351
|
LncRNA H19 promotes the differentiation of bovine skeletal muscle satellite cells by suppressing Sirt1/FoxO1. Cell Mol Biol Lett 2017; 22:10. [PMID: 28652859 PMCID: PMC5481879 DOI: 10.1186/s11658-017-0040-6] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2016] [Accepted: 06/09/2017] [Indexed: 12/31/2022] Open
Abstract
Background H19 is a well-characterized Long noncoding RNA (lncRNA) that has been proven to promote myoblast differentiation in humans and mice. However, its mechanism of action is still not fully interpreted. Methods Using RT-qPCR, we examined H19 RNA levels in various tissues from 1-week, 1-month, 6-month and 36-month old male cattle (i.e., newborn, infant, young and adult). The protein and mRNA levels of MyoG, MyHC, Sirt1 and FoxO1 in the satellite and C2C12 cells with an H19 silencing or overexpression vector were respectively detected using western blot and real-time qPCR. Results H19 was highly expressed in skeletal muscle at all the studied ages. High expression of H19 was required for the differentiation of bovine satellite cells. Knockdown of H19 caused a remarkable increase in the myoblast-inhibitory genes Sirt1/FoxO1, suggesting that H19 suppresses Sirt1/FoxO1 expression during myogenesis. Western blotting analysis of co-transfection of Sirt1 or FoxO1 expression vectors with pcDNA-H19 indicated that Sirt1/FoxO1 overexpression neutralized the promotion of myoblast differentiation through transfection of pcDNA-H19. Conclusion H19 promoted the differentiation of bovine skeletal muscle satellite cells by suppressing Sirt1/FoxO1. Electronic supplementary material The online version of this article (doi:10.1186/s11658-017-0040-6) contains supplementary material, which is available to authorized users.
Collapse
|
352
|
García K, Yáñez C, Plaza N, Peña F, Sepúlveda P, Pérez-Reytor D, Espejo RT. Gene expression of Vibrio parahaemolyticus growing in laboratory isolation conditions compared to those common in its natural ocean environment. BMC Microbiol 2017; 17:118. [PMID: 28525966 PMCID: PMC5437538 DOI: 10.1186/s12866-017-1030-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2016] [Accepted: 05/12/2017] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Vibrio parahaemolyticus is an autochthonous marine bacterial species comprising strains able to grow in broth containing bile salts at 37 °C, a condition seldom found in the ocean. However, this condition is used for isolation in the laboratory because it is considered a necessary property for pathogenesis. In this context, revealing how gene expression enables V. parahaemolyticus to adapt to this particular condition -common to almost all V. parahaemolyticus isolates- will improve our understanding of the biology of this important pathogen. To determine the genes of V. parahaemolyticus differentially expressed when growing in isolation condition (37 °C, 0.9% NaCl, and 0.04% bile salts) referred to those at the temperature and salt concentration prevailing in ocean south of Chile (marine-like condition; 12 °C, 3% NaCl, and absence of bile salts) we used high-throughput sequencing of RNA. RESULTS Our results showed that in the isolation condition, among the 5034 genes annotated in the V. parahaemolyticus RIMD2210633 genome, 344 were upregulated and 433 downregulated referred to the marine-like condition, managing an adjusted P-value (Padj) < E-5. Between the 50 more highly expressed genes, among the small RNAs (sRNA), the three carbon storage regulators B (CsrB) were up four to six times, while RyhB, related to iron metabolism besides motility control, was down about eight times. Among proteins, BfdA, a hemolysin-co-regulated protein (Hcp1) secreted by T6SS1, one of the most highly expressed genes, was about 140 times downregulated in isolation condition. The highest changes in relative expression were found among neighboring genes coding for proteins related to respiration, which were about 40 times upregulated. CONCLUSIONS When V. parahaemolyticus is grown in conditions used for laboratory isolation 777 genes are up- or downregulated referred to conditions prevailing in the marine-like condition; the most significantly overrepresented categories among upregulated processes were those related to transport and localization, while secretion and pathogenesis were overrepresented among downregulated genes. Genes with the highest differential expression included the sRNAs CsrB and RhyB and the mRNAs related with secretion, nutritional upshift, respiration and rapid growing.
Collapse
Affiliation(s)
- Katherine García
- Centro de Investigación Biomédica, Facultad de Ciencias de la Salud, Instituto de Ciencias Biomédicas, Universidad Autónoma de Chile, Av. El Llano Subercaseaux, 2801 Santiago, Chile
| | - Cristian Yáñez
- Institute of Nutrition and Food Technology, Universidad de Chile, Av. El Líbano 5524, Macul, Santiago, Chile
| | - Nicolás Plaza
- Centro de Investigación Biomédica, Facultad de Ciencias de la Salud, Instituto de Ciencias Biomédicas, Universidad Autónoma de Chile, Av. El Llano Subercaseaux, 2801 Santiago, Chile
- Institute of Nutrition and Food Technology, Universidad de Chile, Av. El Líbano 5524, Macul, Santiago, Chile
| | - Francisca Peña
- School of Bioinformatics Engineering, University of Talca, Talca, Chile
| | - Pedro Sepúlveda
- School of Bioinformatics Engineering, University of Talca, Talca, Chile
| | - Diliana Pérez-Reytor
- Centro de Investigación Biomédica, Facultad de Ciencias de la Salud, Instituto de Ciencias Biomédicas, Universidad Autónoma de Chile, Av. El Llano Subercaseaux, 2801 Santiago, Chile
| | - Romilio T. Espejo
- Institute of Nutrition and Food Technology, Universidad de Chile, Av. El Líbano 5524, Macul, Santiago, Chile
| |
Collapse
|
353
|
Lipidomics and RNA-Seq Study of Lipid Regulation in Aphis gossypii parasitized by Lysiphlebia japonica. Sci Rep 2017; 7:1364. [PMID: 28465512 PMCID: PMC5431011 DOI: 10.1038/s41598-017-01546-1] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2016] [Accepted: 03/30/2017] [Indexed: 12/12/2022] Open
Abstract
The cotton-melon aphid, Aphis gossypii Glover, is a major insect pest worldwide. Lysiphlebia japonica (Ashmead) is an obligate parasitic wasp of A. gossypii, and has the ability to regulate lipid metabolism of the cotton-melon aphid. Lipids are known to play critical roles in energy homeostasis, membrane structure, and signaling. However, the parasitoid genes that regulate fat metabolism and lipid composition in aphids are not known. 34 glycerolipids and 248 glycerophospholipids were identified in this study. We have shown that a 3-day parasitism of aphids can induce significant changes in the content and acyl chain composition of triacylglycerols (TAGs) and subspecies composition of glycerophospholipids content and acyl chains. It also upregulate the expression of several genes involved in triacylglycerol synthesis and glycerophospholipid metabolism. Pathway analysis showed that a higher expression of genes involved in the tricarboxylic acid cycle and glycolysis pathways may contribute to TAGs synthesis in parasitized aphids. Interestingly, the higher expression of genes in the sphingomyelin pathway and reduced sphingomyelin content may be related to the reproductive ability of A. gossypii. We provide a comprehensive resource describing the molecular signature of parasitized A. gossypii particularly the changes associated with the lipid metabolism and discuss the biological and ecological significance of this change.
Collapse
|
354
|
Purhonen J, Rajendran J, Mörgelin M, Uusi-Rauva K, Katayama S, Krjutskov K, Einarsdottir E, Velagapudi V, Kere J, Jauhiainen M, Fellman V, Kallijärvi J. Ketogenic diet attenuates hepatopathy in mouse model of respiratory chain complex III deficiency caused by a Bcs1l mutation. Sci Rep 2017; 7:957. [PMID: 28424480 PMCID: PMC5430426 DOI: 10.1038/s41598-017-01109-4] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2016] [Accepted: 03/23/2017] [Indexed: 02/03/2023] Open
Abstract
Mitochondrial disorders are among the most prevalent inborn errors of metabolism but largely lack treatments and have poor outcomes. High-fat, low-carbohydrate ketogenic diets (KDs) have shown beneficial effects in mouse models of mitochondrial myopathies, with induction of mitochondrial biogenesis as the suggested main mechanism. We fed KD to mice with respiratory chain complex III (CIII) deficiency and progressive hepatopathy due to mutated BCS1L, a CIII assembly factor. The mutant mice became persistently ketotic and tolerated the KD for up to 11 weeks. Liver disease progression was attenuated by KD as shown by delayed fibrosis, reduced cell death, inhibition of hepatic progenitor cell response and stellate cell activation, and normalization of liver enzyme activities. Despite no clear signs of increased mitochondrial biogenesis in the liver, CIII assembly and activity were improved and mitochondrial morphology in hepatocytes normalized. Induction of hepatic glutathione transferase genes and elevated total glutathione level were normalized by KD. Histological findings and transcriptome changes indicated modulation of liver macrophage populations by the mutation and the diet. These results reveal a striking beneficial hepatic response to KD in mice with mitochondrial hepatopathy and warrant further investigations of dietary modification in the management of these conditions in patients.
Collapse
Affiliation(s)
- Janne Purhonen
- Folkhälsan Research Center, Helsinki, Finland.,Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Jayasimman Rajendran
- Folkhälsan Research Center, Helsinki, Finland.,Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Matthias Mörgelin
- Division of Infection Medicine, Clinical Sciences, Lund University, Lund, Sweden
| | | | - Shintaro Katayama
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
| | - Kaarel Krjutskov
- Folkhälsan Research Center, Helsinki, Finland.,Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden.,Competence Centre on Health Technologies, Tartu, Estonia.,Molecular Neurology Research Program, University of Helsinki, Helsinki, Finland
| | - Elisabet Einarsdottir
- Folkhälsan Research Center, Helsinki, Finland.,Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden.,Molecular Neurology Research Program, University of Helsinki, Helsinki, Finland
| | - Vidya Velagapudi
- Metabolomics Unit, Institute for Molecular Medicine, University of Helsinki, Helsinki, Finland
| | - Juha Kere
- Folkhälsan Research Center, Helsinki, Finland.,Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden.,Molecular Neurology Research Program, University of Helsinki, Helsinki, Finland.,Department of Genetics and Molecular Medicine, King's College London, England, UK
| | | | - Vineta Fellman
- Folkhälsan Research Center, Helsinki, Finland.,Department of Clinical Sciences, Lund, Pediatrics, Lund University, Lund, Sweden.,Children's Hospital, Helsinki University Hospital, University of Helsinki, Helsinki, Finland
| | | |
Collapse
|
355
|
Integrated host and viral transcriptome analyses reveal pathology and inflammatory response mechanisms to ALV-J injection in SPF chickens. Sci Rep 2017; 7:46156. [PMID: 28401895 PMCID: PMC5388866 DOI: 10.1038/srep46156] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2016] [Accepted: 03/09/2017] [Indexed: 12/31/2022] Open
Abstract
Avian leukosis virus (ALV) is detrimental to poultry health and causes substantial economic losses from mortality and decreased performance. Because tumorigenesis is a complex mechanism, the regulatory architecture of the immune system is likely to include the added dimensions of modulation by miRNAs and long-noncoding RNA (lncRNA). To characterize the response to ALV challenge, we developed a novel methodology that combines four datasets: mRNA expression and the associated regulatory factors of miRNA and lncRNA, and ALV gene expression. Specific Pathogen-Free (SPF) layer chickens were infected with ALV-J or maintained as non-injected controls. Spleen samples were collected at 40 days post injection (dpi), and sequenced. There were 864 genes, 7 miRNAs and 17 lncRNAs differentially expressed between infected and non-infected birds. The combined analysis of the 4 RNA expression datasets revealed that ALV infection is detected by pattern-recognition receptors (TLR9 and TLR3) leading to a type-I IFN mediated innate immune response that is modulated by IRF7 and IRF1. Co-expression network analysis of mRNA with miRNA, lncRNA and virus genes identified key elements within the complex networks utilized during ALV response. The integration of information from the host transcriptomic, epigenetic and virus response also has the potential to provide deeper insights into other host-pathogen interactions.
Collapse
|
356
|
Bräutigam K, Soolanayakanahally R, Champigny M, Mansfield S, Douglas C, Campbell MM, Cronk Q. Sexual epigenetics: gender-specific methylation of a gene in the sex determining region of Populus balsamifera. Sci Rep 2017; 7:45388. [PMID: 28345647 PMCID: PMC5366940 DOI: 10.1038/srep45388] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2016] [Accepted: 02/27/2017] [Indexed: 12/27/2022] Open
Abstract
Methylation has frequently been implicated in gender determination in plants. The recent discovery of the sex determining region (SDR) of balsam poplar, Populus balsamifera, pinpointed 13 genes with differentiated X and Y copies. We tested these genes for differential methylation using whole methylome sequencing of xylem tissue of multiple individuals grown under field conditions in two common gardens. The only SDR gene to show a marked pattern of gender-specific methylation is PbRR9, a member of the two component response regulator (type-A) gene family, involved in cytokinin signalling. It is an ortholog of Arabidopsis genes ARR16 and ARR17. The strongest patterns of differential methylation (mostly male-biased) are found in the putative promoter and the first intron. The 4th intron is strongly methylated in both sexes and the 5th intron is unmethylated in both sexes. Using a statistical learning algorithm we find that it is possible accurately to assign trees to gender using genome-wide methylation patterns alone. The strongest predictor is the region coincident with PbRR9, showing that this gene stands out against all genes in the genome in having the strongest sex-specific methylation pattern. We propose the hypothesis that PbRR9 has a direct, epigenetically mediated, role in poplar sex determination.
