enologia (CIRVE), Via XXVIII Aprile, 14-31015 Conegliano (TV), Italy
| | - Mondher Bouzayen
- Genomics and Biotechnology of Fruit (GBF) Laboratory, Institut National Polytechnique de Toulouse, Avenue de l'Agrobiopole, F-31326 Castanet-Tolosan Cedex (Toulouse), France
| | - Claudio Bonghi
- Department of Agronomy, Food, Natural resources, Animals and Environment (DAFNAE), University of Padova Agripolis, 35020 Legnaro, Italy Centro Interdipartimentale per la Ricerca in Viticoltura ed Enologia (CIRVE), Via XXVIII Aprile, 14-31015 Conegliano (TV), Italy
| | - Margherita Lucchin
- Department of Agronomy, Food, Natural resources, Animals and Environment (DAFNAE), University of Padova Agripolis, 35020 Legnaro, Italy Centro Interdipartimentale per la Ricerca in Viticoltura ed Enologia (CIRVE), Via XXVIII Aprile, 14-31015 Conegliano (TV), Italy
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Hefer CA, Mizrachi E, Myburg AA, Douglas CJ, Mansfield SD. Comparative interrogation of the developing xylem transcriptomes of two wood-forming species: Populus trichocarpa and Eucalyptus grandis. New Phytol 2015; 206:1391-405. [PMID: 25659405 DOI: 10.1111/nph.13277] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2014] [Accepted: 12/04/2014] [Indexed: 05/15/2023]
Abstract
Wood formation is a complex developmental process governed by genetic and environmental stimuli. Populus and Eucalyptus are fast-growing, high-yielding tree genera that represent ecologically and economically important species suitable for generating significant lignocellulosic biomass. Comparative analysis of the developing xylem and leaf transcriptomes of Populus trichocarpa and Eucalyptus grandis together with phylogenetic analyses identified clusters of homologous genes preferentially expressed during xylem formation in both species. A conserved set of 336 single gene pairs showed highly similar xylem preferential expression patterns, as well as evidence of high functional constraint. Individual members of multi-gene orthologous clusters known to be involved in secondary cell wall biosynthesis also showed conserved xylem expression profiles. However, species-specific expression as well as opposite (xylem versus leaf) expression patterns observed for a subset of genes suggest subtle differences in the transcriptional regulation important for xylem development in each species. Using sequence similarity and gene expression status, we identified functional homologs likely to be involved in xylem developmental and biosynthetic processes in Populus and Eucalyptus. Our study suggests that, while genes involved in secondary cell wall biosynthesis show high levels of gene expression conservation, differential regulation of some xylem development genes may give rise to unique xylem properties.
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Affiliation(s)
- Charles A Hefer
- Department of Botany, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - Eshchar Mizrachi
- Department of Genetics, Forestry and Agricultural Biotechnology Institute (FABI), Genomics Research Institute (GRI), University of Pretoria, Private bag X20, Pretoria, 0028, South Africa
| | - Alexander A Myburg
- Department of Genetics, Forestry and Agricultural Biotechnology Institute (FABI), Genomics Research Institute (GRI), University of Pretoria, Private bag X20, Pretoria, 0028, South Africa
| | - Carl J Douglas
- Department of Botany, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - Shawn D Mansfield
- Department of Wood Science, Faculty of Forestry, University of British Columbia, Forest Sciences Centre, 4030-2424 Main Mall, Vancouver, BC, V6T 1Z4, Canada
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Wang Z, Dai M, Wang Y, Cooper KL, Zhu T, Dong D, Zhang J, Zhang S. Unique expression patterns of multiple key genes associated with the evolution of mammalian flight. Proc Biol Sci 2014; 281:20133133. [PMID: 24695426 DOI: 10.1098/rspb.2013.3133] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Bats are the only mammals capable of true flight. Critical adaptations for flight include a pair of dramatically elongated hands with broad wing membranes. To study the molecular mechanisms of bat wing evolution, we perform genomewide mRNA sequencing and in situ hybridization for embryonic bat limbs. We identify seven key genes that display unique expression patterns in embryonic bat wings and feet, compared with mouse fore- and hindlimbs. The expression of all 5'HoxD genes (Hoxd9-13) and Tbx3, six known crucial transcription factors for limb and digit development, is extremely high and prolonged in the elongating wing area. The expression of Fam5c, a tumour suppressor, in bat limbs is bat-specific and significantly high in all short digit regions (the thumb and foot digits). These results suggest multiple genetic changes occurred independently during the evolution of bat wings to elongate the hand digits, promote membrane growth and keep other digits short. Our findings also indicate that the evolution of limb morphology depends on the complex integration of multiple gene regulatory networks and biological processes that control digit formation and identity, chondrogenesis, and interdigital regression or retention.
