General Information of the m6A Target Gene (ID: M6ATAR00452)
Target Name Y-box-binding protein 1 (YBX1)
Synonyms
YB-1; CCAAT-binding transcription factor I subunit A; CBF-A; DNA-binding protein B; DBPB; Enhancer factor I subunit A; EFI-A; Nuclease-sensitive element-binding protein 1; Y-box transcription factor; NSEP1; YB1
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Gene Name YBX1
Chromosomal Location 1p34.2
Family YBX1 family
Function
DNA- and RNA-binding protein involved in various processes, such as translational repression, RNA stabilization, mRNA splicing, DNA repair and transcription regulation. Predominantly acts as a RNA-binding protein: binds preferentially to the 5'-[CU]CUGCG-3' RNA motif and specifically recognizes mRNA transcripts modified by C5-methylcytosine (m5C). Promotes mRNA stabilization: acts by binding to m5C-containing mRNAs and recruiting the mRNA stability maintainer ELAVL1, thereby preventing mRNA decay. Component of the CRD-mediated complex that promotes MYC mRNA stability. Contributes to the regulation of translation by modulating the interaction between the mRNA and eukaryotic initiation factors (By similarity). Plays a key role in RNA composition of extracellular exosomes by defining the sorting of small non-coding RNAs, such as tRNAs, Y RNAs, Vault RNAs and miRNAs. Probably sorts RNAs in exosomes by recognizing and binding C5-methylcytosine (m5C)-containing RNAs. Acts as a key effector of epidermal progenitors by preventing epidermal progenitor senescence: acts by regulating the translation of a senescence-associated subset of cytokine mRNAs, possibly by binding to m5C-containing mRNAs. Also involved in pre-mRNA alternative splicing regulation: binds to splice sites in pre-mRNA and regulates splice site selection. Also able to bind DNA: regulates transcription of the multidrug resistance gene MDR1 is enhanced in presence of the APEX1 acetylated form at 'Lys-6' and 'Lys-7'. Binds to promoters that contain a Y-box (5'-CTGATTGGCCAA-3'), such as MDR1 and HLA class II genes. Promotes separation of DNA strands that contain mismatches or are modified by cisplatin. Has endonucleolytic activity and can introduce nicks or breaks into double-stranded DNA, suggesting a role in DNA repair. The secreted form acts as an extracellular mitogen and stimulates cell migration and proliferation.
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Gene ID 4904
Uniprot ID
YBOX1_HUMAN
HGNC ID
HGNC:8014
Ensembl Gene ID
ENSG00000065978
KEGG ID
hsa:4904
Full List of m6A Methylation Regulator of This Target Gene and Corresponding Disease/Drug Response(s)
YBX1 can be regulated by the following regulator(s), and cause disease/drug response(s). You can browse detail information of regulator(s) or disease/drug response(s).
Browse Regulator
Browse Disease
Insulin-like growth factor 2 mRNA-binding protein 1 (IGF2BP1) [READER]
Representative RNA-seq result indicating the expression of this target gene regulated by IGF2BP1
Cell Line PANC-1 cell line Homo sapiens
Treatment: siIGF2BP1 PANC-1 cells
Control: siControl PANC-1 cells
GSE161087
Regulation
logFC: -6.25E-01
p-value: 4.95E-03
More Results Click to View More RNA-seq Results
In total 2 item(s) under this regulator
Experiment 1 Reporting the m6A Methylation Regulator of This Target Gene [1]
Response Summary Y-box-binding protein 1 (YBX1) selectively functions in regulating survival of myeloid leukemia cells. YBX1 interacts with insulin-like growth factor 2 messenger RNA (mRNA)-binding proteins (IGF2BPs) and stabilizes m6A-tagged RNA. YBX1 deficiency dysregulates the expression of apoptosis-related genes and promotes mRNA decay of MYC and BCL2 in an m6A-dependent manner, which contributes to the defective survival that results from deletion of YBX1.
Target Regulation Up regulation
Responsed Disease Myeloid leukaemia ICD-11: 2B33.1
Cell Process Cell apoptosis
In-vitro Model Leukemia stem cell line (Leukemia stem cell line)
Kasumi-1 Myeloid leukemia with maturation Homo sapiens CVCL_0589
MOLM-13 Adult acute myeloid leukemia Homo sapiens CVCL_2119
THP-1 Childhood acute monocytic leukemia Homo sapiens CVCL_0006
MV4-11 Childhood acute monocytic leukemia Homo sapiens CVCL_0064
BV-173 Chronic myelogenous leukemia Homo sapiens CVCL_0181
NOMO-1 Adult acute monocytic leukemia Homo sapiens CVCL_1609
K-562 Chronic myelogenous leukemia Homo sapiens CVCL_0004
KG-1a Adult acute myeloid leukemia Homo sapiens CVCL_1824
Experiment 2 Reporting the m6A Methylation Regulator of This Target Gene [2]
Response Summary GSEA revealed that KIAA1429, METTL3, and IGF2BP1 were significantly related to multiple biological behaviors, including proliferation, apoptosis, metastasis, energy metabolism, drug resistance, and recurrence, and that KIAA1429 and IGF2BP1 had potential target genes, including E2F3, WTAP, CCND1, CDK4, EGR2, Y-box-binding protein 1 (YBX1), and TLX, which were associated with lung cancers.