Collapse
Affiliation(s)
- Katharina Bräutigam
- Department of Biology, University of Toronto Missisauga, Mississauga ON, L5L 1C6, Canada
| | - Raju Soolanayakanahally
- Saskatoon Research and Development Centre, Agriculture and Agri-Food Canada, 107 Science Place, Saskatoon SK, S7N OX2, Canada
| | - Marc Champigny
- Department of Biological Sciences, University of Toronto Scarborough, Toronto, ON M1C 1A4, Canada
| | - Shawn Mansfield
- Department of Wood Science, University of British Columbia, 4030-2424 Main Mall, Vancouver BC, V6T 1Z4, Canada
| | - Carl Douglas
- Department of Botany, University of British Columbia, Vancouver BC, V6T 1Z4, Canada
| | - Malcolm M Campbell
- Department of Molecular and Cellular Biology, University of Guelph, Guelph ON N1G 2W1, Canada
| | - Quentin Cronk
- Department of Botany, University of British Columbia, Vancouver BC, V6T 1Z4, Canada
| |
Collapse
|
357
|
AlShareef S, Ling Y, Butt H, Mariappan KG, Benhamed M, Mahfouz MM. Herboxidiene triggers splicing repression and abiotic stress responses in plants. BMC Genomics 2017; 18:260. [PMID: 28347276 PMCID: PMC5369228 DOI: 10.1186/s12864-017-3656-z] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2016] [Accepted: 03/22/2017] [Indexed: 12/28/2022] Open
Abstract
Background Constitutive and alternative splicing of pre-mRNAs from multiexonic genes controls the diversity of the proteome; these precisely regulated processes also fine-tune responses to cues related to growth, development, and stresses. Small-molecule inhibitors that perturb splicing provide invaluable tools for use as chemical probes to uncover the molecular underpinnings of splicing regulation and as potential anticancer compounds. Results Here, we show that herboxidiene (GEX1A) inhibits both constitutive and alternative splicing. Moreover, GEX1A activates genome-wide transcriptional patterns involved in abiotic stress responses in plants. GEX1A treatment -activated ABA-inducible promoters, and led to stomatal closure. Interestingly, GEX1A and pladienolide B (PB) elicited similar cellular changes, including alterations in the patterns of transcription and splicing, suggesting that these compounds might target the same spliceosome complex in plant cells. Conclusions Our study establishes GEX1A as a potent splicing inhibitor in plants that can be used to probe the assembly, dynamics, and molecular functions of the spliceosome and to study the interplay between splicing stress and abiotic stresses, as well as having potential biotechnological applications. Electronic supplementary material The online version of this article (doi:10.1186/s12864-017-3656-z) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Sahar AlShareef
- Laboratory for Genome Engineering, Division of Biological Sciences, 4700 King Abdullah University of Science and Technology, Thuwal, 23955-6900, Saudi Arabia
| | - Yu Ling
- Laboratory for Genome Engineering, Division of Biological Sciences, 4700 King Abdullah University of Science and Technology, Thuwal, 23955-6900, Saudi Arabia
| | - Haroon Butt
- Laboratory for Genome Engineering, Division of Biological Sciences, 4700 King Abdullah University of Science and Technology, Thuwal, 23955-6900, Saudi Arabia
| | - Kiruthiga G Mariappan
- Laboratory for Genome Engineering, Division of Biological Sciences, 4700 King Abdullah University of Science and Technology, Thuwal, 23955-6900, Saudi Arabia
| | - Moussa Benhamed
- Laboratory for Genome Engineering, Division of Biological Sciences, 4700 King Abdullah University of Science and Technology, Thuwal, 23955-6900, Saudi Arabia
| | - Magdy M Mahfouz
- Laboratory for Genome Engineering, Division of Biological Sciences, 4700 King Abdullah University of Science and Technology, Thuwal, 23955-6900, Saudi Arabia.
| |
Collapse
|
358
|
Lee YH, Hsueh YW, Peng YH, Chang KC, Tsai KJ, Sun HS, Su IJ, Chiang PM. Low-cell-number, single-tube amplification (STA) of total RNA revealed transcriptome changes from pluripotency to endothelium. BMC Biol 2017; 15:22. [PMID: 28327113 PMCID: PMC5360049 DOI: 10.1186/s12915-017-0359-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2017] [Accepted: 02/15/2017] [Indexed: 12/24/2022] Open
Abstract
Background In addition to messenger RNA (mRNA), noncoding RNAs (ncRNAs) are essential components in cellular machineries for translation and splicing. Besides their housekeeping functions, ncRNAs are involved in cell type-specific regulation of translation, mRNA stability, genome structure, and accessibility. To have a comprehensive understanding of the identities and functions of different cell types, a method to comprehensively quantify both mRNA and ncRNA in a sensitive manner is highly desirable. Methods Here we tried to develop a system capable of concurrently profiling both mRNA and ncRNA by polyadenylating RNA in samples before reverse transcription. The sensitivity of the system was maximized by avoiding purification from cell lysis to amplified cDNA and by optimizing the buffer conditions. The single-tube amplification (STA) system was applied to single to 100 cells of 293T cells, human pluripotent stem cells (hPSCs) and their differentiated endothelial progenies to validate its quantitative power and sensitivity by qPCR and high-throughput sequencing. Results Using microRNA (miRNA) as an example, we showed that complementary DNA (cDNA) from ncRNAs could be amplified and specifically detected from a few cells within a single tube. The sensitivity of the system was maximized by avoiding purification from cell lysis to amplified cDNA and by optimizing the buffer conditions. With 100 human embryonic stem cells (hESCs) and their differentiated endothelial cells as input for high-throughput sequencing, the single-tube amplification (STA) system revealed both well-known and other miRNAs selectively enriched in each cell type. The selective enrichment of the miRNAs was further verified by qPCR with 293FT cells and a human induced pluripotent stem cell (hiPSC) line. In addition, the detection of other non-miRNA transcripts indicated that the STA target was not limited to miRNA, but extended to other ncRNAs and mRNAs as well. Finally, the STA system was capable of detecting miRNA and mRNA expression down to single cells, albeit with some loss of sensitivity and power. Conclusions Overall, STA offered a simple and sensitive way to concurrently quantify both mRNA and ncRNA expression in low-cell-number samples for both qPCR and high-throughput sequencing. Electronic supplementary material The online version of this article (doi:10.1186/s12915-017-0359-5) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Yi-Hsuan Lee
- Department of Pathology, National Taiwan University Hospital, Taipei, Taiwan
| | - Ya-Wen Hsueh
- Institute of Clinical Medicine, College of Medicine, National Cheng Kung University, No. 35, Xiaodong Rd, Tainan, 70457, Taiwan
| | - Yao-Hung Peng
- Institute of Clinical Medicine, College of Medicine, National Cheng Kung University, No. 35, Xiaodong Rd, Tainan, 70457, Taiwan
| | - Kung-Chao Chang
- Department of Pathology, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Kuen-Jer Tsai
- Institute of Clinical Medicine, College of Medicine, National Cheng Kung University, No. 35, Xiaodong Rd, Tainan, 70457, Taiwan
| | - H Sunny Sun
- Institute of Molecular Medicine, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Ih-Jen Su
- Division of Infectious Diseases, National Health Research Institutes, Tainan, Taiwan
| | - Po-Min Chiang
- Institute of Clinical Medicine, College of Medicine, National Cheng Kung University, No. 35, Xiaodong Rd, Tainan, 70457, Taiwan.
| |
Collapse
|
359
|
Tsuzuki M, Motomura K, Kumakura N, Takeda A. Interconnections between mRNA degradation and RDR-dependent siRNA production in mRNA turnover in plants. JOURNAL OF PLANT RESEARCH 2017; 130:211-226. [PMID: 28197782 DOI: 10.1007/s10265-017-0906-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/24/2016] [Accepted: 12/08/2016] [Indexed: 06/06/2023]
Abstract
Accumulation of an mRNA species is determined by the balance between the synthesis and the degradation of the mRNA. Individual mRNA molecules are selectively and actively degraded through RNA degradation pathways, which include 5'-3' mRNA degradation pathway, 3'-5' mRNA degradation pathway, and RNA-dependent RNA polymerase-mediated mRNA degradation pathway. Recent studies have revealed that these RNA degradation pathways compete with each other in mRNA turnover in plants and that plants have a hidden layer of non-coding small-interfering RNA production from a set of mRNAs. In this review, we summarize the current information about plant mRNA degradation pathways in mRNA turnover and discuss the potential roles of a novel class of the endogenous siRNAs derived from plant mRNAs.
Collapse
Affiliation(s)
- Masayuki Tsuzuki
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, Tokyo, 153-8902, Japan
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Kazuki Motomura
- Institute of Transformative Bio-Molecules, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi, 464-8601, Japan
| | - Naoyoshi Kumakura
- Center for Sustainable Resource Science, RIKEN, Suehiro-cho 1-7-22, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan
| | - Atsushi Takeda
- Department of Biotechnology, Graduate School of Life Sciences, Ritsumeikan University, Shiga, 525-8577, Japan.
| |
Collapse
|
360
|
Rajpathak SN, Deobagkar DD. Micro RNAs and DNA methylation are regulatory players in human cells with altered X chromosome to autosome balance. Sci Rep 2017; 7:43235. [PMID: 28233878 PMCID: PMC5324395 DOI: 10.1038/srep43235] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2016] [Accepted: 01/20/2017] [Indexed: 01/04/2023] Open
Abstract
The gene balance hypothesis predicts that an imbalance in the dosage sensitive genes affects the cascade of gene networks that may influence the fitness of individuals. The phenotypes associated with chromosomal aneuploidies demonstrate the importance of gene dosage balance. We have employed untransformed human fibroblast cells with different number of X chromosomes to assess the expression of miRNAs and autosomal genes in addition to the DNA methylation status. High throughput NGS analysis using illumina Next seq500 has detected several autosomal as well as X linked miRNAs as differentially expressed in X monosomy and trisomy cells. Two of these miRNAs (hsa-miR-125a-5p and 335-5p) are likely to be involved in regulation of the autosomal gene expression. Additionally, our data demonstrates altered expression and DNA methylation signatures of autosomal genes in X monosomy and trisomy cells. In addition to miRNAs, expression of DNMT1 which is an important epigenetic player involved in many processes including cancer, is seen to be altered. Overall, present study provides a proof for regulatory roles of micro RNAs and DNA methylation in human X aneuploidy cells opening up possible new ways for designing therapeutic strategies.
Collapse
Affiliation(s)
- Shriram N Rajpathak
- Centre for Advanced Studies, Department of Zoology, Savitribai Phule Pune University, Pune 411007, India
| | - Deepti D Deobagkar
- Centre for Advanced Studies, Department of Zoology, Savitribai Phule Pune University, Pune 411007, India.,Bioinformatics Center, Savitribai Phule Pune University, Pune 411007, India
| |
Collapse
|
361
|
Shen EM, Singh SK, Ghosh JS, Patra B, Paul P, Yuan L, Pattanaik S. The miRNAome of Catharanthus roseus: identification, expression analysis, and potential roles of microRNAs in regulation of terpenoid indole alkaloid biosynthesis. Sci Rep 2017; 7:43027. [PMID: 28223695 PMCID: PMC5320439 DOI: 10.1038/srep43027] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2016] [Accepted: 01/18/2017] [Indexed: 12/02/2022] Open
Abstract
MicroRNAs (miRNAs) regulate numerous crucial biological processes in plants. However, information is limited on their involvement in the biosynthesis of specialized metabolites in plants, including Catharanthus roseus that produces a number of pharmaceutically valuable, bioactive terpenoid indole alkaloids (TIAs). Using small RNA-sequencing, we identified 181 conserved and 173 novel miRNAs (cro-miRNAs) in C. roseus seedlings. Genome-wide expression analysis revealed that a set of cro-miRNAs are differentially regulated in response to methyl jasmonate (MeJA). In silico target prediction identified 519 potential cro-miRNA targets that include several auxin response factors (ARFs). The presence of cleaved transcripts of miRNA-targeted ARFs in C. roseus cells was confirmed by Poly(A) Polymerase-Mediated Rapid Amplification of cDNA Ends (PPM-RACE). We showed that auxin (indole acetic acid, IAA) repressed the expression of key TIA pathway genes in C. roseus seedlings. Moreover, we demonstrated that a miRNA-regulated ARF, CrARF16, binds to the promoters of key TIA pathway genes and repress their expression. The C. roseus miRNAome reported here provides a comprehensive account of the cro-miRNA populations, as well as their abundance and expression profiles in response to MeJA. In addition, our findings underscore the importance of miRNAs in posttranscriptional control of the biosynthesis of specialized metabolites.
Collapse
Affiliation(s)
- Ethan M Shen
- Department of Plant and Soil Sciences, University of Kentucky, 1401 University Drive, Lexington, KY 40546, USA.,Math, Science, and Technology Center, Paul Laurence Dunbar High School, 1600 Man o' War Boulevard, Lexington, KY 40513, USA
| | - Sanjay K Singh
- Department of Plant and Soil Sciences, University of Kentucky, 1401 University Drive, Lexington, KY 40546, USA
| | - Jayadri S Ghosh
- Department of Plant and Soil Sciences, University of Kentucky, 1401 University Drive, Lexington, KY 40546, USA
| | - Barunava Patra
- Department of Plant and Soil Sciences, University of Kentucky, 1401 University Drive, Lexington, KY 40546, USA
| | - Priyanka Paul
- Department of Plant and Soil Sciences, University of Kentucky, 1401 University Drive, Lexington, KY 40546, USA
| | - Ling Yuan
- Department of Plant and Soil Sciences, University of Kentucky, 1401 University Drive, Lexington, KY 40546, USA
| | - Sitakanta Pattanaik
- Department of Plant and Soil Sciences, University of Kentucky, 1401 University Drive, Lexington, KY 40546, USA
| |
Collapse
|
362
|
Mishra N, Friedson L, Hanin G, Bekenstein U, Volovich M, Bennett ER, Greenberg DS, Soreq H. Antisense miR-132 blockade via the AChE-R splice variant mitigates cortical inflammation. Sci Rep 2017; 7:42755. [PMID: 28209997 PMCID: PMC5314396 DOI: 10.1038/srep42755] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2016] [Accepted: 01/12/2017] [Indexed: 01/05/2023] Open
Abstract
MicroRNA (miR)-132 brain-to-body messages suppress inflammation by targeting acetylcholinesterase (AChE), but the target specificity of 3'-AChE splice variants and the signaling pathways involved remain unknown. Using surface plasmon resonance (SPR), we identified preferential miR-132 targeting of soluble AChE-R over synaptic-bound AChE-S, potentiating miR-132-mediated brain and body cholinergic suppression of pro-inflammatory cytokines. Inversely, bacterial lipopolysaccharide (LPS) reduced multiple miR-132 targets, suppressed AChE-S more than AChE-R and elevated inflammatory hallmarks. Furthermore, blockade of peripheral miR-132 by chemically protected AM132 antisense oligonucleotide elevated muscle AChE-R 10-fold over AChE-S, and cortical miRNA-sequencing demonstrated inverse brain changes by AM132 and LPS in immune-related miRs and neurotransmission and cholinergic signaling pathways. In neuromuscular junctions, AM132 co-elevated the nicotinic acetylcholine receptor and AChE, re-balancing neurotransmission and reaching mild muscle incoordination. Our findings demonstrate preferential miR-132-induced modulation of AChE-R which ignites bidirectional brain and body anti-inflammatory regulation, underscoring splice-variant miR-132 specificity as a new complexity level in inflammatory surveillance.