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Affiliation(s)
- Zhe Wang
- Institute of Molecular Ecology and Evolution (iAIR), East China Normal University, , Shanghai 200062, People's Republic of China, Division of Biological Sciences, University of California, , San Diego, CA 92093, USA, Department of Genetics, Harvard Medical School, , Boston, MA 02115, USA
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Damhofer H, Medema JP, Veenstra VL, Badea L, Popescu I, Roelink H, Bijlsma MF. Assessment of the stromal contribution to Sonic Hedgehog-dependent pancreatic adenocarcinoma. Mol Oncol 2013; 7:1031-42. [PMID: 23998958 DOI: 10.1016/j.molonc.2013.08.004] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2013] [Accepted: 08/08/2013] [Indexed: 01/05/2023] Open
Abstract
Pancreatic ductal adenocarcinoma (PDAC) remains one of the most lethal malignancies. It is typically detected at an advanced stage, at which the therapeutic options are very limited. One remarkable feature of PDAC that contributes to its resilience to treatment is the extreme stromal activation seen in these tumors. Often, the vast majority of tumor bulk consists of non-tumor cells that together provide a tumor-promoting environment. One of the signals that maintains and activates the stroma is the developmental protein Sonic Hedgehog (SHH). As the disease progresses, tumor cells produce increasing amounts of SHH, which activates the surrounding stroma to aid in tumor progression. To better understand this response and identify targets for inhibition, we aimed to elucidate the proteins that mediate the SHH-driven stromal response in PDAC. For this a novel mixed-species coculture model was set up in which the cancer cells are human, and the stroma is modeled by mouse fibroblasts. In conjunction with next-generation sequencing we were able to use the sequence difference between these species to genetically distinguish between the epithelial and stromal responses to SHH. The stromal SHH-dependent genes from this analysis were validated and their relevance for human disease was subsequently determined in two independent patient cohorts. In non-microdissected tissue from PDAC patients, in which a large amount of stroma is present, the targets were confirmed to associate with tumor stroma versus normal pancreatic tissue. Patient survival analysis and immunohistochemistry identified CDA, EDIL3, ITGB4, PLAUR and SPOCK1 as SHH-dependent stromal factors that are associated with poor prognosis in PDAC patients. Summarizing, the presented data provide insight into the role of the activated stroma in PDAC, and how SHH acts to mediate this response. In addition, the study has yielded several candidates that are interesting therapeutic targets for a disease for which treatment options are still inadequate.
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Affiliation(s)
- Helene Damhofer
- Laboratory for Experimental Oncology and Radiobiology, Academic Medical Center, University of Amsterdam, Meibergdreef 9, 1105AZ Amsterdam, The Netherlands.
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Bhattacharjee M, Gupta R, Davuluri RV. Estimation of Gene Expression at Isoform Level from mRNA-Seq Data by Bayesian Hierarchical Modeling. Front Genet 2013; 3:239. [PMID: 23293650 PMCID: PMC3536024 DOI: 10.3389/fgene.2012.00239] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2011] [Accepted: 10/18/2012] [Indexed: 11/16/2022] Open
Abstract
mRNA-Seq is a precise and highly reproducible technique for measurement of transcripts levels and yields sequence information of a transcriptome at a single nucleotide base-level thus enabling us to determine splice junctions and alternative splicing events with high confidence. Often analysis of mRNA-Seq data does not attempt to quantify the expressions at isoform level. In this paper our objective would be use the mRNA-Seq data to infer expression at isoform level, where splicing patterns of a gene is assumed to be known. A Bayesian latent variable based modeling framework is proposed here, where the parameterization enables us to infer at various levels. For example, expression variability of an isoform across different conditions; the model parameterization also allows us to carry out two-sample comparisons, e.g., using a Bayesian t-test, in addition simple presence or absence of an isoform can also be estimated by the use of the latent variables present in the model. In this paper we would carry out inference on isoform expression under different normalization techniques, since it has been recently shown that one of the most prominent sources of variation in differential call using mRNA-Seq data is the normalization method used. The statistical framework is developed for multiple isoforms and easily extends to reads mapping to multiple genes. This could be achieved by slight conceptual modifications in definitions of what we consider as a gene and what as an exon. Additionally proposed framework can be extended by appropriate modeling of the design matrix to infer about yet unknown novel transcripts. However such attempts should be made judiciously since the input date used in the proposed model does not use reads from splice junctions.
