EuRBPDB: a comprehensive resource for annotation, functional and oncological investigation of eukaryotic RNA binding proteins (RBPs)

Liao, Jian-You; Yang, Bing; Zhang, Yuchan; Wang, Xiao-Juan; Ye, Yushan; Peng, Jingwen; Yang, Zhi-Zhi; He, Jun; Zhang, Yin; Hu, Kaishun; Lin, De–Chen; Ding, Yin

doi:10.1101/713164

Cited by 16 publications

(18 citation statements)

References 35 publications

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“…Given the DECTG motif, the potential binding proteins were predicted using the databases of EuRBPDB (http://eurbpdb.syshospital. org/index.php), 17 RegRNA 2.0 (http://regrna2.mbc.nctu.edu.tw/ index.html), 18 and ATtRACT (https://attract.cnic.es/). 19 Nuclear cap-binding subunit 3 (NCBP3), EWS RNA binding protein 1 (EWSR1), and developmentally regulated GTP binding protein 2 (DRG2) were identified as the candidates with top three confidential scores ( Figure 6A) and also as DEGs in MH and SH compared to NC in vivo and in vitro (Table S3).…”

Section: Translation Process Facilitated By Dectg Motif Binding Protementioning

confidence: 99%

Translatome and Transcriptome Profiling of Hypoxic-Induced Rat Cardiomyocytes

Shen

Zeng

Zhang

2020

Molecular Therapy - Nucleic Acids

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Adult cardiac hypoxia as a crucial pathogenesis factor can induce detrimental effects on cardiac injury and dysfunction. The global transcriptome and translatome reflecting the cellular response to hypoxia have not yet been extensively studied in myocardium. In this study, we conducted RNA sequencing (RNA-seq) and ribosome profiling technique (polyribo-seq) in rat heart tissues and H9C2 cells exposed to different periods of hypoxia stress in vivo and in vitro. The temporal gene-expression profiling displayed the distinction of transcriptome and translatome, which were mainly concentrated in cell apoptosis, autophagy, DNA repair, angiogenesis, vascular process, and cardiac cell proliferation and differentiation. A large number of genes such as GNAI3, SEPT4, FANCL, BNIP3, TBX3, ESR2, PTGS2, KLF4, and ADRB2, whose transcript and translation levels are closely correlated, were identified to own a common RNA motif "5 0-GAAGCUGCC-3 0 " in 5 0 UTR. NCBP3 was further determined to recognize this RNA motif and facilitate translational process in myocardium under hypoxia stress. Taken together, our data show the close connection between alterations of transcriptome and translatome after hypoxia exposure, emphasizing the significance of translational regulation in related studies. The profiled molecular responses in current study may be valuable resources for advanced understanding of the mechanisms underlying hypoxia-induced effect on heart diseases.

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Section: Translation Process Facilitated By Dectg Motif Binding Protementioning

confidence: 99%

Translatome and Transcriptome Profiling of Hypoxic-Induced Rat Cardiomyocytes

Shen

Zeng

Zhang

2020

Molecular Therapy - Nucleic Acids

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“…We reanalyzed microarray expression data of samples from 64 medulloblastoma patients to analyze RNA-binding proteins (RBPs) expression in patients across the four reported sub-groups [ 35 ]. Among a list of 1220 canonical RBPs represented on the microarray [ 36 ], we found that YBX1 is ubiquitously expressed in medulloblastoma patient samples across all sub-types and ranks among the top expressed RBPs on average ( Figure 1 a). However, there was no clustering of the medulloblastoma subgroups SHH, WNT, group 3 and group 4 based on YBX1 expression.…”

Section: Resultsmentioning

confidence: 99%

YBX1 Indirectly Targets Heterochromatin-Repressed Inflammatory Response-Related Apoptosis Genes through Regulating CBX5 mRNA

Kloetgen

Duggimpudi

Schuschel

et al. 2020

IJMS

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Medulloblastomas arise from undifferentiated precursor cells in the cerebellum and account for about 20% of all solid brain tumors during childhood; standard therapies include radiation and chemotherapy, which oftentimes come with severe impairment of the cognitive development of the young patients. Here, we show that the posttranscriptional regulator Y-box binding protein 1 (YBX1), a DNA- and RNA-binding protein, acts as an oncogene in medulloblastomas by regulating cellular survival and apoptosis. We observed different cellular responses upon YBX1 knockdown in several medulloblastoma cell lines, with significantly altered transcription and subsequent apoptosis rates. Mechanistically, PAR-CLIP for YBX1 and integration with RNA-Seq data uncovered direct posttranscriptional control of the heterochromatin-associated gene CBX5; upon YBX1 knockdown and subsequent CBX5 mRNA instability, heterochromatin-regulated genes involved in inflammatory response, apoptosis and death receptor signaling were de-repressed. Thus, YBX1 acts as an oncogene in medulloblastoma through indirect transcriptional regulation of inflammatory genes regulating apoptosis and represents a promising novel therapeutic target in this tumor entity.

