Knockout of the DNA binding domains in human-specific lncRNAs causes changed expression of target genes
Ontology highlight
ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE213231 | GEO | 2022/09/16
REPOSITORIES: GEO
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Project description:Downregulations of TCAM1P-004 and RP11-598D14.1 were frequently observed in HCC tumors as compared to adjacent non-tumor tissues. To further study the molecular functions of TCAM1P-004 and RP11-598D14.1, we attempted to identify the gene targets regulated by either lncRNAs. Knockdown of TCAM1P-004 or RP11-598D14.1 were achieved by transduction of lentivirus carrying respective shRNAs in non-tumor hepatocyte MIHA cells. Diffferentially expressed genes after knockdown of the lncRNAs were compared to cells tranduced with lentivirus carrying scramble shRNAs.
2018-10-24 | E-MTAB-7280 | biostudies-arrayexpress
Project description:Arraystar SE-lncRNAs Arrays was used to systematically profile the differentially expressed SE-lncRNAs along with corresponding SE-regulated protein coding genes from eight leiomyomas and paired myometrium. The analysis indicated 7680 SE-lncRNAs were expressed, of which 721 SE-lncRNAs were increased, while 247 SE-lncRNAs were decreased by 1.5-fold or greater in leiomyoma. Thirteen novel SE-lncRNAs and their corresponding protein coding genes were selected, and their expression was confirmed in eighty-one paired leiomyoma tissues by quantitative real-time PCR. The thirteen pairs of SE-lncRNAs and their corresponding protein coding genes included RP11-353N14.2/CBX4, SOCS2-AS1/SOCS2, RP1-170O19.14/HOXA11, CASC15/PRL, EGFLAM-AS1/EGFLAM, RP11-225H22/NEURL1, RP5-1086K13.1/CD58, AC092839.3/SPTBN1, RP11-69I8.3/CTGF, TM4SF1-AS1/TM4SF1, RP11-373D23/FOSL2, RP11-399K21.11/COMTD1 and CTB-113P19.1/SPARC. Collectively, our results indicate that the differential expression of SE in fibroids is another mechanism contributing to dysregulation of protein coding genes in fibroids.
2022-01-11 | GSE193320 | GEO
Project description:Gene silencing in bacteria is mediated by chromatin proteins, of which Escherichia coli H-NS is a paradigmatic example. H-NS forms nucleoprotein filaments with either one or two DNA duplexes. However, the overall structures, arrangements of DNA-binding domains (DBDs), positions of DBD–DNA contacts, and determinants of genomic distribution for these linear and bridged filaments are uncertain. To connect H-NS structures that silence genes in vivo with features elucidated in vitro, we developed a multimodal multiscale analysis that combines a new method for chromatin reconstitution and mapping (Nitro-seq), ChIP-seq, tethered-nuclease mapping of DBD–DNA contacts (TEN-map), ·OH footprinting, molecular dynamics, and bioinformatics. We find that DNA sequence principally governs H-NS-filament location with indistinguishable sequence specificity in bridged or linear forms with or without the H-NS modifiers StpA and Hha and that DBD–DNA contacts vary in orientation and position with ~10-bp average spacing. Our results support a hemi-sequestration model of linear-to-bridged filament switching.
2023-09-01 | GSE157512 | GEO
Project description:The Arraystar Human LncRNA Array v2.0 was designed for researchers who were interested in profiling both LncRNAs and protein-coding RNAs in human genome. 33,045 LncRNAs were collected from the authoritative data sources including RefSeq, UCSC knowngenes, Ensembl and many related literatures. This experiment is to profile lncRNAs and protein-coding RNAs using Arraystar Human LncRNA Array v2.0. Identification of coding RNAs and lncRNAs that are diffrentially expressed in colorectal cancer by comparing sample A-E (normal colorectal cells) vs sample F-J (colorectal tumor cells) and c-MYC-regulating lncRNAs by comparing sample 1-3 (triplicate of HCT116 cells treated with control siRNA) vs sample 4-6 (triplicate of HCT116 cells treated with siRNA targeting MYC) and sample 7-9 (triplicate of RKO cells treated with control siRNA) vs sample 10-12 (triplicate of RKO cells treated with siRNA targeting MYC) .