Collapse
Affiliation(s)
- Nibha Mishra
- The Edmond and Lily Safra Center for Brain Sciences, The Hebrew University of Jerusalem, The Edmond Safra Campus, Givat Ram, Jerusalem 9190401, Israel
- The Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, The Edmond Safra Campus, Givat Ram, Jerusalem 9190401, Israel
| | - Lyndon Friedson
- The Edmond and Lily Safra Center for Brain Sciences, The Hebrew University of Jerusalem, The Edmond Safra Campus, Givat Ram, Jerusalem 9190401, Israel
- The Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, The Edmond Safra Campus, Givat Ram, Jerusalem 9190401, Israel
| | - Geula Hanin
- The Edmond and Lily Safra Center for Brain Sciences, The Hebrew University of Jerusalem, The Edmond Safra Campus, Givat Ram, Jerusalem 9190401, Israel
- The Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, The Edmond Safra Campus, Givat Ram, Jerusalem 9190401, Israel
| | - Uriya Bekenstein
- The Edmond and Lily Safra Center for Brain Sciences, The Hebrew University of Jerusalem, The Edmond Safra Campus, Givat Ram, Jerusalem 9190401, Israel
- The Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, The Edmond Safra Campus, Givat Ram, Jerusalem 9190401, Israel
| | - Meshi Volovich
- The Edmond and Lily Safra Center for Brain Sciences, The Hebrew University of Jerusalem, The Edmond Safra Campus, Givat Ram, Jerusalem 9190401, Israel
| | - Estelle R. Bennett
- The Edmond and Lily Safra Center for Brain Sciences, The Hebrew University of Jerusalem, The Edmond Safra Campus, Givat Ram, Jerusalem 9190401, Israel
- The Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, The Edmond Safra Campus, Givat Ram, Jerusalem 9190401, Israel
| | - David S. Greenberg
- The Edmond and Lily Safra Center for Brain Sciences, The Hebrew University of Jerusalem, The Edmond Safra Campus, Givat Ram, Jerusalem 9190401, Israel
- The Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, The Edmond Safra Campus, Givat Ram, Jerusalem 9190401, Israel
| | - Hermona Soreq
- The Edmond and Lily Safra Center for Brain Sciences, The Hebrew University of Jerusalem, The Edmond Safra Campus, Givat Ram, Jerusalem 9190401, Israel
- The Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, The Edmond Safra Campus, Givat Ram, Jerusalem 9190401, Israel
| |
Collapse
|
363
|
Transcriptome profiling of Galaxea fascicularis and its endosymbiont Symbiodinium reveals chronic eutrophication tolerance pathways and metabolic mutualism between partners. Sci Rep 2017; 7:42100. [PMID: 28181581 PMCID: PMC5299600 DOI: 10.1038/srep42100] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2016] [Accepted: 01/06/2017] [Indexed: 01/10/2023] Open
Abstract
In the South China Sea, coastal eutrophication in the Beibu Gulf has seriously threatened reef habitats by subjecting corals to chronic physiological stress. To determine how coral holobionts may tolerate such conditions, we examined the transcriptomes of healthy colonies of the galaxy coral Galaxea fascicularis and its endosymbiont Symbiodinium from two reef sites experiencing pristine or eutrophied nutrient regimes. We identified 236 and 205 genes that were differentially expressed in eutrophied hosts and symbionts, respectively. Both gene sets included pathways related to stress responses and metabolic interactions. An analysis of genes originating from each partner revealed striking metabolic integration with respect to vitamins, cofactors, amino acids, fatty acids, and secondary metabolite biosynthesis. The expression levels of these genes supported the existence of a continuum of mutualism in this coral-algal symbiosis. Additionally, large sets of transcription factors, cell signal transduction molecules, biomineralization components, and galaxin-related proteins were expanded in G. fascicularis relative to other coral species.
Collapse
|
364
|
Gershoni M, Pietrokovski S. The landscape of sex-differential transcriptome and its consequent selection in human adults. BMC Biol 2017; 15:7. [PMID: 28173793 PMCID: PMC5297171 DOI: 10.1186/s12915-017-0352-z] [Citation(s) in RCA: 149] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2016] [Accepted: 01/19/2017] [Indexed: 01/08/2023] Open
Abstract
BACKGROUND The prevalence of several human morbid phenotypes is sometimes much higher than intuitively expected. This can directly arise from the presence of two sexes, male and female, in one species. Men and women have almost identical genomes but are distinctly dimorphic, with dissimilar disease susceptibilities. Sexually dimorphic traits mainly result from differential expression of genes present in both sexes. Such genes can be subject to different, and even opposing, selection constraints in the two sexes. This can impact human evolution by differential selection on mutations with dissimilar effects on the two sexes. RESULTS We comprehensively mapped human sex-differential genetic architecture across 53 tissues. Analyzing available RNA-sequencing data from 544 adults revealed thousands of genes differentially expressed in the reproductive tracts and tissues common to both sexes. Sex-differential genes are related to various biological systems, and suggest new insights into the pathophysiology of diverse human diseases. We also identified a significant association between sex-specific gene transcription and reduced selection efficiency and accumulation of deleterious mutations, which might affect the prevalence of different traits and diseases. Interestingly, many of the sex-specific genes that also undergo reduced selection efficiency are essential for successful reproduction in men or women. This seeming paradox might partially explain the high incidence of human infertility. CONCLUSIONS This work provides a comprehensive overview of the sex-differential transcriptome and its importance to human evolution and human physiology in health and in disease.
Collapse
Affiliation(s)
- Moran Gershoni
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Shmuel Pietrokovski
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| |
Collapse
|
365
|
Nguyen CC, Nakaminami K, Matsui A, Watanabe S, Kanno Y, Seo M, Seki M. Overexpression of oligouridylate binding protein 1b results in ABA hypersensitivity. PLANT SIGNALING & BEHAVIOR 2017; 12:e1282591. [PMID: 28112571 PMCID: PMC5351729 DOI: 10.1080/15592324.2017.1282591] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Oligouridylate binding protein 1b (UBP1b), a marker protein of plant stress granules (SGs), plays a role in heat stress tolerance in plants. A previous microarray analysis revealed that the expression of several ABA signaling-related genes is higher in UBP1b-overexpressing Arabidopsis plants (UBP1b-ox) subjected to both non-stressed and heat stress conditions. Root elongation and seed germination assays demonstrated that UBP1b-ox exhibited hypersensitivity to ABA. RT-qPCR analysis confirmed that mitogen-activated protein kinase (MAPK) cascade genes, such as MPK3, MKK4, and MKK9 were upregulated in UBP1b-ox plants. ABA receptor genes, including PYL5 and PYL6, were also upregulated in UBP1b-ox plants. mRNA of WRKY33 - a downstream gene of MPK3 and an upstream gene of ethylene biosynthesis, exhibited high levels of accumulation, although the level of endogenous ABA was not significantly different between UBP1b-ox and control plants. In addition, RNA decay analysis revealed that WRKY33 was more stable in UBP1b-ox plants, indicating that the mRNA of WRKY33 was protected within UBP1b SGs. Collectively, these data demonstrate that UBP1b plays an important role in plant response to ABA.
Collapse
Affiliation(s)
- Cam Chau Nguyen
- Plant Genomic Network Research Team, RIKEN Center for Sustainable Resource Science (CSRS), Yokohama, Kanagawa, Japan
- Kihara Institute for Biological Research, Yokohama City University, Yokohama, Kanagawa, Japan
| | - Kentaro Nakaminami
- Plant Genomic Network Research Team, RIKEN Center for Sustainable Resource Science (CSRS), Yokohama, Kanagawa, Japan
| | - Akihiro Matsui
- Plant Genomic Network Research Team, RIKEN Center for Sustainable Resource Science (CSRS), Yokohama, Kanagawa, Japan
| | - Shunsuke Watanabe
- Dormancy and Adaptation Research Unit, RIKEN Center for Sustainable Resource Science (CSRS), Yokohama, Kanagawa, Japan
| | - Yuri Kanno
- Dormancy and Adaptation Research Unit, RIKEN Center for Sustainable Resource Science (CSRS), Yokohama, Kanagawa, Japan
| | - Mitsunori Seo
- Dormancy and Adaptation Research Unit, RIKEN Center for Sustainable Resource Science (CSRS), Yokohama, Kanagawa, Japan
| | - Motoaki Seki
- Plant Genomic Network Research Team, RIKEN Center for Sustainable Resource Science (CSRS), Yokohama, Kanagawa, Japan
- Kihara Institute for Biological Research, Yokohama City University, Yokohama, Kanagawa, Japan
- CREST, JST, Honcho, Kawaguchi, Saitama, Japan
- CONTACT Motoaki Seki Plant Genomic Network Research Team, RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| |
Collapse
|
366
|
Deng X, Cao X. Roles of pre-mRNA splicing and polyadenylation in plant development. CURRENT OPINION IN PLANT BIOLOGY 2017; 35:45-53. [PMID: 27866125 DOI: 10.1016/j.pbi.2016.11.003] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2016] [Revised: 11/01/2016] [Accepted: 11/03/2016] [Indexed: 05/20/2023]
Abstract
Plants possess amazing plasticity of growth and development, allowing them to adjust continuously and rapidly to changes in the environment. Over the past two decades, numerous molecular studies have illuminated the role of transcriptional regulation in plant development and environmental responses. However, emerging studies in Arabidopsis have uncovered an unexpectedly widespread role for post-transcriptional regulation in development and responses to environmental changes. In this review, we summarize recent discoveries detailing the contribution of two post-transcriptional mechanisms, pre-mRNA splicing and polyadenylation, to the regulation of plant development, with an emphasis on the control of flowering time. We also discuss future directions in the field and new technological approaches.
Collapse
Affiliation(s)
- Xian Deng
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, CAS Center for Excellence in Molecular Plant Sciences, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Xiaofeng Cao
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, CAS Center for Excellence in Molecular Plant Sciences, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China.
| |
Collapse
|
367
|
Collado-Torres L, Nellore A, Frazee AC, Wilks C, Love MI, Langmead B, Irizarry RA, Leek JT, Jaffe AE. Flexible expressed region analysis for RNA-seq with derfinder. Nucleic Acids Res 2017; 45:e9. [PMID: 27694310 PMCID: PMC5314792 DOI: 10.1093/nar/gkw852] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2016] [Revised: 08/25/2016] [Accepted: 09/15/2016] [Indexed: 12/20/2022] Open
Abstract
Differential expression analysis of RNA sequencing (RNA-seq) data typically relies on reconstructing transcripts or counting reads that overlap known gene structures. We previously introduced an intermediate statistical approach called differentially expressed region (DER) finder that seeks to identify contiguous regions of the genome showing differential expression signal at single base resolution without relying on existing annotation or potentially inaccurate transcript assembly.We present the derfinder software that improves our annotation-agnostic approach to RNA-seq analysis by: (i) implementing a computationally efficient bump-hunting approach to identify DERs that permits genome-scale analyses in a large number of samples, (ii) introducing a flexible statistical modeling framework, including multi-group and time-course analyses and (iii) introducing a new set of data visualizations for expressed region analysis. We apply this approach to public RNA-seq data from the Genotype-Tissue Expression (GTEx) project and BrainSpan project to show that derfinder permits the analysis of hundreds of samples at base resolution in R, identifies expression outside of known gene boundaries and can be used to visualize expressed regions at base-resolution. In simulations, our base resolution approaches enable discovery in the presence of incomplete annotation and is nearly as powerful as feature-level methods when the annotation is complete.derfinder analysis using expressed region-level and single base-level approaches provides a compromise between full transcript reconstruction and feature-level analysis. The package is available from Bioconductor at www.bioconductor.org/packages/derfinder.
Collapse
Affiliation(s)
- Leonardo Collado-Torres
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA
- Center for Computational Biology, Johns Hopkins University, Baltimore, MD 21205, USA
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD 21205, USA
| | - Abhinav Nellore
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA
- Center for Computational Biology, Johns Hopkins University, Baltimore, MD 21205, USA
- Department of Computer Science, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Alyssa C Frazee
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA
- Center for Computational Biology, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Christopher Wilks
- Center for Computational Biology, Johns Hopkins University, Baltimore, MD 21205, USA
- Department of Computer Science, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Michael I Love
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
- Dana-Farber Cancer Institute, Harvard University, Boston, MA 02215, USA
| | - Ben Langmead
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA
- Center for Computational Biology, Johns Hopkins University, Baltimore, MD 21205, USA
- Department of Computer Science, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Rafael A Irizarry
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
- Dana-Farber Cancer Institute, Harvard University, Boston, MA 02215, USA
| | - Jeffrey T Leek
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA
- Center for Computational Biology, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Andrew E Jaffe
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA
- Center for Computational Biology, Johns Hopkins University, Baltimore, MD 21205, USA
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD 21205, USA
- Department of Mental Health, Johns Hopkins University, Baltimore, MD 21205, USA
| |
Collapse
|
368
|
Riege K, Hölzer M, Klassert TE, Barth E, Bräuer J, Collatz M, Hufsky F, Mostajo N, Stock M, Vogel B, Slevogt H, Marz M. Massive Effect on LncRNAs in Human Monocytes During Fungal and Bacterial Infections and in Response to Vitamins A and D. Sci Rep 2017; 7:40598. [PMID: 28094339 PMCID: PMC5240112 DOI: 10.1038/srep40598] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2016] [Accepted: 12/06/2016] [Indexed: 02/08/2023] Open
Abstract
Mycoses induced by C.albicans or A.fumigatus can cause important host damage either by deficient or exaggerated immune response. Regulation of chemokine and cytokine signaling plays a crucial role for an adequate inflammation, which can be modulated by vitamins A and D. Non-coding RNAs (ncRNAs) as transcription factors or cis-acting antisense RNAs are known to be involved in gene regulation. However, the processes during fungal infections and treatment with vitamins in terms of therapeutic impact are unknown. We show that in monocytes both vitamins regulate ncRNAs involved in amino acid metabolism and immune system processes using comprehensive RNA-Seq analyses. Compared to protein-coding genes, fungi and bacteria induced an expression change in relatively few ncRNAs, but with massive fold changes of up to 4000. We defined the landscape of long-ncRNAs (lncRNAs) in response to pathogens and observed variation in the isoforms composition for several lncRNA following infection and vitamin treatment. Most of the involved antisense RNAs are regulated and positively correlated with their sense protein-coding genes. We investigated lncRNAs with stimulus specific immunomodulatory activity as potential marker genes: LINC00595, SBF2-AS1 (A.fumigatus) and RP11-588G21.2, RP11-394l13.1 (C.albicans) might be detectable in the early phase of infection and serve as therapeutic targets in the future.
