Landscape of super-enhancer-associated lncRNAs in hepatocellular carcinoma [ChIP-seq]
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ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE181753 | GEO | 2024/08/07
REPOSITORIES: GEO
Similar Datasets
Project description:Super-enhancer (SE) plays a vital role in the determination of cell identity and cell fate through the control of cell- or tissue-specific gene regulation. Upregulated expression of coding genes is frequently associated with SE. However, the transcription dysregulation driven by SE, from long non-coding RNAs (lncRNAs) viewpoint, remains unclear. Here, SE-associated lncRNAs in HCC were comprehensively screened. The result shows that pol2-mediated transcription of SE-associated lncRNAs is more sensitive to JQ1 treatment in a genome-wide manner.
2024-08-07 | GSE181754 | GEO
Project description:Prostate cancer (PCa) is one of the most commonly diagnosed cancers in males worldwide. lncRNAs (long non-coding RNAs) play a significant role in the occurrence and development of PCa. eRNAs (enhancer RNA) and SE-lncRNAs (super-enhancer lncRNA) are important elements of lncRNAs, but the role of eRNAs and SE-lncRNAs in PCa remains largely unclear. In this work, we identified 681 eRNAs and 292 SE-lncRNAs that were expressed differentially in PCa using a microarray. We constructed a transcriptional regulation network that eRNA related enhancer and the target genes shared the same TF binding motifs. Further, we investigated whether CTCF played a role in mediating the transcriptional regulation network. eRNAs, especially those that regulate androgen response genes, may be candidates for prognostic biomarkers and therapy targets. Our work provide a new perspective for developing medical treatments and therapies for prostate cancer.
2020-10-13 | GSE155056 | GEO
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:A vast portion of the mammalian genome is transcribed as long non-coding RNAs (lncRNAs) acting in the cytoplasm with largely unknown functions. Surprisingly, lncRNAs have been shown to interact with ribosomes, encode uncharacterized proteins, or act as ribosome sponges. These functions still remain mostly undetected and understudied owing to the lack of efficient tools for genome-wide simultaneous identification of ribosome-associated lncRNAs and peptide-producing lncRNAs. Here we present AHARIBO, a method for the detection of lncRNAs either untranslated, but associated with ribosomes, or encoding small peptides. Using AHARIBO in mouse embryonic stem cells during neuronal differentiation, we isolated ribosome-protected RNA fragments, translated RNAs and corresponding de novo synthesized polypeptides. Besides identifying mRNAs under active translation and associated ribosomes, we found and distinguished lncRNAs acting as ribosome sponges or encoding micropeptides, laying the ground for a better functional understanding of hundreds lncRNAs.
2021-09-09 | PXD022679 | Pride
Project description:Landscape of super-enhancer-associated lncRNAs in hepatocellular carcinoma
| PRJNA753288 | ENA
Project description:Differentially expressed SE-lncRNAs in lung adenocarcinoma
| PRJNA805532 | ENA
Project description:Background: Long non-coding RNAs (lncRNAs) are an important class of pervasive genes involved in a variety of biological functions. They are aberrantly expressed in many types of diseases. We want to study the lncRNAs profiles in preeclampsia. Preeclampsia has been observed in patients with molar pregnancy where a fetus is absent demonstrating that the placenta is sufficient to cause the condition. So we analyze the lncRNAs profiles in preeclampsia placentas. In this study, we described the lncRNAs profiles in 6 preeclampsia placentas (T) and 5 matched normal pregnancy placentas (N) tissues by microarray. Methodology/Principal Findings: With abundant and varied probes accounting 33,045 LncRNAs in our microarray, the number of lncRNAs that expressed at a certain level could be detected is 28,443. From the data we found there were 738 lncRNAs that differentially expressed (M-bM-^IM-%1.5 fold-change) among preeclampsia placentas compared with matched controls. Up to 18,063 coding transcripts could be detected in placenta samples through 30,215 coding transcripts probes. Coding-non-coding gene co-expression networks (CNC network) were constructed based on the correlation analysis between the differential expressed lncRNAs and mRNAs. According to the GO-Pathway analysis of differential expressed lncRNAs/mRNAs, we choose three lncRNAs to analyze the relationship between lncRNAs and preeclampsia. LOC391533, LOC284100, CEACAMP8 were evaluated by qPCR in 40 of preeclampsia placentas and 40 of controls. The results showed three lncRNAs were aberrantly expressed in preeclampsia placentas compared with controls. Conclusions/Significance: Our study is the first one to determine genome-wide lncRNAs expression patterns in preeclampsia placenta by microarray. The results displayed that clusters of lncRNAs were aberrantly expressed in preeclampsia placenta compared with controls, which revealed that lncRNAs differentially expressed in preeclampsia placenta may exert a partial or key role in preeclampsia development. Misregulation of LOC391533, LOC284100, CEACAMP8 might be associated with preeclampsia. Taken together, this study may provide potential targets for future treatment of preeclampsia and novel insights into preeclampsia biology. LncRNAs/mRNAs profiles in 6 preeclampsia placentas and 5 matched normal pregnancy placentas tissues by microarray using Arraystar v2.0.
