Transcriptomic, proteomic, and metabolomic landscape of positional memory in the caudal fin of zebrafish

Regeneration requires cells to regulate proliferation and patterning according to their spatial position. Positional memory is a property that enables regenerating cells to recall spatial information from the uninjured tissue. Positional memory is hypothesized to rely on gradients of molecules, few of which have been identified. Here, we quantified the global abundance of transcripts, proteins, and metabolites along the proximodistal axis of caudal fins of uninjured and regenerating adult zebrafish. Using this approach, we uncovered complex overlapping expression patterns for hundreds of molecules involved in diverse cellular functions, including development, bioelectric signaling, and amino acid and lipid metabolism. Moreover, 32 genes differentially expressed at the RNA level had concomitant differential expression of the encoded proteins. Thus, the identification of proximodistal differences in levels of RNAs, proteins, and metabolites will facilitate future functional studies of positional memory during appendage regeneration.

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New Insights into the p38γ and p38δ MAPK Pathways

Journal of Signal Transduction ◽

10.1155/2012/520289 ◽

2012 ◽

Vol 2012 ◽

pp. 1-8 ◽

Cited By ~ 35

Author(s):

Ana Risco ◽

Ana Cuenda

Keyword(s):

Amino Acid ◽

Amino Acid Sequence ◽

Protein Kinases ◽

Expression Patterns ◽

Cellular Functions ◽

Mitogen Activated Protein Kinases ◽

Pathological Conditions ◽

Mitogen Activated Protein ◽

Distinct Role ◽

Made In

The mammalian p38 mitogen-activated protein kinases (MAPKs) family is composed of four members (p38α, p38β, p38γ, and p38δ), which are very similar in amino acid sequence but differ in their expression patterns. This suggests that they may have specific functions in different organs. In the last years most of the effort has been centred on the study of the function of the p38α isoform, which is widely referred to as p38 in the literature. However, the role that other p38 isoforms play in cellular functions and their implication in some of the pathological conditions have not been precisely defined so far. In this paper we highlight recent advances made in defining the functions of the two less studied alternative p38MAPKs, p38γ and p38δ. We describe that these p38MAPKs show similarities to the classical p38α isoform, although they may play central and distinct role in certain physiological and pathological processes.

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Differential expression of the ras gene family in mice

Molecular and Cellular Biology ◽

10.1128/mcb.7.4.1535-1540.1987 ◽

1987 ◽

Vol 7 (4) ◽

pp. 1535-1540 ◽

Cited By ~ 1

Author(s):

J Leon ◽

I Guerrero ◽

A Pellicer

Keyword(s):

Gene Family ◽

Differential Expression ◽

Adult Mouse ◽

Expression Patterns ◽

Cellular Functions ◽

Ras Gene ◽

Ras Genes ◽

Mouse Tissues

We compared the expression of the ras gene family (H-ras, K-ras, and N-ras) in adult mouse tissues and during development. We found substantial variations in expression among different organs and in the amounts of the different transcripts originating from each gene, especially for the N-ras gene. The expression patterns were consistent with the reported preferential tissue activation of ras genes and suggested different cellular functions for each of the ras genes.

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Differential expression of the ras gene family in mice.

Molecular and Cellular Biology ◽

10.1128/mcb.7.4.1535 ◽

1987 ◽

Vol 7 (4) ◽

pp. 1535-1540 ◽

Cited By ~ 132

Author(s):

J Leon ◽

I Guerrero ◽

A Pellicer

Keyword(s):

Gene Family ◽

Differential Expression ◽

Adult Mouse ◽

Expression Patterns ◽

Cellular Functions ◽

Ras Gene ◽

Ras Genes ◽

Mouse Tissues

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Differential gene expression in liposarcoma: Insight into pathways for dedifferentiation?

Journal of Clinical Oncology ◽

10.1200/jco.2012.30.15_suppl.10048 ◽

2012 ◽

Vol 30 (15_suppl) ◽

pp. 10048-10048

Author(s):

Dale Han ◽

Gregory C Bloom ◽

Marilyn M Bui ◽

Steven Enkemann ◽

Hideko Yamauchi ◽

...