Collapse
Affiliation(s)
- Konstantin Riege
- Friedrich Schiller University, Bioinformatics/High Throughput Analysis, Jena, 07743, Germany
| | - Martin Hölzer
- Friedrich Schiller University, Bioinformatics/High Throughput Analysis, Jena, 07743, Germany
| | - Tilman E Klassert
- Jena University Hospital, Septomics Research Center, Jena, 07745, Germany
| | - Emanuel Barth
- Friedrich Schiller University, Bioinformatics/High Throughput Analysis, Jena, 07743, Germany.,FLI Leibniz Institute for Age Research, 07745 Jena, Germany
| | - Julia Bräuer
- Jena University Hospital, Septomics Research Center, Jena, 07745, Germany
| | - Maximilian Collatz
- Friedrich Schiller University, Bioinformatics/High Throughput Analysis, Jena, 07743, Germany.,Institute of Virology, Philipps-University Marburg, 35043 Marburg, Germany
| | - Franziska Hufsky
- Friedrich Schiller University, Bioinformatics/High Throughput Analysis, Jena, 07743, Germany.,Chair of Bioinformatics, Friedrich-Schiller-University Jena, 07743 Jena, Germany
| | - Nelly Mostajo
- Friedrich Schiller University, Bioinformatics/High Throughput Analysis, Jena, 07743, Germany.,Institute of Virology, Philipps-University Marburg, 35043 Marburg, Germany
| | - Magdalena Stock
- Jena University Hospital, Septomics Research Center, Jena, 07745, Germany
| | - Bertram Vogel
- Friedrich Schiller University, Bioinformatics/High Throughput Analysis, Jena, 07743, Germany.,Institute of Virology, Philipps-University Marburg, 35043 Marburg, Germany
| | - Hortense Slevogt
- Jena University Hospital, Septomics Research Center, Jena, 07745, Germany
| | - Manja Marz
- Friedrich Schiller University, Bioinformatics/High Throughput Analysis, Jena, 07743, Germany.,FLI Leibniz Institute for Age Research, 07745 Jena, Germany
| |
Collapse
|
369
|
van der Velde KJ, de Boer EN, van Diemen CC, Sikkema-Raddatz B, Abbott KM, Knopperts A, Franke L, Sijmons RH, de Koning TJ, Wijmenga C, Sinke RJ, Swertz MA. GAVIN: Gene-Aware Variant INterpretation for medical sequencing. Genome Biol 2017; 18:6. [PMID: 28093075 PMCID: PMC5240400 DOI: 10.1186/s13059-016-1141-7] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2016] [Accepted: 12/19/2016] [Indexed: 01/08/2023] Open
Abstract
We present Gene-Aware Variant INterpretation (GAVIN), a new method that accurately classifies variants for clinical diagnostic purposes. Classifications are based on gene-specific calibrations of allele frequencies from the ExAC database, likely variant impact using SnpEff, and estimated deleteriousness based on CADD scores for >3000 genes. In a benchmark on 18 clinical gene sets, we achieve a sensitivity of 91.4% and a specificity of 76.9%. This accuracy is unmatched by 12 other tools. We provide GAVIN as an online MOLGENIS service to annotate VCF files and as an open source executable for use in bioinformatic pipelines. It can be found at http://molgenis.org/gavin.
Collapse
Affiliation(s)
- K Joeri van der Velde
- University of Groningen, University Medical Center Groningen, Genomics Coordination Center, Groningen, The Netherlands.,Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Eddy N de Boer
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Cleo C van Diemen
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Birgit Sikkema-Raddatz
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Kristin M Abbott
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Alain Knopperts
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Lude Franke
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Rolf H Sijmons
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Tom J de Koning
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Cisca Wijmenga
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Richard J Sinke
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Morris A Swertz
- University of Groningen, University Medical Center Groningen, Genomics Coordination Center, Groningen, The Netherlands. .,Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands.
| |
Collapse
|
370
|
Rodriguez-Lujan I, Hasty J, Huerta R. FBB: a fast Bayesian-bound tool to calibrate RNA-seq aligners. Bioinformatics 2017; 33:210-218. [DOI: 10.1093/bioinformatics/btw608] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2016] [Revised: 09/08/2016] [Accepted: 09/16/2016] [Indexed: 11/12/2022] Open
|
371
|
Ling Y, Alshareef S, Butt H, Lozano-Juste J, Li L, Galal AA, Moustafa A, Momin AA, Tashkandi M, Richardson DN, Fujii H, Arold S, Rodriguez PL, Duque P, Mahfouz MM. Pre-mRNA splicing repression triggers abiotic stress signaling in plants. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2017; 89:291-309. [PMID: 27664942 DOI: 10.1111/tpj.13383] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2016] [Revised: 09/15/2016] [Accepted: 09/21/2016] [Indexed: 05/24/2023]
Abstract
Alternative splicing (AS) of precursor RNAs enhances transcriptome plasticity and proteome diversity in response to diverse growth and stress cues. Recent work has shown that AS is pervasive across plant species, with more than 60% of intron-containing genes producing different isoforms. Mammalian cell-based assays have discovered various inhibitors of AS. Here, we show that the macrolide pladienolide B (PB) inhibits constitutive splicing and AS in plants. Also, our RNA sequencing (RNA-seq) data revealed that PB mimics abiotic stress signals including salt, drought and abscisic acid (ABA). PB activates the abiotic stress- and ABA-responsive reporters RD29A::LUC and MAPKKK18::uidA in Arabidopsis thaliana and mimics the effects of ABA on stomatal aperture. Genome-wide analysis of AS by RNA-seq revealed that PB perturbs the splicing machinery and leads to a striking increase in intron retention and a reduction in other forms of AS. Interestingly, PB treatment activates the ABA signaling pathway by inhibiting the splicing of clade A PP2C phosphatases while still maintaining to some extent the splicing of ABA-activated SnRK2 kinases. Taken together, our data establish PB as an inhibitor and modulator of splicing and a mimic of abiotic stress signals in plants. Thus, PB reveals the molecular underpinnings of the interplay between stress responses, ABA signaling and post-transcriptional regulation in plants.
Collapse
Affiliation(s)
- Yu Ling
- Laboratory for Genome Engineering, Division of Biological Sciences, 4700 King Abdullah University of Science and Technology, Thuwal, 23955-6900, Saudi Arabia
| | - Sahar Alshareef
- Laboratory for Genome Engineering, Division of Biological Sciences, 4700 King Abdullah University of Science and Technology, Thuwal, 23955-6900, Saudi Arabia
| | - Haroon Butt
- Laboratory for Genome Engineering, Division of Biological Sciences, 4700 King Abdullah University of Science and Technology, Thuwal, 23955-6900, Saudi Arabia
| | - Jorge Lozano-Juste
- Instituto de Biologia Molecular y Celular de Plantas, Consejo Superior de Investigaciones Cientificas-Universidad Politecnica de Valencia, ES-46022, Valencia, Spain
| | - Lixin Li
- Laboratory for Genome Engineering, Division of Biological Sciences, 4700 King Abdullah University of Science and Technology, Thuwal, 23955-6900, Saudi Arabia
| | - Aya A Galal
- Department of Biology and Biotechnology Graduate Program, American University in Cairo, New Cairo, 11835, Egypt
| | - Ahmed Moustafa
- Department of Biology and Biotechnology Graduate Program, American University in Cairo, New Cairo, 11835, Egypt
| | - Afaque A Momin
- Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal, 23955-6900, Saudi Arabia
| | - Manal Tashkandi
- Laboratory for Genome Engineering, Division of Biological Sciences, 4700 King Abdullah University of Science and Technology, Thuwal, 23955-6900, Saudi Arabia
| | - Dale N Richardson
- Instituto Gulbenkian de Ciência, Rua da Quinta Grande 6, 2780-156, Oeiras, Portugal
| | - Hiroaki Fujii
- Molecular Plant Biology, Department of Biochemistry, University of Turku, FI-20014, Turku, Finland
| | - Stefan Arold
- Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal, 23955-6900, Saudi Arabia
| | - Pedro L Rodriguez
- Instituto de Biologia Molecular y Celular de Plantas, Consejo Superior de Investigaciones Cientificas-Universidad Politecnica de Valencia, ES-46022, Valencia, Spain
| | - Paula Duque
- Instituto Gulbenkian de Ciência, Rua da Quinta Grande 6, 2780-156, Oeiras, Portugal
| | - Magdy M Mahfouz
- Laboratory for Genome Engineering, Division of Biological Sciences, 4700 King Abdullah University of Science and Technology, Thuwal, 23955-6900, Saudi Arabia
| |
Collapse
|
372
|
Consiglio A, Mencar C, Grillo G, Marzano F, Caratozzolo MF, Liuni S. A fuzzy method for RNA-Seq differential expression analysis in presence of multireads. BMC Bioinformatics 2016; 17:345. [PMID: 28185579 PMCID: PMC5123383 DOI: 10.1186/s12859-016-1195-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
Background When the reads obtained from high-throughput RNA sequencing are mapped against a reference database, a significant proportion of them - known as multireads - can map to more than one reference sequence. These multireads originate from gene duplications, repetitive regions or overlapping genes. Removing the multireads from the mapping results, in RNA-Seq analyses, causes an underestimation of the read counts, while estimating the real read count can lead to false positives during the detection of differentially expressed sequences. Results We present an innovative approach to deal with multireads and evaluate differential expression events, entirely based on fuzzy set theory. Since multireads cause uncertainty in the estimation of read counts during gene expression computation, they can also influence the reliability of differential expression analysis results, by producing false positives. Our method manages the uncertainty in gene expression estimation by defining the fuzzy read counts and evaluates the possibility of a gene to be differentially expressed with three fuzzy concepts: over-expression, same-expression and under-expression. The output of the method is a list of differentially expressed genes enriched with information about the uncertainty of the results due to the multiread presence. We have tested the method on RNA-Seq data designed for case-control studies and we have compared the obtained results with other existing tools for read count estimation and differential expression analysis. Conclusions The management of multireads with the use of fuzzy sets allows to obtain a list of differential expression events which takes in account the uncertainty in the results caused by the presence of multireads. Such additional information can be used by the biologists when they have to select the most relevant differential expression events to validate with laboratory assays. Our method can be used to compute reliable differential expression events and to highlight possible false positives in the lists of differentially expressed genes computed with other tools. Electronic supplementary material The online version of this article (doi:10.1186/s12859-016-1195-2) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Arianna Consiglio
- Institute for Biomedical Technologies of Bari - ITB, National Research Council, Bari, 70126, Italy.
| | - Corrado Mencar
- Department of Informatics, University of Bari Aldo Moro, Bari, 70121, Italy
| | - Giorgio Grillo
- Institute for Biomedical Technologies of Bari - ITB, National Research Council, Bari, 70126, Italy
| | - Flaviana Marzano
- Institute for Biomedical Technologies of Bari - ITB, National Research Council, Bari, 70126, Italy
| | | | - Sabino Liuni
- Institute for Biomedical Technologies of Bari - ITB, National Research Council, Bari, 70126, Italy
| |
Collapse
|
373
|
Quigley KM, Willis BL, Bay LK. Maternal effects and Symbiodinium community composition drive differential patterns in juvenile survival in the coral Acropora tenuis. ROYAL SOCIETY OPEN SCIENCE 2016; 3:160471. [PMID: 27853562 PMCID: PMC5098987 DOI: 10.1098/rsos.160471] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2016] [Accepted: 09/12/2016] [Indexed: 05/24/2023]
Abstract
Coral endosymbionts in the dinoflagellate genus Symbiodinium are known to impact host physiology and have led to the evolution of reef-building, but less is known about how symbiotic communities in early life-history stages and their interactions with host parental identity shape the structure of coral communities on reefs. Differentiating the roles of environmental and biological factors driving variation in population demographic processes, particularly larval settlement, early juvenile survival and the onset of symbiosis is key to understanding how coral communities are structured and to predicting how they are likely to respond to climate change. We show that maternal effects (that here include genetic and/or effects related to the maternal environment) can explain nearly 24% of variation in larval settlement success and 5-17% of variation in juvenile survival in an experimental study of the reef-building scleractinian coral, Acropora tenuis. After 25 days on the reef, Symbiodinium communities associated with juvenile corals differed significantly between high mortality and low mortality families based on estimates of taxonomic richness, composition and relative abundance of taxa. Our results highlight that maternal and familial effects significantly explain variation in juvenile survival and symbiont communities in a broadcast-spawning coral, with Symbiodinium type A3 possibly a critical symbiotic partner during this early life stage.
Collapse
Affiliation(s)
- Kate M. Quigley
- College of Marine and Environmental Sciences, and ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, Queensland 4811, Australia
- AIMS@JCU, Australian Institute of Marine Science and James Cook University, Townsville, Queensland 4811, Australia
| | - Bette L. Willis
- College of Marine and Environmental Sciences, and ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, Queensland 4811, Australia
- AIMS@JCU, Australian Institute of Marine Science and James Cook University, Townsville, Queensland 4811, Australia
| | - Line K. Bay
- AIMS@JCU, Australian Institute of Marine Science and James Cook University, Townsville, Queensland 4811, Australia
- Australian Institute of Marine Science, PMB 3, Townsville, Queensland 4810, Australia
| |
Collapse
|
374
|
Quigley KM, Willis BL, Bay LK. Maternal effects and Symbiodinium community composition drive differential patterns in juvenile survival in the coral Acropora tenuis. ROYAL SOCIETY OPEN SCIENCE 2016. [PMID: 27853562 DOI: 10.5061/dryad.8b5g6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
Coral endosymbionts in the dinoflagellate genus Symbiodinium are known to impact host physiology and have led to the evolution of reef-building, but less is known about how symbiotic communities in early life-history stages and their interactions with host parental identity shape the structure of coral communities on reefs. Differentiating the roles of environmental and biological factors driving variation in population demographic processes, particularly larval settlement, early juvenile survival and the onset of symbiosis is key to understanding how coral communities are structured and to predicting how they are likely to respond to climate change. We show that maternal effects (that here include genetic and/or effects related to the maternal environment) can explain nearly 24% of variation in larval settlement success and 5-17% of variation in juvenile survival in an experimental study of the reef-building scleractinian coral, Acropora tenuis. After 25 days on the reef, Symbiodinium communities associated with juvenile corals differed significantly between high mortality and low mortality families based on estimates of taxonomic richness, composition and relative abundance of taxa. Our results highlight that maternal and familial effects significantly explain variation in juvenile survival and symbiont communities in a broadcast-spawning coral, with Symbiodinium type A3 possibly a critical symbiotic partner during this early life stage.