2013-09-20 | E-GEOD-39846 | biostudies-arrayexpress
Project description:Objective: To analysis lncRNAs expression profiles and identify differentially expressed lncRNAs in CD4+ T cells response to T. pallidum infection in neurosyphilis patients. Methods: CD4+ T cells were isolated from peripheral blood mononuclear cells. RNA extraction was performed to conduct further experiments. Expression profiles of mRNAs and lncRNAs in CD4+ T cells isolated from neurosyphilis patients and healthy controls were analyzed by using microarray assay. Four lncRNAs were selected to conduct validation by using real time-quantitative polymerase chain reaction and the expression levels of those above mentioned lncRNAs in neurosyphilis patients and healthy controls were compared. Results: In total, 17, 278 lncRNAs and 15, 840 mRNA were found to be differentially expressed when comparing the CD4+ T cells between neurosyphilis patients and healthy control individuals. Of these transcripts, 2258 lncRNAs and 1728 mRNAs were significantly over or under expressed, respectively. Compared with healthy controls, AC068282.3 (fold change: 21.90) and CTD-3064M3.3 (fold change: 23.93) were the most over-expressed and under-expressed lncRNAs in neurosyphilis patients. The majority of differentially expressed lncRNAs are from intergenic regions (~ 57.5%), intronic antisense to protein-coding loci (~ 15.0%), natural antisense to protein-coding loci (~12.1%). It is worth noting that 59 lncRNAs were significant difference along with significantly different mRNA. Among the 59 pairs of genes, LOC7999 mRNA was positively correlated with lncRNA RP11-160E2.16, RP11-160E2.11, RP11-160E2.19, respectively; NKX1-1 mRNA was positively correlated with lncRNA RP11-1398P2.1, RP11-160E2.19, XLOC_003422, respectively. The following five mRNAs were correlated with two differential lncRNAs, namely DUSP16, AP000349.1, FAM115C, TIMM8A, SMCHD1. GO analysis revealed that the differentially expressed coding genes were mainly involved in the biological processes, and among them, the most significant association was observed in defense response to fungus, defense response to bacterium, killing cells of other organism and disruption of cells of other organism. Subsequent pathway analysis was also conducted, and T cell receptor signaling pathway, MAPK signaling pathway, TGF-beta signaling pathway, etc. were found out to be associated with differentially expressed mRNAs. Conclusion: The present study revealed the differential expression profiles of lncRNAs in CD4+ T cells response to T. pallidum infection in neurosyphilis patients. LncRNAs are involved in the key biological process in CD4+ T cell response to T. pallidum infection.
2017-09-08 | GSE103599 | GEO
Project description:To further explore t of the role lncRNAs in glaucoma patients, we have employed lncRNAs microarray expression profiling as a discovery platform to identify abnormal genes under oxidative stress in HTMCs. Our results revealed that lncRNA-RP11 was significantly up-regulated under oxidative stress in HTMCs. Further studies found that lncRNA-RP11-820 directly binds miR-3178, through which regulates the expression of MYOD1. Importantly, MYOD1 can transcriptionally activate ECM genes. Furthermore, MYOD1 binds STAT3 to form a transcription complex, and transcriptionally activates ECM genes expression in HTMCs. Taken together, our data established taht oxidative stress induced lncRNA-RP11-820 plays a key role in regulating miR-3178/MYOD1/ECM axis in HTMCs.
2019-02-07 | GSE126170 | GEO
Project description:Long non-coding RNAs (lncRNAs) play important roles in numerous diseases and represent an emerging layer of cancer biology. However, the role that lncRNAs play in the pathogenesis of pediatric B-cell leukemia (B-ALL) with t(12;21) (ETV6-RUNX1) translocation is largely unknown. In this study, we assessed the lncRNA expression profiles of 42 pediatric B-ALL (24 with and 18 without the t(12;21) translocation) and 4 bone marrows from healthy donors. We identified 117 lncRNAs that were differentially expressed (fold change> 1.5 and FDR > 0.05) between the B-ALL subgroups (ETV6-RUNX1-positive and ETV6-RUNX1-negative). The most upregulated lncRNAs in ETV6-RUNX1 positive B-ALL were TCL6, RP4-697K14.3, LOC100292680, RP11-345I18.1, LINC00599 and TRAF3IP2-AS1, while the most downregulated were RP11-135F9.1, RP11-561B11.1, AK095221, RP11-463H12.1, AC007283.4 and CCDC26. Coding-non-coding gene co-expression networks were constructed to identify lncRNAs with potential functions in ETV6-RUNX1 translocation. Levels of representative lncRNA-mRNA pairs were further detected by RT-qPCR in patients with pediatric B-ALL. Importantly, pediatric B-ALL patients who expressed low levels of the lncRNA TCL6 had lower disease-free survival than patients with high levels of TCL6. Thus, these findings provide the first detailed description of lncRNA expression profiles related to t(12;21) translocation in pediatric B-ALL. Such lncRNAs profiles might play important roles in driving normal cells to leukemic cells. These lncRNAs may provide novel molecular biomarkers and offer new basis for combating pediatric B-ALL.