Keyword(s):

Gene Expression ◽

Lipid Metabolism ◽

Network Analysis ◽

Differential Expression ◽

Differential Gene Expression ◽

Gene Networks ◽

Expression Patterns ◽

Differential Regulation ◽

Gene Expression Patterns ◽

Differential Gene

10048 Background: Liposarcoma (LPS) dedifferentiation signifies conversion to a clinically aggressive phenotype, but the biologic processes required for this change have not been determined. We describe differential gene expression patterns between well-differentiated (WD) and dedifferentiated (DD) tumors to determine pathways involved in LPS dedifferentiation. Methods: From 1999 to 2006, 121 fatty tumors were resected at a single institution. Twenty tumors, consisting of atypical lipomatous tumors (ALT), WD LPS or DD LPS, were randomly selected and clinicopathologic characteristics were retrospectively reviewed. Gene expression profiling was performed on extracted RNA using the Affymetrix GeneChip platform. Differentially expressed genes were obtained and gene network analysis was done using GeneGO by MetaCore. Results: Median age was 59 years and 70% of cases were male. WD tumors, consisting of 3 ALT and 6 WD LPS, were compared with 11 DD LPS. After a median follow-up of 64 months, 7 patients had died of whom 6 had DD LPS. DD histology was associated with lower overall survival (p<0.05). Significance Analysis of Microarrays for WD tumors vs. DD LPS using a 0% false discovery rate showed differential expression of 188 genes. Network analysis of genes from WD tumors vs. DD LPS showed significant (p<0.001) differential regulation of glucose-activated transcription factor ChREBP (carbohydrate response element binding protein), a key element involved in lipogenesis, gluconeogenesis and glycolysis. There was also significant differential regulation of insulin signaling, PI3K-dependent and PKA signal transduction pathways and of amino acid, fatty acid and glucose metabolism pathways (p<0.05). These pathways, based on Gene Ontology cellular processes, mapped to gene networks primarily involved in lipid metabolism (p<0.05). Conclusions: Differential expression of genes involved in lipid metabolism networks is seen in DD LPS and changes in lipid metabolism may be associated with dedifferentiation. These differential gene expression patterns may help identify fatty tumors potentially at risk for progressing to a malignant or DD state and provide prognostic factors and therapeutic targets for patients with LPS.

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Analysis of the Differential Expression Patterns of Sumoylation Enzymes E1, E2 and E3 in Ocular Cell Lines

Current Molecular Medicine ◽

10.2174/1566524019666190112143636 ◽

2019 ◽

Vol 18 (8) ◽

pp. 509-515 ◽

Cited By ~ 1

Author(s):

Qian Nie ◽

Jie Xie ◽

Xiaodong Gong ◽

Zhongwen Luo ◽

Ling Wang ◽

...

Keyword(s):

Differential Expression ◽

Cell Lines ◽

Expression Patterns

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Differential expression and correlation analysis of miRNA–mRNA profiles in swine testicular cells infected with porcine epidemic diarrhea virus

Scientific Reports ◽

10.1038/s41598-021-81189-5 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Xiaoqian Zhang ◽

Chang Li ◽

Bingzhou Zhang ◽

Zhonghua Li ◽

Wei Zeng ◽

...

Keyword(s):

Differential Expression ◽

Porcine Epidemic Diarrhea Virus ◽

Expression Profiles ◽

Expression Patterns ◽

Bacterial Invasion ◽

Sequencing Data ◽

Diarrhea Virus ◽

Comparison Groups ◽

Porcine Epidemic Diarrhea

AbstractThe variant virulent porcine epidemic diarrhea virus (PEDV) strain (YN15) can cause severe porcine epidemic diarrhea (PED); however, the attenuated vaccine-like PEDV strain (YN144) can induce immunity in piglets. To investigate the differences in pathogenesis and epigenetic mechanisms between the two strains, differential expression and correlation analyses of the microRNA (miRNA) and mRNA in swine testicular (ST) cells infected with YN15, YN144, and mock were performed on three comparison groups (YN15 vs Control, YN144 vs Control, and YN15 vs YN144). The mRNA and miRNA expression profiles were obtained using next-generation sequencing (NGS), and the differentially expressed (DE) (p-value < 0.05) mRNA and miRNA were obtained using DESeq R package. mRNAs targeted by DE miRNAs were predicted using the miRanda algortithm. 8039, 8631 and 3310 DE mRNAs, and 36, 36, and 22 DE miRNAs were identified in the three comparison groups, respectively. 14,140, 15,367 and 3771 DE miRNA–mRNA (targeted by DE miRNAs) interaction pairs with negatively correlated expression patterns were identified, and interaction networks were constructed using Cytoscape. Six DE miRNAs and six DE mRNAs were randomly selected to verify the sequencing data by real-time relative quantitative reverse transcription polymerase chain reaction (qRT-PCR). Based on bioinformatics analysis, we discovered the differences were mostly involved in host immune responses and viral pathogenicity, including NF-κB signaling pathway and bacterial invasion of epithelial cells, etc. This is the first comprehensive comparison of DE miRNA–mRNA pairs in YN15 and YN144 infection in vitro, which could provide novel strategies for the prevention and control of PED.