Collapse
Affiliation(s)
- Kate M Quigley
- College of Marine and Environmental Sciences, and ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, Queensland 4811, Australia; AIMS@JCU, Australian Institute of Marine Science and James Cook University, Townsville, Queensland 4811, Australia
| | - Bette L Willis
- College of Marine and Environmental Sciences, and ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, Queensland 4811, Australia; AIMS@JCU, Australian Institute of Marine Science and James Cook University, Townsville, Queensland 4811, Australia
| | - Line K Bay
- AIMS@JCU, Australian Institute of Marine Science and James Cook University, Townsville, Queensland 4811, Australia; Australian Institute of Marine Science, PMB 3, Townsville, Queensland 4810, Australia
| |
Collapse
|
375
|
Kawa D, Testerink C. Regulation of mRNA decay in plant responses to salt and osmotic stress. Cell Mol Life Sci 2016; 74:1165-1176. [PMID: 27677492 PMCID: PMC5346435 DOI: 10.1007/s00018-016-2376-x] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2016] [Revised: 09/09/2016] [Accepted: 09/21/2016] [Indexed: 11/24/2022]
Abstract
Plant acclimation to environmental stresses requires fast signaling to initiate changes in developmental and metabolic responses. Regulation of gene expression by transcription factors and protein kinases acting upstream are important elements of responses to salt and drought. Gene expression can be also controlled at the post-transcriptional level. Recent analyses on mutants in mRNA metabolism factors suggest their contribution to stress signaling. Here we highlight the components of mRNA decay pathways that contribute to responses to osmotic and salt stress. We hypothesize that phosphorylation state of proteins involved in mRNA decapping affect their substrate specificity.
Collapse
Affiliation(s)
- Dorota Kawa
- Plant Cell Biology, Swammerdam Institute for Life Sciences, University of Amsterdam, Postbus 94215, 1090 GE, Amsterdam, The Netherlands
| | - Christa Testerink
- Plant Cell Biology, Swammerdam Institute for Life Sciences, University of Amsterdam, Postbus 94215, 1090 GE, Amsterdam, The Netherlands.
| |
Collapse
|
376
|
Wyatt LE, Strickler SR, Mueller LA, Mazourek M. Comparative analysis of Cucurbita pepo metabolism throughout fruit development in acorn squash and oilseed pumpkin. HORTICULTURE RESEARCH 2016; 3:16045. [PMID: 27688889 PMCID: PMC5030761 DOI: 10.1038/hortres.2016.45] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2016] [Revised: 08/20/2016] [Accepted: 08/22/2016] [Indexed: 05/23/2023]
Abstract
Both the fruit mesocarp and the seeds of winter squash can be used for consumption, although the focus of breeding efforts varies by cultivar. Cultivars bred for fruit consumption are selected for fruit mesocarp quality traits such as carotenoid content, percent dry matter, and percent soluble solids, while these traits are essentially ignored in oilseed pumpkins. To compare fruit development in these two types of squash, we sequenced the fruit transcriptome of two cultivars bred for different purposes: an acorn squash, 'Sweet REBA', and an oilseed pumpkin, 'Lady Godiva'. Putative metabolic pathways were developed for carotenoid, starch, and sucrose synthesis in winter squash fruit and squash homologs were identified for each of the structural genes in the pathways. Gene expression, especially of known rate-limiting and branch point genes, corresponded with metabolite accumulation both across development and between the two cultivars. Thus, developmental regulation of metabolite genes is an important factor in winter squash fruit quality.
Collapse
Affiliation(s)
- Lindsay E Wyatt
- School of Integrative Plant Sciences, Section of Plant Breeding and Genetics, Cornell University, Ithaca, NY 14850, USA
| | | | - Lukas A Mueller
- Boyce Thompson Institute for Plant Research, Ithaca, NY 14853, USA
| | - Michael Mazourek
- School of Integrative Plant Sciences, Section of Plant Breeding and Genetics, Cornell University, Ithaca, NY 14850, USA
| |
Collapse
|
377
|
Najafova Z, Tirado-Magallanes R, Subramaniam M, Hossan T, Schmidt G, Nagarajan S, Baumgart SJ, Mishra VK, Bedi U, Hesse E, Knapp S, Hawse JR, Johnsen SA. BRD4 localization to lineage-specific enhancers is associated with a distinct transcription factor repertoire. Nucleic Acids Res 2016; 45:127-141. [PMID: 27651452 PMCID: PMC5224504 DOI: 10.1093/nar/gkw826] [Citation(s) in RCA: 79] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2016] [Revised: 09/05/2016] [Accepted: 09/08/2016] [Indexed: 12/14/2022] Open
Abstract
Proper temporal epigenetic regulation of gene expression is essential for cell fate determination and tissue development. The Bromodomain-containing Protein-4 (BRD4) was previously shown to control the transcription of defined subsets of genes in various cell systems. In this study we examined the role of BRD4 in promoting lineage-specific gene expression and show that BRD4 is essential for osteoblast differentiation. Genome-wide analyses demonstrate that BRD4 is recruited to the transcriptional start site of differentiation-induced genes. Unexpectedly, while promoter-proximal BRD4 occupancy correlated with gene expression, genes which displayed moderate expression and promoter-proximal BRD4 occupancy were most highly regulated and sensitive to BRD4 inhibition. Therefore, we examined distal BRD4 occupancy and uncovered a specific co-localization of BRD4 with the transcription factors C/EBPb, TEAD1, FOSL2 and JUND at putative osteoblast-specific enhancers. These findings reveal the intricacies of lineage specification and provide new insight into the context-dependent functions of BRD4.
Collapse
Affiliation(s)
- Zeynab Najafova
- Department of General, Visceral and Pediatric Surgery, University Medical Center Göttingen, 37075 Göttingen, Germany
| | - Roberto Tirado-Magallanes
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), CNRS, Inserm, Ecole Normale Supérieure, PSL Research University, F-75005 Paris, France
| | | | - Tareq Hossan
- Department of General, Visceral and Pediatric Surgery, University Medical Center Göttingen, 37075 Göttingen, Germany
| | - Geske Schmidt
- Department of General, Visceral and Pediatric Surgery, University Medical Center Göttingen, 37075 Göttingen, Germany
| | - Sankari Nagarajan
- Department of General, Visceral and Pediatric Surgery, University Medical Center Göttingen, 37075 Göttingen, Germany
| | - Simon J Baumgart
- Department of General, Visceral and Pediatric Surgery, University Medical Center Göttingen, 37075 Göttingen, Germany
| | - Vivek Kumar Mishra
- Department of General, Visceral and Pediatric Surgery, University Medical Center Göttingen, 37075 Göttingen, Germany
| | - Upasana Bedi
- Department of General, Visceral and Pediatric Surgery, University Medical Center Göttingen, 37075 Göttingen, Germany
| | - Eric Hesse
- Heisenberg-Group for Molecular Skeletal Biology, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany.,Department of Anatomy and Cell Biology, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Stefan Knapp
- Institute for Pharmaceutical Chemistry, Goethe-University Frankfurt, 60323 Frankfurt am Main, Germany.,Nuffield Department of Clinical Medicine, University of Oxford, Old Road Campus, Oxford OX3 7DQ, UK
| | - John R Hawse
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN 55905, USA
| | - Steven A Johnsen
- Department of General, Visceral and Pediatric Surgery, University Medical Center Göttingen, 37075 Göttingen, Germany
| |
Collapse
|
378
|
Li H, Hu C, Bai L, Li H, Li M, Zhao X, Czajkowsky DM, Shao Z. Ultra-deep sequencing of ribosome-associated poly-adenylated RNA in early Drosophila embryos reveals hundreds of conserved translated sORFs. DNA Res 2016; 23:571-580. [PMID: 27559081 PMCID: PMC5144680 DOI: 10.1093/dnares/dsw040] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2016] [Accepted: 07/11/2016] [Indexed: 11/23/2022] Open
Abstract
There is growing recognition that small open reading frames (sORFs) encoding peptides shorter than 100 amino acids are an important class of functional elements in the eukaryotic genome, with several already identified to play critical roles in growth, development, and disease. However, our understanding of their biological importance has been hindered owing to the significant technical challenges limiting their annotation. Here we combined ultra-deep sequencing of ribosome-associated poly-adenylated RNAs with rigorous conservation analysis to identify a comprehensive population of translated sORFs during early Drosophila embryogenesis. In total, we identify 399 sORFs, including those previously annotated but without evidence of translational capacity, those found within transcripts previously classified as non-coding, and those not previously known to be transcribed. Further, we find, for the first time, evidence for translation of many sORFs with different isoforms, suggesting their regulation is as complex as longer ORFs. Furthermore, many sORFs are found not associated with ribosomes in late-stage Drosophila S2 cells, suggesting that many of the translated sORFs may have stage-specific functions during embryogenesis. These results thus provide the first comprehensive annotation of the sORFs present during early Drosophila embryogenesis, a necessary basis for a detailed delineation of their function in embryogenesis and other biological processes.
Collapse
Affiliation(s)
- Hongmei Li
- Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Chuansheng Hu
- Bio-ID Center, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Ling Bai
- Bio-ID Center, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Hua Li
- Bio-ID Center, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Mingfa Li
- School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Xiaodong Zhao
- Bio-ID Center, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Daniel M Czajkowsky
- Bio-ID Center, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Zhifeng Shao
- Bio-ID Center, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
| |
Collapse
|
379
|
Cayer DM, Nazor KL, Schork NJ. Mission critical: the need for proteomics in the era of next-generation sequencing and precision medicine. Hum Mol Genet 2016; 25:R182-R189. [DOI: 10.1093/hmg/ddw214] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2016] [Accepted: 06/29/2016] [Indexed: 12/14/2022] Open
|
380
|
Untiet V, Moeller LM, Ibarra-Soria X, Sánchez-Andrade G, Stricker M, Neuhaus EM, Logan DW, Gensch T, Spehr M. Elevated Cytosolic Cl- Concentrations in Dendritic Knobs of Mouse Vomeronasal Sensory Neurons. Chem Senses 2016; 41:669-76. [PMID: 27377750 DOI: 10.1093/chemse/bjw077] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
In rodents, the vomeronasal system controls social and sexual behavior. However, several mechanistic aspects of sensory signaling in the vomeronasal organ remain unclear. Here, we investigate the biophysical basis of a recently proposed vomeronasal signal transduction component-a Ca(2+)-activated Cl(-) current. As the physiological role of such a current is a direct function of the Cl(-) equilibrium potential, we determined the intracellular Cl(-) concentration in dendritic knobs of vomeronasal neurons. Quantitative fluorescence lifetime imaging of a Cl(-)-sensitive dye at the apical surface of the intact vomeronasal neuroepithelium revealed increased cytosolic Cl(-) levels in dendritic knobs, a substantially lower Cl(-) concentration in vomeronasal sustentacular cells, and an apparent Cl(-) gradient in vomeronasal neurons along their dendritic apicobasal axis. Together, our data provide a biophysical basis for sensory signal amplification in vomeronasal neuron microvilli by opening Ca(2+)-activated Cl(-) channels.
Collapse
Affiliation(s)
- Verena Untiet
- Institute of Complex Systems, Cellular Biophysics (ICS-4), Forschungszentrum Jülich, Leo-Brandt-Straße, D-52428 Jülich, Germany
| | - Lisa M Moeller
- Department of Chemosensation, Institute for Biology II, RWTH Aachen University, Worringerweg 3, D-52074 Aachen, Germany
| | - Ximena Ibarra-Soria
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | | | - Miriam Stricker
- Institute of Complex Systems, Cellular Biophysics (ICS-4), Forschungszentrum Jülich, Leo-Brandt-Straße, D-52428 Jülich, Germany
| | - Eva M Neuhaus
- Pharmacology and Toxicology, University Hospital Jena, Drackendorfer Straße 1, Friedrich Schiller University Jena, D-07743 Jena, Germany and
| | - Darren W Logan
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK, Monell Chemical Senses Center, 3500 Market Street, Philadelphia, PA 19104, USA
| | - Thomas Gensch
- Institute of Complex Systems, Cellular Biophysics (ICS-4), Forschungszentrum Jülich, Leo-Brandt-Straße, D-52428 Jülich, Germany
| | - Marc Spehr
- Department of Chemosensation, Institute for Biology II, RWTH Aachen University, Worringerweg 3, D-52074 Aachen, Germany,
| |
Collapse
|
381
|
Cairns J, Freire-Pritchett P, Wingett SW, Várnai C, Dimond A, Plagnol V, Zerbino D, Schoenfelder S, Javierre BM, Osborne C, Fraser P, Spivakov M. CHiCAGO: robust detection of DNA looping interactions in Capture Hi-C data. Genome Biol 2016; 17:127. [PMID: 27306882 PMCID: PMC4908757 DOI: 10.1186/s13059-016-0992-2] [Citation(s) in RCA: 252] [Impact Index Per Article: 31.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2016] [Accepted: 05/25/2016] [Indexed: 12/14/2022] Open
Abstract
Capture Hi-C (CHi-C) is a method for profiling chromosomal interactions involving targeted regions of interest, such as gene promoters, globally and at high resolution. Signal detection in CHi-C data involves a number of statistical challenges that are not observed when using other Hi-C-like techniques. We present a background model and algorithms for normalisation and multiple testing that are specifically adapted to CHi-C experiments. We implement these procedures in CHiCAGO ( http://regulatorygenomicsgroup.org/chicago ), an open-source package for robust interaction detection in CHi-C. We validate CHiCAGO by showing that promoter-interacting regions detected with this method are enriched for regulatory features and disease-associated SNPs.
Collapse
Affiliation(s)
- Jonathan Cairns
- Nuclear Dynamics Programme, Babraham Institute, Cambridge, UK
| | | | - Steven W Wingett
- Nuclear Dynamics Programme, Babraham Institute, Cambridge, UK
- Bioinformatics Group, Babraham Institute, Cambridge, UK
| | - Csilla Várnai
- Nuclear Dynamics Programme, Babraham Institute, Cambridge, UK
| | - Andrew Dimond
- Nuclear Dynamics Programme, Babraham Institute, Cambridge, UK
| | | | - Daniel Zerbino
- European Molecular Biology Laboratory, European Bioinformatics Institute, Cambridge, UK
| | | | | | - Cameron Osborne
- Department of Medical and Molecular Genetics, King's College, London, UK
| | - Peter Fraser
- Nuclear Dynamics Programme, Babraham Institute, Cambridge, UK
| | | |
Collapse
|
382
|
Correa BR, de Araujo PR, Qiao M, Burns SC, Chen C, Schlegel R, Agarwal S, Galante PAF, Penalva LOF. Functional genomics analyses of RNA-binding proteins reveal the splicing regulator SNRPB as an oncogenic candidate in glioblastoma. Genome Biol 2016; 17:125. [PMID: 27287018 PMCID: PMC4901439 DOI: 10.1186/s13059-016-0990-4] [Citation(s) in RCA: 70] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2016] [Accepted: 05/24/2016] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Glioblastoma (GBM) is the most common and aggressive type of brain tumor. Currently, GBM has an extremely poor outcome and there is no effective treatment. In this context, genomic and transcriptomic analyses have become important tools to identify new avenues for therapies. RNA-binding proteins (RBPs) are master regulators of co- and post-transcriptional events; however, their role in GBM remains poorly understood. To further our knowledge of novel regulatory pathways that could contribute to gliomagenesis, we have conducted a systematic study of RBPs in GBM. RESULTS By measuring expression levels of 1542 human RBPs in GBM samples and glioma stem cell samples, we identified 58 consistently upregulated RBPs. Survival analysis revealed that increased expression of 21 RBPs was also associated with a poor prognosis. To assess the functional impact of those RBPs, we modulated their expression in GBM cell lines and performed viability, proliferation, and apoptosis assays. Combined results revealed a prominent oncogenic candidate, SNRPB, which encodes core spliceosome machinery components. To reveal the impact of SNRPB on splicing and gene expression, we performed its knockdown in a GBM cell line followed by RNA sequencing. We found that the affected genes were involved in RNA processing, DNA repair, and chromatin remodeling. Additionally, genes and pathways already associated with gliomagenesis, as well as a set of general cancer genes, also presented with splicing and expression alterations. CONCLUSIONS Our study provides new insights into how RBPs, and specifically SNRPB, regulate gene expression and directly impact GBM development.