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“…The lncRNAs were applied to analyze their possible binding proteins using the web interface of lncSEA, a new comprehensive human lncRNA sets resource and enrichment analysis platform which also integrates RNA binding proteins rooted in large-scale crosslinking-immunprecipitation sequencing (CLIP-Seq) data from StarBase, RNAInter (RNA interactome database) and EuRBPDB (a comprehensive and user-friendly database for eukaryotic RNA binding proteins) [32][33][34][35].…”

Section: Identi Cation Of the Cerna-gene Relationship Pairsmentioning

confidence: 99%

LncRNA- and circRNA-associated competing endogenous RNA (ceRNA) networks in leukocytes in traditional Chinese medicine (TCM)-defined Pi-qi-deficiency syndrome and Pi-wei damp-heat syndrome resulting from chronic atrophic gastritis

You

Wang

et al. 2021

Preprint

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Background To investigate lncRNA/circRNA-associated competing endogenous RNA (ceRNA)-gene regulation underlying leukocyte functions and characteristics, especially the potential ceRNA biomarkers, implicated in traditional Chinese medicine (TCM)-defined Pi-qi-deficiency syndrome (PQDS) and Pi-wei damp-heat syndrome (PDHS) resulting from chronic atrophic gastritis (CAG). Methods Based on RNA-sequencing approach, comparing with healthy control population, we identified the PDHS- or PQDS-specific lncRNAs/circRNAs in leukocytes, especially the Zheng (syndrome)-specific ceRNAs and their corresponding ceRNA regulatory networks, further decoding their potential functions and pathways. Results Despite being the TCM-defined Zhengs resulting from the same disease of CAG, the Zheng-specific lncRNAs/circRNAs in leukocytes were not same in PQDS and PDHS. There were the Zheng-specific lncRNA/circRNA-associated ceRNAs identified in the leukocytes, and their corresponding ceRNA regulatory networks were generated, including the ceRNA-gene binary relationship networks and the miRNA-centered ceRNA-miRNA-gene triple relationship networks. In the generated Zheng-specific ceRNA networks, the PQDS-specific ceRNA-governed genes in leukocytes, keeping more complex interactions with each other, were enriched in pathways related to MAPK signaling, receptor tyrosine kinases signaling as well as complement and coagulation cascades. Notably, the enriched pathways associated with adherens junction, focal adhesion, ECM-receptor interaction, ECM-organization and cell surface interactions, were implicated in cell-to-cell adhesion/junction and communication, probably contributing to the characteristics and functions of leukocytes. The PDHS-specific ceRNA-regulated genes, seemed to have no more interactions with each other, were enriched in the biological processes related to regulation of cell morphogenesis, neutrophil activation and degranulation, and lymphocyte mediated immunity such as B-cell receptor signaling, complement and coagulation cascades, and regulation of NK/T-cell mediated cytotoxicity. Importantly, the five exosome-encapsuled ceRNAs, containing ZFAS1 (NR_036658.2), AL353719.1 (ENST00000566847), LOH12CR2 (NR_024061.1) and two new lncRNAs (TCONS_00038035 and TCONS_00027600), particularly higher expression in the leukocytes in PQDS rather than PDHS, could be the potential ceRNA biomarkers for differentiation of the TCM-defined PQDS and PDHS among CAG patients. Conclusions These results may provide new insights into the characteristic and functional changes of leukocytes in the two TCM Zhengs, especially the Zheng-specific ceRNA-mediated gene regulation underlying leukocyte characteristics and functions, with potential leukocyte biomarkers for future application in integrative medicine.

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EuRBPDB: a comprehensive resource for annotation, functional and oncological investigation of eukaryotic RNA binding proteins (RBPs)

Cited by 16 publications

References 35 publications

Translatome and Transcriptome Profiling of Hypoxic-Induced Rat Cardiomyocytes

Translatome and Transcriptome Profiling of Hypoxic-Induced Rat Cardiomyocytes

YBX1 Indirectly Targets Heterochromatin-Repressed Inflammatory Response-Related Apoptosis Genes through Regulating CBX5 mRNA

LncRNA- and circRNA-associated competing endogenous RNA (ceRNA) networks in leukocytes in traditional Chinese medicine (TCM)-defined Pi-qi-deficiency syndrome and Pi-wei damp-heat syndrome resulting from chronic atrophic gastritis

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