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Phylogenetic comparison and splice site conservation of eukaryotic U1 snRNP-specific U1-70K gene family

Scientific Reports ◽

10.1038/s41598-021-91693-3 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Tao Fan ◽

Yu-Zhen Zhao ◽

Jing-Fang Yang ◽

Qin-Lai Liu ◽

Yuan Tian ◽

...

Keyword(s):

Gene Family ◽

Splice Site ◽

Messenger Rna ◽

Expression Patterns ◽

Protein Structures ◽

Single Copy ◽

Central Component ◽

Animal Kingdom ◽

Functional Studies ◽

U1 Snrnp

AbstractEukaryotic cells can expand their coding ability by using their splicing machinery, spliceosome, to process precursor mRNA (pre-mRNA) into mature messenger RNA. The mega-macromolecular spliceosome contains multiple subcomplexes, referred to as small nuclear ribonucleoproteins (snRNPs). Among these, U1 snRNP and its central component, U1-70K, are crucial for splice site recognition during early spliceosome assembly. The human U1-70K has been linked to several types of human autoimmune and neurodegenerative diseases. However, its phylogenetic relationship has been seldom reported. To this end, we carried out a systemic analysis of 95 animal U1-70K genes and compare these proteins to their yeast and plant counterparts. Analysis of their gene and protein structures, expression patterns and splicing conservation suggest that animal U1-70Ks are conserved in their molecular function, and may play essential role in cancers and juvenile development. In particular, animal U1-70Ks display unique characteristics of single copy number and a splicing isoform with truncated C-terminal, suggesting the specific role of these U1-70Ks in animal kingdom. In summary, our results provide phylogenetic overview of U1-70K gene family in vertebrates. In silico analyses conducted in this work will act as a reference for future functional studies of this crucial U1 splicing factor in animal kingdom.

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The methyltransferase METTL9 mediates pervasive 1-methylhistidine modification in mammalian proteomes

Nature Communications ◽

10.1038/s41467-020-20670-7 ◽

2021 ◽

Vol 12 (1) ◽

Author(s):

Erna Davydova ◽

Tadahiro Shimazu ◽

Maren Kirstin Schuhmacher ◽

Magnus E. Jakobsson ◽

Hanneke L. D. M. Willemen ◽

...

Keyword(s):

Amino Acid ◽

Protein Function ◽

Crucial Role ◽

Complex I ◽

Protein Modification ◽

Zinc Binding ◽

Functional Studies ◽

Mitochondrial Respiratory Complex ◽

Respiratory Complex I ◽

Broad Specificity

AbstractPost-translational methylation plays a crucial role in regulating and optimizing protein function. Protein histidine methylation, occurring as the two isomers 1- and 3-methylhistidine (1MH and 3MH), was first reported five decades ago, but remains largely unexplored. Here we report that METTL9 is a broad-specificity methyltransferase that mediates the formation of the majority of 1MH present in mouse and human proteomes. METTL9-catalyzed methylation requires a His-x-His (HxH) motif, where “x” is preferably a small amino acid, allowing METTL9 to methylate a number of HxH-containing proteins, including the immunomodulatory protein S100A9 and the NDUFB3 subunit of mitochondrial respiratory Complex I. Notably, METTL9-mediated methylation enhances respiration via Complex I, and the presence of 1MH in an HxH-containing peptide reduced its zinc binding affinity. Our results establish METTL9-mediated 1MH as a pervasive protein modification, thus setting the stage for further functional studies on protein histidine methylation.

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