Collapse
Affiliation(s)
- Bruna R Correa
- Centro de Oncologia Molecular, Hospital Sírio-Libanês, São Paulo, Brazil
- Children's Cancer Research Institute, UTHSCSA, San Antonio, TX, USA
| | | | - Mei Qiao
- Children's Cancer Research Institute, UTHSCSA, San Antonio, TX, USA
| | - Suzanne C Burns
- Children's Cancer Research Institute, UTHSCSA, San Antonio, TX, USA
| | - Chen Chen
- Georgetown University Medical Center, Washington, DC, USA
| | | | - Seema Agarwal
- Georgetown University Medical Center, Washington, DC, USA
| | - Pedro A F Galante
- Centro de Oncologia Molecular, Hospital Sírio-Libanês, São Paulo, Brazil.
| | - Luiz O F Penalva
- Children's Cancer Research Institute, UTHSCSA, San Antonio, TX, USA.
- Department of Cellular and Structural Biology, UTHSCSA, San Antonio, TX, USA.
| |
Collapse
|
383
|
Hébert FO, Grambauer S, Barber I, Landry CR, Aubin-Horth N. Transcriptome sequences spanning key developmental states as a resource for the study of the cestode Schistocephalus solidus, a threespine stickleback parasite. Gigascience 2016; 5:24. [PMID: 27259971 PMCID: PMC4891850 DOI: 10.1186/s13742-016-0128-3] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2015] [Accepted: 05/11/2016] [Indexed: 01/06/2023] Open
Abstract
Background Schistocephalus solidus is a well-established model organism for studying the complex life cycle of cestodes and the mechanisms underlying host-parasite interactions. However, very few large-scale genetic resources for this species are available. We have sequenced and de novo-assembled the transcriptome of S. solidus using tissues from whole worms at three key developmental states - non-infective plerocercoid, infective plerocercoid and adult plerocercoid - to provide a resource for studying the evolution of complex life cycles and, more specifically, how parasites modulate their interactions with their hosts during development. Findings The de novo transcriptome assembly reconstructed the coding sequence of 10,285 high-confidence unigenes from which 24,765 non-redundant transcripts were derived. 7,920 (77 %) of these unigenes were annotated with a protein name and 7,323 (71 %) were assigned at least one Gene Ontology term. Our raw transcriptome assembly (unfiltered transcripts) covers 92 % of the predicted transcriptome derived from the S. solidus draft genome assembly currently available on WormBase. It also provides new ecological information and orthology relationships to further annotate the current WormBase transcriptome and genome. Conclusion This large-scale transcriptomic dataset provides a foundation for studies on how parasitic species with complex life cycles modulate their response to changes in biotic and abiotic conditions experienced inside their various hosts, which is a fundamental objective of parasitology. Furthermore, this resource will help in the validation of the S solidus gene features that have been predicted based on genomic sequence. Electronic supplementary material The online version of this article (doi:10.1186/s13742-016-0128-3) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- François Olivier Hébert
- Institut de Biologie Intégrative et des Systèmes (IBIS), Département de Biologie, Université Laval, Pavillon Charles-Eugène-Marchand, Québec, G1V 0A6, Canada.
| | - Stephan Grambauer
- Department of Neuroscience, Psychology and Behaviour, Adrian Building, University of Leicester, University Road, Leicester, LE1 7RH, UK
| | - Iain Barber
- Department of Neuroscience, Psychology and Behaviour, Adrian Building, University of Leicester, University Road, Leicester, LE1 7RH, UK
| | - Christian R Landry
- Institut de Biologie Intégrative et des Systèmes (IBIS), Département de Biologie, Université Laval, Pavillon Charles-Eugène-Marchand, Québec, G1V 0A6, Canada
| | - Nadia Aubin-Horth
- Institut de Biologie Intégrative et des Systèmes (IBIS), Département de Biologie, Université Laval, Pavillon Charles-Eugène-Marchand, Québec, G1V 0A6, Canada
| |
Collapse
|
384
|
Powell D, Knibb W, Nguyen NH, Elizur A. Transcriptional Profiling of Banana Shrimp Fenneropenaeus merguiensis with Differing Levels of Viral Load. Integr Comp Biol 2016; 56:1131-1143. [PMID: 27252205 DOI: 10.1093/icb/icw029] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Viral pathogens are of serious concern to the culture of penaeid shrimps worldwide. However, little is known about the molecular response of shrimp to viral infection. Selective breeding has been suggested as an effective long-term strategy to manage viral disease, though more information on gene function is needed to help inform breeding programs. The study of cultured banana shrimp (Fenneropenaeus merguiensis) infected with hepatopancreatic parvo-like virus (HPV) provides a unique opportunity to explore the host response to viral infection independent of challenge testing. To gain insight into the genetic mechanisms underlying resistance to high levels of HPV, we examined hepatopancreas tissue from six full-sib groups of banana shrimp with differing levels of HPV infection for differences in gene expression. A total of 404 differentially expressed genes were identified with 180 being over-expressed and 224 under-expressed among high-HPV full-sib groups. Based on homology analysis, a large proportion of these genes were associated with processes reported to be involved in the immune response of crustaceans, including pattern recognition proteins, antimicrobial peptides, components of the prophenoloxidase system, and antiviral activity. The results indicate shrimp from high-HPV full-sib groups appear to have a lower presence of important immune response elements, yet possess upregulated putative antiviral pathways. Within the differentially expressed genes, over 4000 sequence variants were identified to be exclusive to either the high- or low-HPV full-sib groups. To our knowledge, this is the first report of differential expression analysis using RNA-Seq to explore differences in viral load among high- and low-HPV full-sib groups of cultured shrimp. This research has provided additional insight into our understanding of the mechanisms involved in the response of this shrimp species to a naturally occurring viral pathogen. Sequence variants identified in this study offer an exceptional resource for mining gene-associated markers of HPV resistance.
Collapse
Affiliation(s)
- Daniel Powell
- Faculty of Science, Health, Education and Engineering, Genecology Research Centre, University of the Sunshine Coast, Maroochydore DC, Queensland 4558, Australia
| | - Wayne Knibb
- Faculty of Science, Health, Education and Engineering, Genecology Research Centre, University of the Sunshine Coast, Maroochydore DC, Queensland 4558, Australia
| | - Nguyen Hong Nguyen
- Faculty of Science, Health, Education and Engineering, Genecology Research Centre, University of the Sunshine Coast, Maroochydore DC, Queensland 4558, Australia
| | - Abigail Elizur
- Faculty of Science, Health, Education and Engineering, Genecology Research Centre, University of the Sunshine Coast, Maroochydore DC, Queensland 4558, Australia
| |
Collapse
|
385
|
Germain PL, Vitriolo A, Adamo A, Laise P, Das V, Testa G. RNAontheBENCH: computational and empirical resources for benchmarking RNAseq quantification and differential expression methods. Nucleic Acids Res 2016; 44:5054-67. [PMID: 27190234 PMCID: PMC4914128 DOI: 10.1093/nar/gkw448] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2016] [Accepted: 05/09/2016] [Indexed: 11/13/2022] Open
Abstract
RNA sequencing (RNAseq) has become the method of choice for transcriptome analysis, yet no consensus exists as to the most appropriate pipeline for its analysis, with current benchmarks suffering important limitations. Here, we address these challenges through a rich benchmarking resource harnessing (i) two RNAseq datasets including ERCC ExFold spike-ins; (ii) Nanostring measurements of a panel of 150 genes on the same samples; (iii) a set of internal, genetically-determined controls; (iv) a reanalysis of the SEQC dataset; and (v) a focus on relative quantification (i.e. across-samples). We use this resource to compare different approaches to each step of RNAseq analysis, from alignment to differential expression testing. We show that methods providing the best absolute quantification do not necessarily provide good relative quantification across samples, that count-based methods are superior for gene-level relative quantification, and that the new generation of pseudo-alignment-based software performs as well as established methods, at a fraction of the computing time. We also assess the impact of library type and size on quantification and differential expression analysis. Finally, we have created a R package and a web platform to enable the simple and streamlined application of this resource to the benchmarking of future methods.
Collapse
Affiliation(s)
- Pierre-Luc Germain
- European Institute of Oncology, Department of Experimental Oncology, Via Adamello 16, 20139 Milano, Italy
| | - Alessandro Vitriolo
- European Institute of Oncology, Department of Experimental Oncology, Via Adamello 16, 20139 Milano, Italy University of Milan, Department of Oncology and Hemato-Oncology, Via Festa del Perdono 7, 20122 Milano, Italy
| | - Antonio Adamo
- European Institute of Oncology, Department of Experimental Oncology, Via Adamello 16, 20139 Milano, Italy
| | - Pasquale Laise
- European Institute of Oncology, Department of Experimental Oncology, Via Adamello 16, 20139 Milano, Italy
| | - Vivek Das
- European Institute of Oncology, Department of Experimental Oncology, Via Adamello 16, 20139 Milano, Italy University of Milan, Department of Oncology and Hemato-Oncology, Via Festa del Perdono 7, 20122 Milano, Italy
| | - Giuseppe Testa
- European Institute of Oncology, Department of Experimental Oncology, Via Adamello 16, 20139 Milano, Italy University of Milan, Department of Oncology and Hemato-Oncology, Via Festa del Perdono 7, 20122 Milano, Italy
| |
Collapse
|
386
|
Abstract
Gene body methylation (gbM) is an ancestral and widespread feature in Eukarya, yet its adaptive value and evolutionary implications remain unresolved. The occurrence of gbM within protein-coding sequences is particularly puzzling, because methylation causes cytosine hypermutability and hence is likely to produce deleterious amino acid substitutions. We investigate this enigma using an evolutionarily basal group of Metazoa, the stony corals (order Scleractinia, class Anthozoa, phylum Cnidaria). We show that patterns of coral gbM are similar to other invertebrate species, predicting wide and active transcription and slower sequence evolution. We also find a strong correlation between gbM and codon bias, resulting from systematic replacement of CpG bearing codons. We conclude that gbM has strong effects on codon evolution and speculate that this may influence establishment of optimal codons.
Collapse
Affiliation(s)
- Groves B Dixon
- Institute for Cell and Molecular Biology, University of Texas
| | - Line K Bay
- Australian Institute of Marine Science, Townsville, QLD, Australia ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, QLD, Australia
| | | |
Collapse
|
387
|
Kawakami E, Nakaoka S, Ohta T, Kitano H. Weighted enrichment method for prediction of transcription regulators from transcriptome and global chromatin immunoprecipitation data. Nucleic Acids Res 2016; 44:5010-21. [PMID: 27131787 PMCID: PMC4914117 DOI: 10.1093/nar/gkw355] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2015] [Accepted: 04/20/2016] [Indexed: 11/12/2022] Open
Abstract
Predicting responsible transcription regulators on the basis of transcriptome data is one of the most promising computational approaches to understanding cellular processes and characteristics. Here, we present a novel method employing vast amounts of chromatin immunoprecipitation (ChIP) experimental data to address this issue. Global high-throughput ChIP data was collected to construct a comprehensive database, containing 8 578 738 binding interactions of 454 transcription regulators. To incorporate information about heterogeneous frequencies of transcription factor (TF)-binding events, we developed a flexible framework for gene set analysis employing the weighted t-test procedure, namely weighted parametric gene set analysis (wPGSA). Using transcriptome data as an input, wPGSA predicts the activities of transcription regulators responsible for observed gene expression. Validation of wPGSA with published transcriptome data, including that from over-expressed TFs, showed that the method can predict activities of various TFs, regardless of cell type and conditions, with results totally consistent with biological observations. We also applied wPGSA to other published transcriptome data and identified potential key regulators of cell reprogramming and influenza virus pathogenesis, generating compelling hypotheses regarding underlying regulatory mechanisms. This flexible framework will contribute to uncovering the dynamic and robust architectures of biological regulation, by incorporating high-throughput experimental data in the form of weights.