Responsed Disease Lung cancer ICD-11: 2C25
Cell Process Cell apoptosis
In-vitro Model A-549 Lung adenocarcinoma Homo sapiens CVCL_0023
NCI-H520 Lung squamous cell carcinoma Homo sapiens CVCL_1566
HBE (Human bronchial epithelial cell line)
LTEP-a2 Endocervical adenocarcinoma Homo sapiens CVCL_6929
SK-MES-1 Lung squamous cell carcinoma Homo sapiens CVCL_0630
Insulin-like growth factor 2 mRNA-binding protein 2 (IGF2BP2) [READER]
Representative RIP-seq result supporting the interaction between YBX1 and the regulator
Cell Line HEK293T Homo sapiens
Regulation logFC: 1.14E+00 GSE90639
In total 1 item(s) under this regulator
Experiment 1 Reporting the m6A Methylation Regulator of This Target Gene [1]
Response Summary Y-box-binding protein 1 (YBX1) selectively functions in regulating survival of myeloid leukemia cells. YBX1 interacts with insulin-like growth factor 2 messenger RNA (mRNA)-binding proteins (IGF2BPs) and stabilizes m6A-tagged RNA. YBX1 deficiency dysregulates the expression of apoptosis-related genes and promotes mRNA decay of MYC and BCL2 in an m6A-dependent manner, which contributes to the defective survival that results from deletion of YBX1.
Target Regulation Up regulation
Responsed Disease Myeloid leukaemia ICD-11: 2B33.1
Cell Process Cell apoptosis
In-vitro Model Leukemia stem cell line (Leukemia stem cell line)
Kasumi-1 Myeloid leukemia with maturation Homo sapiens CVCL_0589
MOLM-13 Adult acute myeloid leukemia Homo sapiens CVCL_2119
THP-1 Childhood acute monocytic leukemia Homo sapiens CVCL_0006
MV4-11 Childhood acute monocytic leukemia Homo sapiens CVCL_0064
BV-173 Chronic myelogenous leukemia Homo sapiens CVCL_0181
NOMO-1 Adult acute monocytic leukemia Homo sapiens CVCL_1609
K-562 Chronic myelogenous leukemia Homo sapiens CVCL_0004
KG-1a Adult acute myeloid leukemia Homo sapiens CVCL_1824
Insulin-like growth factor 2 mRNA-binding protein 3 (IGF2BP3) [READER]
Representative RIP-seq result supporting the interaction between YBX1 and the regulator
Cell Line HEK293T Homo sapiens
Regulation logFC: 2.22E+00 GSE90639
In total 1 item(s) under this regulator
Experiment 1 Reporting the m6A Methylation Regulator of This Target Gene [1]
Response Summary Y-box-binding protein 1 (YBX1) selectively functions in regulating survival of myeloid leukemia cells. YBX1 interacts with insulin-like growth factor 2 messenger RNA (mRNA)-binding proteins (IGF2BPs) and stabilizes m6A-tagged RNA. YBX1 deficiency dysregulates the expression of apoptosis-related genes and promotes mRNA decay of MYC and BCL2 in an m6A-dependent manner, which contributes to the defective survival that results from deletion of YBX1.
Target Regulation Up regulation
Responsed Disease Myeloid leukaemia ICD-11: 2B33.1
Cell Process Cell apoptosis
In-vitro Model Leukemia stem cell line (Leukemia stem cell line)
Kasumi-1 Myeloid leukemia with maturation Homo sapiens CVCL_0589
MOLM-13 Adult acute myeloid leukemia Homo sapiens CVCL_2119
THP-1 Childhood acute monocytic leukemia Homo sapiens CVCL_0006
MV4-11 Childhood acute monocytic leukemia Homo sapiens CVCL_0064
BV-173 Chronic myelogenous leukemia Homo sapiens CVCL_0181
NOMO-1 Adult acute monocytic leukemia Homo sapiens CVCL_1609
K-562 Chronic myelogenous leukemia Homo sapiens CVCL_0004
KG-1a Adult acute myeloid leukemia Homo sapiens CVCL_1824
Protein virilizer homolog (VIRMA) [WRITER]
In total 1 item(s) under this regulator
Experiment 1 Reporting the m6A Methylation Regulator of This Target Gene [2]
Response Summary GSEA revealed that KIAA1429, METTL3, and IGF2BP1 were significantly related to multiple biological behaviors, including proliferation, apoptosis, metastasis, energy metabolism, drug resistance, and recurrence, and that KIAA1429 and IGF2BP1 had potential target genes, including E2F3, WTAP, CCND1, CDK4, EGR2, Y-box-binding protein 1 (YBX1), and TLX, which were associated with lung cancers.