2019-12-10 | GSE128254 | GEO
Project description:The challenge of oligohydramnios study is multiple causes of oligohydramnios. Long noncoding RNAs (lncRNAs) is a set of RNAs that has been proved to function in multiple biological process. Currently, little is know about their expression and possible role in oligohydramnios. Total RNA was isolated from fetal membranes ressected from oligohydramnios pregnant women (OR) and normal amniotic fluid control (Normal).RNA-sequencing (RNA-seq) obtain that a total of 801 lncRNAs and 367 mRNAs were differentially expressed in OR. Of which, 638 lncRNAs and 189 mRNAs were upregulated, and 163 lncRNAs and 178 mRNAs were downregulated. Of these lncRNAs, 566 of them were intergenic lncRNA, 351 were intronic antisense lncRNA，and 300 natural antisense. The differentially expressed lncRNA were primary located in chromosome 2, 1 and 11. KEGG enrichment pathways revealed the differential expressed mRNAs were enriched in pathway in cancer, Ras signaling pathway, TNF signaling pathway, focal adhesion, and chemokine signaling pathway. The qRT-PCR result confirmed that LINC00515 and RP11-388P9.2 were upregulated in OR. Furthermore, the constructed lncRNA-miRNA-mRNA regulatory network revealed TNR, CFTR, ABCC2, ABCA12, and COL9A2 as the candidate targets of LINC00515 and RP11-388P9.2. A wide range of lncRNAs were alert in OR, in particularly, LINC00515 and RP11-388P9.2 were confirmed to be uprgulated in OR, and their predicted downstream targets were transport and tissue growth and development associated. Further study focused on the role of differential expressed lncRNAs such as LINC00515 and RP11-388P9.2 would provide more insight into the pathophysiology in OR
2019-12-30 | GSE142701 | GEO
Project description:Methods and Materials The high throughput RNA sequencing (RNA-seq) data from kidney biopsies of LN patients and controls was applied studied to screen for candidate lncRNAs. Quantitative real-time polymerase chain reaction(RT-qPCR) was used to detect the expression of lncRNAs and individual IFN-stimulated genes (ISGs). Western blotting and dual-luciferace luciferase reporter assay was adopted to explore the specific function of the candidate lncRNA. Results The expression of lncRNA RP11-2B6.2 was significantly increased in the kidney tissues from LN patients compared with those from healthy controls, and positive correlated with the degree of disease activity and renal injuryinjuries. Additionally, expression of LncRNA RP11-2B6.2 could be stimulated by type I IFN. Silencing it RP11-2B6.2 significantly reduced the expression of a group of interferon-stimulating genes(ISGs) including IFIT1, OAS1, etc., Furthermore, it lncRNA RP11-2B6.2 affected the expression of IFN alpha and beta receptor subunit 1 (IFNAR1), phosphorylation of Jak1 and Stat1, and the luciferase activity induced by interferon stimulated response element(ISRE). Conclusion Long noncoding RNA RP11-2B6.2 is a positive regulator of the type I IFN signaling pathway in LN. It LncRNA RP11-2B6.2 may contribute to the pathogenesis of LN and provide served as a potentially therapeutic target.
2019-05-01 | GSE98422 | GEO
Project description:To explore the mechanisms underlying the radioresistance of colorectal cancer, we established specifically radioresistant HCT116 cell line (HCT116-R cells) and RKO cell line (RKO-R cells) derived from HCT116 and RKO cell lines by repeatedly exposing to multi-fractionated irradiation. Then, the aberrantly expressed miRNA were detected by miRNA sequencing and their bioinformatics were analyzed.
2021-01-10 | GSE159528 | GEO