Collapse
Affiliation(s)
- Eiryo Kawakami
- Laboratory for disease systems modeling, RIKEN Center for Integrated Medical Sciences (IMS), Yokohama, Kanagawa 230-0045, Japan
| | - Shinji Nakaoka
- Laboratory for disease systems modeling, RIKEN Center for Integrated Medical Sciences (IMS), Yokohama, Kanagawa 230-0045, Japan Department of Global Health Policy, Graduate School of Medicine, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Tazro Ohta
- Database Center for Life Science (DBCLS), Research Organization of Information and Systems (ROIS), Mishima, Shizuoka 411-8540, Japan
| | - Hiroaki Kitano
- Laboratory for disease systems modeling, RIKEN Center for Integrated Medical Sciences (IMS), Yokohama, Kanagawa 230-0045, Japan The Systems Biology Institute, Minato-ku, Tokyo 108-0071, Japan Sony Computer Science Laboratories, Inc, Shinagawa-ku, Tokyo 141-0022, Japan Okinawa Institute of Science and Technology, Graduate University, Onna-son, Okinawa 904-0495, Japan
| |
Collapse
|
388
|
Sergushichev AA, Loboda AA, Jha AK, Vincent EE, Driggers EM, Jones RG, Pearce EJ, Artyomov MN. GAM: a web-service for integrated transcriptional and metabolic network analysis. Nucleic Acids Res 2016; 44:W194-200. [PMID: 27098040 PMCID: PMC4987878 DOI: 10.1093/nar/gkw266] [Citation(s) in RCA: 65] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2016] [Accepted: 04/04/2016] [Indexed: 01/14/2023] Open
Abstract
Novel techniques for high-throughput steady-state metabolomic profiling yield information about changes of nearly thousands of metabolites. Such metabolomic profiles, when analyzed together with transcriptional profiles, can reveal novel insights about underlying biological processes. While a number of conceptual approaches have been developed for data integration, easily accessible tools for integrated analysis of mammalian steady-state metabolomic and transcriptional data are lacking. Here we present GAM (‘genes and metabolites’): a web-service for integrated network analysis of transcriptional and steady-state metabolomic data focused on identification of the most changing metabolic subnetworks between two conditions of interest. In the web-service, we have pre-assembled metabolic networks for humans, mice, Arabidopsis and yeast and adapted exact solvers for an optimal subgraph search to work in the context of these metabolic networks. The output is the most regulated metabolic subnetwork of size controlled by false discovery rate parameters. The subnetworks are then visualized online and also can be downloaded in Cytoscape format for subsequent processing. The web-service is available at: https://artyomovlab.wustl.edu/shiny/gam/
Collapse
Affiliation(s)
- Alexey A Sergushichev
- Computer Technologies Department, ITMO University, Saint Petersburg, 197101, Russia Department of Pathology & Immunology, Washington University in St. Louis, St.Louis, MO 63110, USA
| | - Alexander A Loboda
- Computer Technologies Department, ITMO University, Saint Petersburg, 197101, Russia
| | | | - Emma E Vincent
- Goodman Cancer Research Centre, McGill University, Montreal, QC H3A 1A3, Canada Department of Physiology, McGill University, Montreal, QC H3G 1Y6, Canada
| | | | - Russell G Jones
- Goodman Cancer Research Centre, McGill University, Montreal, QC H3A 1A3, Canada Department of Physiology, McGill University, Montreal, QC H3G 1Y6, Canada
| | - Edward J Pearce
- Department of Immunometabolism, Max Planck Institute of Immunobiology and Epigenetics, Freiburg, D-79108, Germany
| | - Maxim N Artyomov
- Computer Technologies Department, ITMO University, Saint Petersburg, 197101, Russia Department of Pathology & Immunology, Washington University in St. Louis, St.Louis, MO 63110, USA
| |
Collapse
|
389
|
Xiao FH, Kong QP, Perry B, He YH. Progress on the role of DNA methylation in aging and longevity. Brief Funct Genomics 2016; 15:454-459. [PMID: 27032421 DOI: 10.1093/bfgp/elw009] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Aging is a major risk factor for individuals' health problems. Moreover, environmental signals have a widespread influence on the aging process. Epigenetic modification, e.g. DNA methylation, represents a link between genetic and environmental signals via the regulation of gene transcription. An abundance of literature indicates that aberrant epigenetic change occurs throughout the aging process at both the cellular and the organismal level. In particular, DNA methylation presents globally decreasing and site-specific increasing in aging. In this review, we focus on the crucial roles of DNA methylation in aging and age-related disease and highlight the great potential of DNA methylation as a therapeutic target in preventing age-related diseases and promoting healthy longevity.
Collapse
|
390
|
Meng Y, Yi X, Li X, Hu C, Wang J, Bai L, Czajkowsky DM, Shao Z. The non-coding RNA composition of the mitotic chromosome by 5'-tag sequencing. Nucleic Acids Res 2016; 44:4934-46. [PMID: 27016738 PMCID: PMC4889943 DOI: 10.1093/nar/gkw195] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2015] [Accepted: 03/15/2016] [Indexed: 12/16/2022] Open
Abstract
Mitotic chromosomes are one of the most commonly recognized sub-cellular structures in eukaryotic cells. Yet basic information necessary to understand their structure and assembly, such as their composition, is still lacking. Recent proteomic studies have begun to fill this void, identifying hundreds of RNA-binding proteins bound to mitotic chromosomes. However, by contrast, there are only two RNA species (U3 snRNA and rRNA) that are known to be associated with the mitotic chromosome, suggesting that there are many mitotic chromosome-associated RNAs (mCARs) not yet identified. Here, using a targeted protocol based on 5'-tag sequencing to profile the mammalian mCAR population, we report the identification of 1279 mCARs, the majority of which are ncRNAs, including lncRNAs that exhibit greater conservation across 60 vertebrate species than the entire population of lncRNAs. There is also a significant enrichment of snoRNAs and specific SINE RNAs. Finally, ∼40% of the mCARs are presently unannotated, many of which are as abundant as the annotated mCARs, suggesting that there are also many novel ncRNAs in the mCARs. Overall, the mCARs identified here, together with the previous proteomic and genomic data, constitute the first comprehensive catalogue of the molecular composition of the eukaryotic mitotic chromosomes.
Collapse
Affiliation(s)
- Yicong Meng
- Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Xianfu Yi
- School of Biomedical Engineering, Tianjin Medical University, Tianjin 300070, China
| | - Xinhui Li
- Bio-ID Center, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Chuansheng Hu
- Bio-ID Center, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Ju Wang
- School of Biomedical Engineering, Tianjin Medical University, Tianjin 300070, China
| | - Ling Bai
- Bio-ID Center, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Daniel M Czajkowsky
- Bio-ID Center, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Zhifeng Shao
- Bio-ID Center, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China State Key Laboratory of Oncogenes & Related Genes, Shanghai Jiao Tong University, Shanghai 200240, China
| |
Collapse
|
391
|
Indoliya Y, Tiwari P, Chauhan AS, Goel R, Shri M, Bag SK, Chakrabarty D. Decoding regulatory landscape of somatic embryogenesis reveals differential regulatory networks between japonica and indica rice subspecies. Sci Rep 2016; 6:23050. [PMID: 26973288 PMCID: PMC4789791 DOI: 10.1038/srep23050] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2015] [Accepted: 02/25/2016] [Indexed: 11/09/2022] Open
Abstract
Somatic embryogenesis is a unique process in plants and has considerable interest for biotechnological application. Compare to japonica, indica rice has been less responsive to in vitro culture. We used Illumina Hiseq 2000 sequencing platform for comparative transcriptome analysis between two rice subspecies at six different developmental stages combined with a tag-based digital gene expression profiling. Global gene expression among different samples showed greater complexity in japonica rice compared to indica which may be due to polyphyletic origin of two rice subspecies. Expression pattern in initial stage indicate major differences in proembryogenic callus induction phase that may serve as key regulator to observe differences between both subspecies. Our data suggests that phytohormone signaling pathways consist of elaborate networks with frequent crosstalk, thereby allowing plants to regulate somatic embryogenesis pathway. However, this crosstalk varies between the two rice subspecies. Down regulation of positive regulators of meristem development (i.e. KNOX, OsARF5) and up regulation of its counterparts (OsRRs, MYB, GA20ox1/GA3ox2) in japonica may be responsible for its better regeneration and differentiation of somatic embryos. Comprehensive gene expression information in the present experiment may also facilitate to understand the monocot specific meristem regulation for dedifferentiation of somatic cell to embryogenic cells.
Collapse
Affiliation(s)
- Yuvraj Indoliya
- Council of Scientific and Industrial Research - National Botanical Research Institute (CSIR-NBRI), Rana Pratap Marg, Lucknow-226001, India.,Academy of Scientific and Innovative Research (AcSIR), Anusandhan Bhawan, 2 Rafi Marg, New Delhi-110 001, India
| | - Poonam Tiwari
- Council of Scientific and Industrial Research - National Botanical Research Institute (CSIR-NBRI), Rana Pratap Marg, Lucknow-226001, India
| | - Abhisekh Singh Chauhan
- Council of Scientific and Industrial Research - National Botanical Research Institute (CSIR-NBRI), Rana Pratap Marg, Lucknow-226001, India
| | - Ridhi Goel
- Council of Scientific and Industrial Research - National Botanical Research Institute (CSIR-NBRI), Rana Pratap Marg, Lucknow-226001, India.,Academy of Scientific and Innovative Research (AcSIR), Anusandhan Bhawan, 2 Rafi Marg, New Delhi-110 001, India
| | - Manju Shri
- Council of Scientific and Industrial Research - National Botanical Research Institute (CSIR-NBRI), Rana Pratap Marg, Lucknow-226001, India
| | - Sumit Kumar Bag
- Council of Scientific and Industrial Research - National Botanical Research Institute (CSIR-NBRI), Rana Pratap Marg, Lucknow-226001, India.,Academy of Scientific and Innovative Research (AcSIR), Anusandhan Bhawan, 2 Rafi Marg, New Delhi-110 001, India
| | - Debasis Chakrabarty
- Council of Scientific and Industrial Research - National Botanical Research Institute (CSIR-NBRI), Rana Pratap Marg, Lucknow-226001, India.,Academy of Scientific and Innovative Research (AcSIR), Anusandhan Bhawan, 2 Rafi Marg, New Delhi-110 001, India
| |
Collapse
|
392
|
Figuet E, Nabholz B, Bonneau M, Mas Carrio E, Nadachowska-Brzyska K, Ellegren H, Galtier N. Life History Traits, Protein Evolution, and the Nearly Neutral Theory in Amniotes. Mol Biol Evol 2016; 33:1517-27. [DOI: 10.1093/molbev/msw033] [Citation(s) in RCA: 58] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
|
393
|
Zeilinger S, Gupta VK, Dahms TES, Silva RN, Singh HB, Upadhyay RS, Gomes EV, Tsui CKM, Nayak S C. Friends or foes? Emerging insights from fungal interactions with plants. FEMS Microbiol Rev 2016; 40:182-207. [PMID: 26591004 PMCID: PMC4778271 DOI: 10.1093/femsre/fuv045] [Citation(s) in RCA: 133] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Revised: 06/11/2015] [Accepted: 10/11/2015] [Indexed: 12/22/2022] Open
Abstract
Fungi interact with plants in various ways, with each interaction giving rise to different alterations in both partners. While fungal pathogens have detrimental effects on plant physiology, mutualistic fungi augment host defence responses to pathogens and/or improve plant nutrient uptake. Tropic growth towards plant roots or stomata, mediated by chemical and topographical signals, has been described for several fungi, with evidence of species-specific signals and sensing mechanisms. Fungal partners secrete bioactive molecules such as small peptide effectors, enzymes and secondary metabolites which facilitate colonization and contribute to both symbiotic and pathogenic relationships. There has been tremendous advancement in fungal molecular biology, omics sciences and microscopy in recent years, opening up new possibilities for the identification of key molecular mechanisms in plant-fungal interactions, the power of which is often borne out in their combination. Our fragmentary knowledge on the interactions between plants and fungi must be made whole to understand the potential of fungi in preventing plant diseases, improving plant productivity and understanding ecosystem stability. Here, we review innovative methods and the associated new insights into plant-fungal interactions.
Collapse
Affiliation(s)
- Susanne Zeilinger
- Institute of Microbiology, University of Innsbruck, Technikerstrasse 25, 6020 Innsbruck, Austria
| | - Vijai K Gupta
- Molecular Glycobiotechnology Group, Discipline of Biochemistry, School of Natural Sciences, National University of Ireland Galway, Galway, Ireland
| | - Tanya E S Dahms
- Department of Chemistry and Biochemistry, University of Regina, SK, Canada
| | - Roberto N Silva
- Department of Biochemistry and Immunology, Ribeirão Preto Medical School, University of São Paulo (USP), 14049-900 Ribeirão Preto, SP, Brazil
| | - Harikesh B Singh
- Department of Mycology and Plant Pathology, Institute of Agricultural Sciences, Banaras Hindu University, Varanasi 221 005, India
| | - Ram S Upadhyay
- Department of Botany, Banaras Hindu University, Varanasi 221 005, India
| | - Eriston Vieira Gomes
- Department of Biochemistry and Immunology, Ribeirão Preto Medical School, University of São Paulo (USP), 14049-900 Ribeirão Preto, SP, Brazil
| | - Clement Kin-Ming Tsui
- Department of Pathology and Laboratory Medicine, the University of British Columbia, Vancouver, BC, Canada V6T 1Z4
| | - Chandra Nayak S
- Department of Biotechnology, University of Mysore, Mysore-570001, Karnataka, India
| |
Collapse
|
394
|
Cui P, Chen T, Qin T, Ding F, Wang Z, Chen H, Xiong L. The RNA Polymerase II C-Terminal Domain Phosphatase-Like Protein FIERY2/CPL1 Interacts with eIF4AIII and Is Essential for Nonsense-Mediated mRNA Decay in Arabidopsis. THE PLANT CELL 2016; 28:770-85. [PMID: 26887918 PMCID: PMC4826008 DOI: 10.1105/tpc.15.00771] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2015] [Revised: 02/04/2016] [Accepted: 02/15/2016] [Indexed: 05/18/2023]
Abstract
Nonsense-mediated decay (NMD) is a posttranscriptional surveillance mechanism in eukaryotes that recognizes and degrades transcripts with premature translation-termination codons. The RNA polymerase II C-terminal domain phosphatase-like protein FIERY2 (FRY2; also known as C-TERMINAL DOMAIN PHOSPHATASE-LIKE1 [CPL1]) plays multiple roles in RNA processing in Arabidopsis thaliana Here, we found that FRY2/CPL1 interacts with two NMD factors, eIF4AIII and UPF3, and is involved in the dephosphorylation of eIF4AIII. This dephosphorylation retains eIF4AIII in the nucleus and limits its accumulation in the cytoplasm. By analyzing RNA-seq data combined with quantitative RT-PCR validation, we found that a subset of alternatively spliced transcripts and 5'-extended mRNAs with NMD-eliciting features accumulated in the fry2-1 mutant, cycloheximide-treated wild type, and upf3 mutant plants, indicating that FRY2 is essential for the degradation of these NMD transcripts.
Collapse
Affiliation(s)
- Peng Cui
- Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia
| | - Tao Chen
- Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia
| | - Tao Qin
- Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia
| | - Feng Ding
- Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia
| | - Zhenyu Wang
- Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia
| | - Hao Chen
- Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia
| | - Liming Xiong
- Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia
| |
Collapse
|
395
|
Du C, Wu X, Li J. Mutation pattern is an influential factor on functional mutation rates in cancer. Cancer Cell Int 2016; 16:2. [PMID: 26865835 PMCID: PMC4748466 DOI: 10.1186/s12935-016-0278-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2015] [Accepted: 02/03/2016] [Indexed: 11/11/2022] Open
Abstract
BACKGROUND Mutation rates are consistently varied in cancer genome and play an important role in tumorigenesis, however, little has been known about their function potential and impact on the distribution of functional mutations. In this study, we investigated genomic features which affect mutation pattern and the function importance of mutation pattern in cancer. METHODS Somatic mutations of clear-cell renal cell carcinoma, liver cancer, lung cancer and melanoma and single nucleotide polymorphisms (SNPs) were intersected with 54 distinct genomic features. Somatic mutation and SNP densities were then computed for each feature type. We constructed 2856 1-Mb windows, in which each row (1-Mb window) contains somatic mutation, SNP densities and 54 feature vectors. Correlation analyses were conducted between somatic mutation, SNP densities and each feature vector. We also built two random forest models, namely somatic mutation model (CSM) and SNP model to predict somatic mutation and SNP densities on a 1-Kb scale. The relation of CSM and SNP scores was further analyzed with the distributions of deleterious coding variants predicted by SIFT and Mutation Assessor, non-coding functional variants evaluated with FunSeq 2 and GWAVA and disease-causing variants from HGMD and ClinVar databases. RESULTS We observed a wide range of genomic features which affect local mutation rates, such as replication time, transcription levels, histone marks and regulatory elements. Repressive histone marks, replication time and promoter contributed most to the CSM models, while, recombination rate and chromatin organizations were most important for the SNP model. We showed low mutated regions preferentially have higher densities of deleterious coding mutations, higher average scores of non-coding variants, higher fraction of functional regions and higher enrichment of disease-causing variants as compared to high mutated regions. CONCLUSIONS Somatic mutation densities vary largely across cancer genome, mutation frequency is a major indication of function and influence on the distribution of functional mutations in cancer.
