HCSGD entry for LMNB1
1. General information
| Official gene symbol | LMNB1 |
|---|---|
| Entrez ID | 4001 |
| Gene full name | lamin B1 |
| Other gene symbols | ADLD LMN LMN2 LMNB |
| Links to Entrez Gene | Links to Entrez Gene |
2. Neighbors in the network
3. Gene ontology annotation
GO ID | GO term | Evidence | Category |
|---|---|---|---|
| GO:0005198 | Structural molecule activity | IEA | molecular_function |
| GO:0005635 | Nuclear envelope | IEA TAS | cellular_component |
| GO:0005637 | Nuclear inner membrane | IEA | cellular_component |
| GO:0005638 | Lamin filament | IEA | cellular_component |
| GO:0005654 | Nucleoplasm | IEA TAS | cellular_component |
| GO:0006915 | Apoptotic process | TAS | biological_process |
| GO:0006921 | Cellular component disassembly involved in execution phase of apoptosis | TAS | biological_process |
| GO:0043274 | Phospholipase binding | IEA | molecular_function |
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4. Expression levels in datasets
- Meta-analysis result
| p-value up | p-value down | FDR up | FDR down |
|---|---|---|---|
| 0.9887936439 | 0.0000100452 | 0.9999902473 | 0.0069833333 |
- Individual experiment result
( "-" represent NA in the specific microarray platform )
( "-" represent NA in the specific microarray platform )
| Data source | Up or down | Log fold change |
|---|---|---|
| GSE11954 | Down | -2.5132701213 |
| GSE13712_SHEAR | Down | -0.4174441119 |
| GSE13712_STATIC | Down | -0.1770814437 |
| GSE19018 | Down | -0.7638278804 |
| GSE19899_A1 | Down | -2.9404355937 |
| GSE19899_A2 | Down | -4.7098091073 |
| PubMed_21979375_A1 | Down | -3.1101610245 |
| PubMed_21979375_A2 | Down | -7.0753576618 |
| GSE35957 | Down | -2.8489558253 |
| GSE36640 | Down | -5.6885157049 |
| GSE54402 | Down | -0.9767291967 |
| GSE9593 | Down | -1.5908709983 |
| GSE43922 | Down | -1.6328950104 |
| GSE24585 | Down | -0.1836461354 |
| GSE37065 | Down | -0.3003484468 |
| GSE28863_A1 | Down | -0.1436976140 |
| GSE28863_A2 | Up | 0.7467983253 |
| GSE28863_A3 | Down | -0.0870039195 |
| GSE28863_A4 | Up | 0.1703820819 |
| GSE48662 | Down | -1.1231778501 |
5. Regulation relationships with compounds/drugs/microRNAs
- Compounds
Not regulated by compounds
- Drugs
Not regulated by drugs
- MicroRNAs
- mirTarBase
- mirTarBase
MiRNA_name | mirBase ID | miRTarBase ID | Experiment | Support type | References (Pubmed ID) |
|---|---|---|---|---|---|
| hsa-miR-373-3p | MIMAT0000726 | MIRT002510 | Microarray//Microarray;Other | Functional MTI (Weak) | 15685193 |
| hsa-miR-124-3p | MIMAT0000422 | MIRT002571 | Proteomics;Microarray | Functional MTI (Weak) | 18668037 |
| hsa-miR-124-3p | MIMAT0000422 | MIRT002571 | Microarray | Functional MTI (Weak) | 15685193 |
| hsa-miR-128-3p | MIMAT0000424 | MIRT022094 | Sequencing | Functional MTI (Weak) | 20371350 |
| hsa-miR-1 | MIMAT0000416 | MIRT023965 | Proteomics | Functional MTI (Weak) | 18668040 |
| hsa-miR-215-5p | MIMAT0000272 | MIRT024320 | Microarray | Functional MTI (Weak) | 19074876 |
| hsa-miR-192-5p | MIMAT0000222 | MIRT026682 | Microarray | Functional MTI (Weak) | 19074876 |
| hsa-miR-101-3p | MIMAT0000099 | MIRT027335 | Sequencing | Functional MTI (Weak) | 20371350 |
| hsa-miR-26b-5p | MIMAT0000083 | MIRT029849 | Microarray | Functional MTI (Weak) | 19088304 |
| hsa-miR-193b-3p | MIMAT0002819 | MIRT041285 | CLASH | Functional MTI (Weak) | 23622248 |
| hsa-miR-484 | MIMAT0002174 | MIRT042270 | CLASH | Functional MTI (Weak) | 23622248 |
| hsa-miR-320a | MIMAT0000510 | MIRT044805 | CLASH | Functional MTI (Weak) | 23622248 |
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- mirRecord
- mirRecord
MicroRNA name | mirBase ID | Target site number | MiRNA mature ID | Test method inter | MiRNA regulation site | Reporter target site | Pubmed ID |
|---|---|---|---|---|---|---|---|
| hsa-miR-373-3p | MIMAT0000726 | NA | hsa-miR-373 | 15685193 |
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6. Text-mining results about the gene
Gene occurances in abstracts of cellular senescence-associated articles: 15 abstracts the gene occurs.