2013-09-12 | E-GEOD-50783 | biostudies-arrayexpress
Project description:Long non-coding RNAs (lncRNAs) are components of epigenetic control mechanisms that ensure appropriate and timely gene expression. The functions of lncRNAs are often mediated through associated gene regulatory activities, but how lncRNAs are distinguished from other RNAs and recruit effector complexes is unclear. Here we utilize the fission yeast Schizosaccharomyces pombe to investigate how lncRNAs engage silencing activities to regulate gene expression in cis. We find that invasion of lncRNA transcription into the downstream gene body incorporates a cryptic intron required for repression of that gene. Our analyses show that lncRNAs containing cryptic introns are targeted by the conserved Pir2ARS2 protein in association with splicing factors, which recruit RNA processing and chromatin modifying activities involved in gene silencing. Pir2 and splicing machinery are broadly required for gene repression. Our finding that human ARS2 also interacts with splicing factors suggests a conserved mechanism mediates gene repression through cryptic introns within lncRNAs.
2020-04-07 | PXD018373 | Pride
Project description:Background: Lung adenocarcinoma (LUAD) is the leading cause of deaths worldwide, and metastasis accounts for the vast majority of cancer-related deaths. Driver mutations play important roles in treatment decision making for LUAD patients, while the complicated metastatic progress cannot be explained by genetic aberrations alone. Epigenomic reprogramming is particularly notable as an important signature of the metastasis transition. However, long noncoding RNAs (lncRNAs) hijacked by super-enhancer (SE), vital regulatory elements in epigenome, remain elusive in the progression of metastasis. Methods: SE associated lncRNAs microarray was utilized to identified the dysregulated lncRNAs related to metastasis. ChIP-seq, Hi-C data analysis and luciferase reporter assay were utilized to confirm LINC01977 was hijacked by SE. In vitro and in vivo assays were applied to elucidate effects of LINC01977 on the malignancy of LUAD. Results: In this study, we identified that LINC01977, a cancer-testis lncRNA, was up-regulated in tumor, which was driven by a …kb-long SE upstream of LINC01977 and sensitive to BRD4 inhibitor. LINC01977-antisense oligonucleotides (ASO) dramatically suppresses proliferation and invasion both in vitro and in vivo. Mechanically, LINC01977 promotes phosphorylation of SMAD3 to facilitate its nuclear retention, and it also act as a scaffold to cooperate the interaction between SMAD3 and CBP/P300, the transcriptional co-activators, to regulate the downstream target gene ZEB1. Interestingly, SMAD3 also positively regulated LINC09177 transcription by binding the promoter and active elements of its SE, which was medicated by canonical TGF-β signaling secreted by M2-like tumor-associated macrophages (TAM2). We also revealed that the expression of LINC01977 was positively correlated with TAM2 infiltration especially in early stage. Additionally, stage I LUAD patients with high LIN01977 expression predicated a shorter progression-free survival (PFS). Conclusions: LINC01977 promotes the malignant progression of LUAD through facilitating the interaction between SMAD3 and CBP/P300. The upregulation of LINC01977 was medicated by super-enhancer and TAM2 infiltration, dependent on canonical TGF-β signaling. LINC01977 could be a valuable therapeutic target especially for early stage patients.
2022-08-24 | GSE196584 | GEO
Project description:To address the role of SE-lncRNAs in CRC tumorigenesis, we performed Arraystar human SE-lncRNA microarray to profile the differentially expressed SE-lncRNAs and mRNA in four CRC and paired peritumoral tissues. According to the filter criteria of Fold Change ≥ 1.5 and P-value < 0.05, a total of 55 significantly upregulated and 29 significantly downregulated SE-LncRNs were identified. These data confirmed that the expression of SE-lncRNA undergoes a change that cannot be ignored during CRC tumorigenesis. We also identified 165 (91 up- and 74 downregulated) differentially expressed mRNA between the two groups（Fold Change > 1.5 and P-value < 0.05）(Fig.1C), which provides help for us to findpotential target genes and further explore the biological function of SE-lncRNA in CRC
2020-05-22 | GSE151021 | GEO