Collapse
Affiliation(s)
- Chuance Du
- Department of Urology, Ganzhou Hospital Affiliated to Nanchang University, Ganzhou, Jiangxi province China
| | - Xiaoyuan Wu
- Department of Rehabilitation, Ganzhou Hospital Affiliated to Nanchang University, Nan Chang, Jiangxi province China
| | - Jia Li
- Department of Thyroid and Breast, Shanghai Tenth People’s Hospital, Tongji University, Shanghai, 200072 China
| |
Collapse
|
396
|
Perea-Resa C, Carrasco-López C, Catalá R, Turečková V, Novak O, Zhang W, Sieburth L, Jiménez-Gómez JM, Salinas J. The LSM1-7 Complex Differentially Regulates Arabidopsis Tolerance to Abiotic Stress Conditions by Promoting Selective mRNA Decapping. THE PLANT CELL 2016; 28:505-20. [PMID: 26764377 PMCID: PMC4790874 DOI: 10.1105/tpc.15.00867] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2015] [Revised: 12/14/2015] [Accepted: 01/08/2016] [Indexed: 05/19/2023]
Abstract
In eukaryotes, the decapping machinery is highly conserved and plays an essential role in controlling mRNA stability, a key step in the regulation of gene expression. Yet, the role of mRNA decapping in shaping gene expression profiles in response to environmental cues and the operating molecular mechanisms are poorly understood. Here, we provide genetic and molecular evidence that a component of the decapping machinery, the LSM1-7 complex, plays a critical role in plant tolerance to abiotic stresses. Our results demonstrate that, depending on the stress, the complex from Arabidopsis thaliana interacts with different selected stress-inducible transcripts targeting them for decapping and subsequent degradation. This interaction ensures the correct turnover of the target transcripts and, consequently, the appropriate patterns of downstream stress-responsive gene expression that are required for plant adaptation. Remarkably, among the selected target transcripts of the LSM1-7 complex are those encoding NCED3 and NCED5, two key enzymes in abscisic acid (ABA) biosynthesis. We demonstrate that the complex modulates ABA levels in Arabidopsis exposed to cold and high salt by differentially controlling NCED3 and NCED5 mRNA turnover, which represents a new layer of regulation in ABA biosynthesis in response to abiotic stress. Our findings uncover an unanticipated functional plasticity of the mRNA decapping machinery to modulate the relationship between plants and their environment.
Collapse
Affiliation(s)
- Carlos Perea-Resa
- Departamento de Biología Medioambiental, Centro de Investigaciones Biológicas, CSIC, 28040 Madrid, Spain
| | - Cristian Carrasco-López
- Departamento de Biología Medioambiental, Centro de Investigaciones Biológicas, CSIC, 28040 Madrid, Spain
| | - Rafael Catalá
- Departamento de Biología Medioambiental, Centro de Investigaciones Biológicas, CSIC, 28040 Madrid, Spain
| | - Veronika Turečková
- Laboratory of Growth Regulators, Institute of Experimental Botany Academy of Sciences of the Czech Republic, v.v.i. & Palacký University, 78371 Olomouc, Czech Republic
| | - Ondrej Novak
- Laboratory of Growth Regulators, Institute of Experimental Botany Academy of Sciences of the Czech Republic, v.v.i. & Palacký University, 78371 Olomouc, Czech Republic
| | - Weiping Zhang
- Department of Biology, University of Utah, Salt Lake City, Utah 84112
| | - Leslie Sieburth
- Department of Biology, University of Utah, Salt Lake City, Utah 84112
| | - José Manuel Jiménez-Gómez
- Department of Plant Breeding and Genetics, Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany INRA, Institut Jean-Pierre Bourgin, UMR 1318, 78026 Versailles, France
| | - Julio Salinas
- Departamento de Biología Medioambiental, Centro de Investigaciones Biológicas, CSIC, 28040 Madrid, Spain
| |
Collapse
|
397
|
Popa A, Lebrigand K, Barbry P, Waldmann R. Pateamine A-sensitive ribosome profiling reveals the scope of translation in mouse embryonic stem cells. BMC Genomics 2016; 17:52. [PMID: 26764022 PMCID: PMC4712605 DOI: 10.1186/s12864-016-2384-0] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2015] [Accepted: 01/06/2016] [Indexed: 01/02/2023] Open
Abstract
Background Open reading frames are common in long noncoding RNAs (lncRNAs) and 5’UTRs of protein coding transcripts (uORFs). The question of whether those ORFs are translated was recently addressed by several groups using ribosome profiling. Most of those studies concluded that certain lncRNAs and uORFs are translated, essentially based on computational analysis of ribosome footprints. However, major discrepancies remain on the scope of translation and the translational status of individual ORFs. In consequence, further criteria are required to reliably identify translated ORFs from ribosome profiling data. Results We examined the effect of the translation inhibitors pateamine A, harringtonine and puromycin on murine ES cell ribosome footprints. We found that pateamine A, a drug that targets eIF4A, allows a far more accurate identification of translated sequences than previously used drugs and computational scoring schemes. Our data show that at least one third but less than two thirds of ES cell lncRNAs are translated. We also identified translated uORFs in hundreds of annotated coding transcripts including key pluripotency transcripts, such as dicer, lin28, trim71, and ctcf. Conclusion Pateamine A inhibition data clearly increase the precision of the detection of translated ORFs in ribosome profiling experiments. Our data show that translation of lncRNAs and uORFs in murine ES cells is rather common although less pervasive than previously suggested. The observation of translated uORFs in several key pluripotency transcripts suggests that translational regulation by uORFs might be part of the network that defines mammalian stem cell identity. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-2384-0) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Alexandra Popa
- Institut de Pharmacologie Moléculaire et Cellulaire (IPMC), University Nice Sophia Antipolis, CNRS, F06560, Sophia-Antipolis, France
| | - Kevin Lebrigand
- Institut de Pharmacologie Moléculaire et Cellulaire (IPMC), University Nice Sophia Antipolis, CNRS, F06560, Sophia-Antipolis, France
| | - Pascal Barbry
- Institut de Pharmacologie Moléculaire et Cellulaire (IPMC), University Nice Sophia Antipolis, CNRS, F06560, Sophia-Antipolis, France.
| | - Rainer Waldmann
- Institut de Pharmacologie Moléculaire et Cellulaire (IPMC), University Nice Sophia Antipolis, CNRS, F06560, Sophia-Antipolis, France
| |
Collapse
|
398
|
Thatcher SR, Danilevskaya ON, Meng X, Beatty M, Zastrow-Hayes G, Harris C, Van Allen B, Habben J, Li B. Genome-Wide Analysis of Alternative Splicing during Development and Drought Stress in Maize. PLANT PHYSIOLOGY 2016; 170:586-99. [PMID: 26582726 PMCID: PMC4704579 DOI: 10.1104/pp.15.01267] [Citation(s) in RCA: 92] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2015] [Accepted: 11/17/2015] [Indexed: 05/18/2023]
Abstract
Alternative splicing plays a crucial role in plant development as well as stress responses. Although alternative splicing has been studied during development and in response to stress, the interplay between these two factors remains an open question. To assess the effects of drought stress on developmentally regulated splicing in maize (Zea mays), 94 RNA-seq libraries from ear, tassel, and leaf of the B73 public inbred line were constructed at four developmental stages under both well-watered and drought conditions. This analysis was supplemented with a publicly available series of 53 libraries from developing seed, embryo, and endosperm. More than 48,000 novel isoforms, often with stage- or condition-specific expression, were uncovered, suggesting that developmentally regulated alternative splicing occurs in thousands of genes. Drought induced large developmental splicing changes in leaf and ear but relatively few in tassel. Most developmental stage-specific splicing changes affected by drought were tissue dependent, whereas stage-independent changes frequently overlapped between leaf and ear. A linear relationship was found between gene expression changes in splicing factors and alternative spicing of other genes during development. Collectively, these results demonstrate that alternative splicing is strongly associated with tissue type, developmental stage, and stress condition.
Collapse
Affiliation(s)
- Shawn R Thatcher
- DuPont Pioneer, Wilmington, Delaware 19880 (S.R.T., B.L.); andDuPont Pioneer, Johnston, Iowa 50131 (O.N.D., X.M., M.B., G.Z.-H., C.H., B.V.A., J.H.)
| | - Olga N Danilevskaya
- DuPont Pioneer, Wilmington, Delaware 19880 (S.R.T., B.L.); andDuPont Pioneer, Johnston, Iowa 50131 (O.N.D., X.M., M.B., G.Z.-H., C.H., B.V.A., J.H.)
| | - Xin Meng
- DuPont Pioneer, Wilmington, Delaware 19880 (S.R.T., B.L.); andDuPont Pioneer, Johnston, Iowa 50131 (O.N.D., X.M., M.B., G.Z.-H., C.H., B.V.A., J.H.)
| | - Mary Beatty
- DuPont Pioneer, Wilmington, Delaware 19880 (S.R.T., B.L.); andDuPont Pioneer, Johnston, Iowa 50131 (O.N.D., X.M., M.B., G.Z.-H., C.H., B.V.A., J.H.)
| | - Gina Zastrow-Hayes
- DuPont Pioneer, Wilmington, Delaware 19880 (S.R.T., B.L.); andDuPont Pioneer, Johnston, Iowa 50131 (O.N.D., X.M., M.B., G.Z.-H., C.H., B.V.A., J.H.)
| | - Charlotte Harris
- DuPont Pioneer, Wilmington, Delaware 19880 (S.R.T., B.L.); andDuPont Pioneer, Johnston, Iowa 50131 (O.N.D., X.M., M.B., G.Z.-H., C.H., B.V.A., J.H.)
| | - Brandon Van Allen
- DuPont Pioneer, Wilmington, Delaware 19880 (S.R.T., B.L.); andDuPont Pioneer, Johnston, Iowa 50131 (O.N.D., X.M., M.B., G.Z.-H., C.H., B.V.A., J.H.)
| | - Jeffrey Habben
- DuPont Pioneer, Wilmington, Delaware 19880 (S.R.T., B.L.); andDuPont Pioneer, Johnston, Iowa 50131 (O.N.D., X.M., M.B., G.Z.-H., C.H., B.V.A., J.H.)
| | - Bailin Li
- DuPont Pioneer, Wilmington, Delaware 19880 (S.R.T., B.L.); andDuPont Pioneer, Johnston, Iowa 50131 (O.N.D., X.M., M.B., G.Z.-H., C.H., B.V.A., J.H.)
| |
Collapse
|
399
|
Okamoto M, Matsui A, Tanaka M, Morosawa T, Ishida J, Iida K, Mochizuki Y, Toyoda T, Seki M. Sm-Like Protein-Mediated RNA Metabolism Is Required for Heat Stress Tolerance in Arabidopsis. FRONTIERS IN PLANT SCIENCE 2016; 7:1079. [PMID: 27493656 PMCID: PMC4954817 DOI: 10.3389/fpls.2016.01079] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2016] [Accepted: 07/08/2016] [Indexed: 05/04/2023]
Abstract
Sm-like proteins play multiple functions in RNA metabolism, which is essential for biological processes such as stress responses in eukaryotes. The Arabidopsis thaliana sad1 mutant has a mutation of sm-like protein 5 (LSM5) and shows impaired drought and salt stress tolerances. The lsm5/sad1 mutant also showed hypersensitivity to heat stress. GFP-fused LSM5/SAD1 was localized in the nucleus under optimal growth conditions. After heat stress treatment, GFP-fused LSM5/SAD1 fluorescence was also observed as small cytoplasmic dots, in addition to nuclear localization. Whole genome transcriptome analysis revealed that many genes in Arabidopsis were drastically changed in response to heat stress. More heat-responsive genes were highly expressed in lsm5/sad1 mutant at both 2 and 6 h after heat stress treatment. Additionally, intron-retained and capped transcripts accumulated in the lsm5/sad1 mutant after heat stress treatment. In this study, we also identified non-Arabidopsis Genome Initiative transcripts that were expressed from unannotated regions. Most of these transcripts were antisense transcripts, and many capped non-AGI transcripts accumulated in the lsm5/sad1 mutant during heat stress treatment. These results indicated that LSM5/SAD1 functions to degrade aberrant transcripts through appropriate mRNA splicing and decapping, and precise RNA metabolic machinery is required for heat stress tolerance.
Collapse
Affiliation(s)
- Masanori Okamoto
- Arid Land Research Center, Tottori UniversityHamasaka, Japan
- RIKEN Center for Sustainable Resource ScienceYokohama, Japan
- PRESTO, Japan Science and Technology AgencyKawaguchi, Japan
| | - Akihiro Matsui
- RIKEN Center for Sustainable Resource ScienceYokohama, Japan
| | - Maho Tanaka
- RIKEN Center for Sustainable Resource ScienceYokohama, Japan
| | - Taeko Morosawa
- RIKEN Center for Sustainable Resource ScienceYokohama, Japan
| | - Junko Ishida
- RIKEN Center for Sustainable Resource ScienceYokohama, Japan
| | - Kei Iida
- Graduate School of Medicine, Kyoto UniversityKyoto, Japan
| | | | - Tetsuro Toyoda
- RIKEN Advanced Center for Computing and CommunicationWako, Japan
| | - Motoaki Seki
- RIKEN Center for Sustainable Resource ScienceYokohama, Japan
- Kihara Institute for Biological Research, Yokohama City UniversityYokohama, Japan
- CREST, Japan Science and Technology AgencyKawaguchi, Japan
- *Correspondence: Motoaki Seki,
| |
Collapse
|
400
|
Bergsveinson J, Ewen E, Friesen V, Ziola B. Transcriptional activity and role of plasmids of Lactobacillus brevis BSO 464 and Pediococcus claussenii ATCC BAA-344T during growth in the presence of hops. AIMS Microbiol 2016. [DOI: 10.3934/microbiol.2016.4.460] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
|