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Affiliation(s)
- M Bhattacharjee
- Department of Statistics, University of Pune Pune, India ; Department of Mathematics and Statistics, University of Hyderabad Hyderabad, India
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Rafehi H, Ververis K, Balcerczyk A, Ziemann M, Ooi J, Hu S, Kwa FAA, Loveridge SJ, Georgiadis GT, El-Osta A, Karagiannis TC. Investigation of the biological properties of Cinnulin PF in the context of diabetes: mechanistic insights by genome-wide mRNA-Seq analysis. Pathobiol Aging Age Relat Dis 2012; 2:PBA-2-11905. [PMID: 22953038 PMCID: PMC3417697 DOI: 10.3402/pba.v2i0.11905] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/07/2011] [Revised: 01/17/2012] [Accepted: 02/01/2012] [Indexed: 01/20/2023]
Abstract
The accumulating evidence of the beneficial effects of cinnamon (Cinnamomum burmanni) in type-2 diabetes, a chronic age-associated disease, has prompted the commercialisation of various supplemental forms of the spice. One such supplement, Cinnulin PF®, represents the water soluble fraction containing relatively high levels of the double-linked procyanidin type-A polymers of flavanoids. The overall aim of this study was to utilize genome-wide mRNA-Seq analysis to characterise the changes in gene expression caused by Cinnulin PF in immortalised human keratinocytes and microvascular endothelial cells, which are relevant with respect to diabetic complications. In summary, our findings provide insights into the mechanisms of action of Cinnulin PF in diabetes and diabetic complications. More generally, we identify relevant candidate genes which could provide the basis for further investigation.
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Affiliation(s)
- Haloom Rafehi
- Epigenomic Medicine, Baker IDI Heart and Diabetes Institute, The Alfred Medical Research and Education Precinct, Melbourne, VIC., Australia
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Mizuno H, Kawahara Y, Wu J, Katayose Y, Kanamori H, Ikawa H, Itoh T, Sasaki T, Matsumoto T. Asymmetric distribution of gene expression in the centromeric region of rice chromosome 5. Front Plant Sci 2011; 2:16. [PMID: 22639581 PMCID: PMC3355683 DOI: 10.3389/fpls.2011.00016] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2011] [Accepted: 06/20/2011] [Indexed: 05/28/2023]
Abstract
There is controversy as to whether gene expression is silenced in the functional centromere. The complete genomic sequences of the centromeric regions in higher eukaryotes have not been fully elucidated, because the presence of highly repetitive sequences complicates many aspects of genomic sequencing. We performed resequencing, assembly, and sequence finishing of two P1-derived artificial chromosome clones in the centromeric region of rice (Oryza sativa L.) chromosome 5 (Cen5). The pericentromeric region, where meiotic recombination is silenced, is located at the center of chromosome 5 and is 2.14 Mb long; a total of six restriction-fragment-length polymorphism markers (R448, C1388, S20487S, E3103S, C53260S, and R2059) genetically mapped at 54.6 cM were located in this region. In the pericentromeric region, 28 genes were annotated on the short arm and 45 genes on the long arm. To quantify all transcripts in this region, we performed massive parallel sequencing of mRNA. Transcriptional density (total length of transcribed region/length of the genomic region) and expression level (number of uniquely mapped reads/length of transcribed region) were calculated on the basis of the mapped reads on the rice genome. Transcriptional density and expression level were significantly lower in Cen5 than in the average of the other chromosomal regions. Moreover, transcriptional density in Cen5 was significantly lower on the short arm than on the long arm; the distribution of transcriptional density was asymmetric. The genomic sequence of Cen5 has been integrated into the most updated reference rice genome sequence constructed by the International Rice Genome Sequencing Project.
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Affiliation(s)
- Hiroshi Mizuno
- Plant Genome Research Unit, Division of Genome and Biodiversity Research, National Institute of Agrobiological SciencesTsukuba, Ibaraki, Japan
| | - Yoshihiro Kawahara
- Bioinformatics Research Unit, Division of Genome and Biodiversity Research, National Institute of Agrobiological SciencesTsukuba, Ibaraki, Japan
| | - Jianzhong Wu
- Plant Genome Research Unit, Division of Genome and Biodiversity Research, National Institute of Agrobiological SciencesTsukuba, Ibaraki, Japan
| | - Yuichi Katayose
- Soybean Genome Research Team, Division of Genome and Biodiversity Research, National Institute of Agrobiological SciencesTsukuba, Ibaraki, Japan
| | - Hiroyuki Kanamori
- Institute of the Society for Techno-innovation of Agriculture, Forestry and FisheriesTsukuba, Ibaraki, Japan
| | - Hiroshi Ikawa
- Institute of the Society for Techno-innovation of Agriculture, Forestry and FisheriesTsukuba, Ibaraki, Japan
| | - Takeshi Itoh
- Bioinformatics Research Unit, Division of Genome and Biodiversity Research, National Institute of Agrobiological SciencesTsukuba, Ibaraki, Japan
| | - Takuji Sasaki
- National Institute of Agrobiological SciencesTsukuba, Ibaraki, Japan
| | - Takashi Matsumoto
- Plant Genome Research Unit, Division of Genome and Biodiversity Research, National Institute of Agrobiological SciencesTsukuba, Ibaraki, Japan
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