Responsed Disease Lung cancer ICD-11: 2C25
Cell Process Cell apoptosis
In-vitro Model A-549 Lung adenocarcinoma Homo sapiens CVCL_0023
NCI-H520 Lung squamous cell carcinoma Homo sapiens CVCL_1566
HBE (Human bronchial epithelial cell line)
LTEP-a2 Endocervical adenocarcinoma Homo sapiens CVCL_6929
SK-MES-1 Lung squamous cell carcinoma Homo sapiens CVCL_0630
Malignant haematopoietic neoplasm [ICD-11: 2B33]
In total 1 item(s) under this disease
Experiment 1 Reporting the m6A-centered Disease Response [1]
Response Summary Y-box-binding protein 1 (YBX1) selectively functions in regulating survival of myeloid leukemia cells. YBX1 interacts with insulin-like growth factor 2 messenger RNA (mRNA)-binding proteins (IGF2BPs) and stabilizes m6A-tagged RNA. YBX1 deficiency dysregulates the expression of apoptosis-related genes and promotes mRNA decay of MYC and BCL2 in an m6A-dependent manner, which contributes to the defective survival that results from deletion of YBX1.
Responsed Disease Myeloid leukaemia [ICD-11: 2B33.1]
Target Regulator Insulin-like growth factor 2 mRNA-binding protein 1 (IGF2BP1) READER
Target Regulation Up regulation
Cell Process Cell apoptosis
In-vitro Model Leukemia stem cell line (Leukemia stem cell line)
Kasumi-1 Myeloid leukemia with maturation Homo sapiens CVCL_0589
MOLM-13 Adult acute myeloid leukemia Homo sapiens CVCL_2119
THP-1 Childhood acute monocytic leukemia Homo sapiens CVCL_0006
MV4-11 Childhood acute monocytic leukemia Homo sapiens CVCL_0064
BV-173 Chronic myelogenous leukemia Homo sapiens CVCL_0181
NOMO-1 Adult acute monocytic leukemia Homo sapiens CVCL_1609
K-562 Chronic myelogenous leukemia Homo sapiens CVCL_0004
KG-1a Adult acute myeloid leukemia Homo sapiens CVCL_1824
Lung cancer [ICD-11: 2C25]
In total 2 item(s) under this disease
Experiment 1 Reporting the m6A-centered Disease Response [2]
Response Summary GSEA revealed that KIAA1429, METTL3, and IGF2BP1 were significantly related to multiple biological behaviors, including proliferation, apoptosis, metastasis, energy metabolism, drug resistance, and recurrence, and that KIAA1429 and IGF2BP1 had potential target genes, including E2F3, WTAP, CCND1, CDK4, EGR2, Y-box-binding protein 1 (YBX1), and TLX, which were associated with lung cancers.
Responsed Disease Lung cancer [ICD-11: 2C25]
Target Regulator Insulin-like growth factor 2 mRNA-binding protein 1 (IGF2BP1) READER
Cell Process Cell apoptosis
In-vitro Model A-549 Lung adenocarcinoma Homo sapiens CVCL_0023
NCI-H520 Lung squamous cell carcinoma Homo sapiens CVCL_1566
HBE (Human bronchial epithelial cell line)
LTEP-a2 Endocervical adenocarcinoma Homo sapiens CVCL_6929
SK-MES-1 Lung squamous cell carcinoma Homo sapiens CVCL_0630
Experiment 2 Reporting the m6A-centered Disease Response [2]
Response Summary GSEA revealed that KIAA1429, METTL3, and IGF2BP1 were significantly related to multiple biological behaviors, including proliferation, apoptosis, metastasis, energy metabolism, drug resistance, and recurrence, and that KIAA1429 and IGF2BP1 had potential target genes, including E2F3, WTAP, CCND1, CDK4, EGR2, Y-box-binding protein 1 (YBX1), and TLX, which were associated with lung cancers.
Responsed Disease Lung cancer [ICD-11: 2C25]
Target Regulator Protein virilizer homolog (VIRMA) WRITER
Cell Process Cell apoptosis
In-vitro Model A-549 Lung adenocarcinoma Homo sapiens CVCL_0023
NCI-H520 Lung squamous cell carcinoma Homo sapiens CVCL_1566
HBE (Human bronchial epithelial cell line)
LTEP-a2 Endocervical adenocarcinoma Homo sapiens CVCL_6929
SK-MES-1 Lung squamous cell carcinoma Homo sapiens CVCL_0630
References
Ref 1 YBX1 is required for maintaining myeloid leukemia cell survival by regulating BCL2 stability in an m6A-dependent manner. Blood. 2021 Jul 8;138(1):71-85. doi: 10.1182/blood.2020009676.
Ref 2 Identification of pathology-specific regulators of m(6)A RNA modification to optimize lung cancer management in the context of predictive, preventive, and personalized medicine. EPMA J. 2020 Jul 29;11(3):485-504. doi: 10.1007/s13167-020-00220-3. eCollection 2020 Sep.