PubMed ID of the article | Sentenece the gene occurs |
|---|---|
| 26654219 | We reveal that the autophagy protein LC3/Atg8 directly interacts with the nuclear lamina protein LMNB1 (lamin B1), and binds to LMN/lamin-associated chromatin domains (LADs) |
| 26354777 | These include the activation of autophagy, a catabolic process operating in the cytoplasm and downregulation of lamin B1, a component of the nuclear lamina |
| 26354777 | We discovered that cells entering BRAF(V600E)- or H-RAS(G12V)-induced senescence downregulate not only lamin B1 but also lamin A, as well as several other nuclear envelope (NE) proteins, resulting in an altered NE morphology |
| 26354777 | Depletion of LMNB1 or LMNA/C was sufficient to recapitulate some OIS features, including cell cycle exit and downregulation of NE proteins |
| 27350809 | Introduction of telomerase gene function in HGPS cells reversed such aging phenotypes along with upregulation of lamin B1 and downregulation of progerin, which is a hallmark of young cells |
| 24861957 | Here, we summarize and review recent findings shedding light on SAHF composition and formation via spatial repositioning of chromatin, with a specific focus on the role of lamin B1 for this process |
| 24380701 | In humans duplication of the LMNB1 gene (encoding lamin B1) causes an adult onset neurodegenerative disorder, termed autosomal dominant leukodystrophy, whilst very recently, LMNB1 has been implicated as a susceptibility gene in neural tube defects |
| 23964094 | Redistribution of the Lamin B1 genomic binding profile affects rearrangement of heterochromatic domains and SAHF formation during senescence |
| 23964094 | Studying a key component of the nuclear lamina lamin B1 (LMNB1), we report dynamic alterations in its genomic profile and their implications for SAHF formation and gene regulation during senescence |
| 23964094 | Genome-wide mapping reveals that LMNB1 is depleted during senescence, preferentially from the central regions of lamina-associated domains (LADs), which are enriched for Lys9 trimethylation on histone H3 (H3K9me3) |
| 23964094 | LMNB1 knockdown facilitates the spatial relocalization of perinuclear H3K9me3-positive heterochromatin, thus promoting SAHF formation, which could be inhibited by ectopic LMNB1 expression |
| 23964094 | Furthermore, despite the global reduction in LMNB1 protein levels, LMNB1 binding increases during senescence in a small subset of gene-rich regions where H3K27me3 also increases and gene expression becomes repressed |
| 23964094 | These results suggest that LMNB1 may contribute to senescence in at least two ways due to its uneven genome-wide redistribution: first, through the spatial reorganization of chromatin and, second, through gene repression |
| 23934658 | Lamin B1 depletion in senescent cells triggers large-scale changes in gene expression and the chromatin landscape |
| 23934658 | While chromatin regulation and lamin B1 down-regulation have been implicated as senescence effectors, functional interactions between them are poorly understood |
| 23934658 | Lamin B1 reduction in proliferating cells triggers senescence and formation of mesas and canyons |
| 23934658 | Our data illustrate profound chromatin reorganization during senescence and suggest that lamin B1 down-regulation in senescence is a key trigger of global and local chromatin changes that impact gene expression, aging, and cancer |
| 23873483 | Duplication of the LMNB1 locus, leading to elevated levels of lamin B1, causes adult-onset autosomal dominant leukodystrophy (ADLD), a rare genetic disease that leads to demyelination in the central nervous system (CNS) |
| 23873483 | How do elevated levels of lamin B1 cause disease and why is the CNS particularly susceptible to lamin B1 fluctuations |
| 23849162 | WRN-mutated fibroblasts showed oxidative stress, increased lamin B1 expression, nuclear dysmorphies and premature senescence |
| 23849162 | Increased expression of lamin B1 with altered lamina architecture observed in WRN-mutated fibroblasts could contribute to premature cellular senescence |
| 23816621 | In senescent cells, lamin A/C-negative, but strongly gamma-H2AX-positive and H3K27me3-positive, cytoplasmic chromatin fragments (CCFs) budded off nuclei, and this was associated with lamin B1 down-regulation and the loss of nuclear envelope integrity |
| 23475125 | Disruption of lamin B1 and lamin B2 processing and localization by farnesyltransferase inhibitors |
| 23475125 | Lamin A and the B-type lamins, lamin B1 and lamin B2, are translated as pre-proteins that are modified at a carboxyl terminal CAAX motif by farnesylation, proteolysis and carboxymethylation |
| 23475125 | Lamin B1 and lamin B2 play important roles in cell proliferation and organ development, but little is known about the role of farnesylation in their functions |
| 23475125 | Treating normal human fibroblasts with farnesyltransferase inhibitors causes the accumulation of unprocessed lamin B2 and lamin A and a decrease in mature lamin B1 |
| 23357361 | Since beta-asarone induced lamin B1 expression, a model is proposed in which beta-asarone inhibits colorectal cancer by inducing senescence through lamin B1 |
| 22496421 | Lamin B1 loss is a senescence-associated biomarker |
| 22496421 | We show here than lamin B1 is lost from primary human and murine cell strains when they are induced to senesce by DNA damage, replicative exhaustion, or oncogene expression |
| 22496421 | However, activation of either the p53 or pRB tumor suppressor pathway was sufficient to induce lamin B1 loss |
| 22496421 | Lamin B1 declined at the mRNA level via a decrease in mRNA stability rather than by the caspase-mediated degradation seen during apoptosis |
| 22496421 | Last, lamin B1 protein and mRNA declined in mouse tissue after senescence was induced by irradiation |
| 22496421 | Our findings suggest that lamin B1 loss can serve as biomarker of senescence both in culture and in vivo |
| 22155925 | Nuclear lamin B1 (LB1) is a major structural component of the nucleus that appears to be involved in the regulation of many nuclear functions |
| 19522540 | Circulating Lamin B1 (LMNB1) biomarker detects early stages of liver cancer in patients |
| 19522540 | LMNB1 functions in nuclear envelope lamina and possesses a transcriptional coregulatory activity having an important role in DNA replication, cellular aging, and stress responses |
| 19522540 | Clinically, the expression level of lamin B1 correlated positively with tumor stages, tumor sizes, and number of nodules |
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