scholarly journals Architectural RNA is required for heterochromatin organization

2019 ◽  
Author(s):  
Jitendra Thakur ◽  
He Fang ◽  
Trizia Llagas ◽  
Christine M. Disteche ◽  
Steven Henikoff
Keyword(s):  
Protein Synthesis ◽  
Chromatin Structure ◽  
Enzyme Catalysis ◽  
Pericentric Heterochromatin ◽  
Chromatin Organization ◽  
Non Coding Rna ◽  
Binding Factor ◽  
Chromatin Profiling ◽  
Long Non Coding Rna

AbstractIn addition to its known roles in protein synthesis and enzyme catalysis, RNA has been proposed to stabilize higher-order chromatin structure. To distinguish presumed architectural roles of RNA from other functions, we applied a ribonuclease digestion strategy to our CUT&RUN in situ chromatin profiling method (CUT&RUN.RNase). We find that depletion of RNA compromises association of the murine nucleolar protein Nucleophosmin with pericentric heterochromatin and alters the chromatin environment of CCCTC-binding factor (CTCF) bound regions. Strikingly, we find that RNA maintains the integrity of both constitutive (H3K9me3 marked) and facultative (H3K27me3 marked) heterochromatic regions as compact domains, but only moderately stabilizes euchromatin. To establish the specificity of heterochromatin stabilization by RNA, we performed CUT&RUN on cells deleted for the Firre long non-coding RNA and observed disruption of H3K27me3 domains on several chromosomes. We conclude that RNA maintains local and global chromatin organization by acting as a structural scaffold for heterochromatic domains.

The Mechanism of Long Non-Coding RNA Plasmacytoma Variant Translocation 1 Regulating Hepatoma Cells Proliferation and Apoptosis—Targeting the Transcription Factor Lymphoid Enhancer-Binding Factor 1 to Promote the Expression of Downstream Baculoviral IAP Repeat Containing 5

2020 ◽  
Vol 10 (12) ◽  
pp. 1851-1857
Author(s):  
Shuyuan Zang ◽  
Zuoan Li ◽  
Fumin Zhang
Keyword(s):  
Cell Proliferation ◽  
Colony Formation ◽  
Normal Liver ◽  
Hepatoma Cells ◽  
Luciferase Assay ◽  
Hippo Signaling ◽  
Non Coding Rna ◽  
Binding Factor ◽  
Apoptosis Protein ◽  
Long Non Coding Rna

Long non-coding RNA (lncRNA) PVT1 has been reported to be involved in the development of hepatocellular carcinoma (HCC). The expression of anti-apoptosis protein baculoviral IAP repeat containing 5 (BIRC5) is also increased in hepatoma cells and can be activated by lymphoid enhancer binding factor 1 (LEF1), which is one of the potential markers for HCC. The objective of this study is to explore the relationship between PVT1, BIRC5, and LEF1, so as to uncover the pathways and mechanisms of PVT1 promoting HCC. BIRC5 and PVT1 expression in normal liver cells and hepatoma cells was analyzed by RT-qPCR and western blotting. PVT1 short hairpin (sh)-RNA plasmids were transfected into PLC/PRF5 hepatoma cells to knockdown PVT1 expression, and then cell proliferation, colony formation, apoptosis and expression of related proteins were assessed. Besides, the interaction between PVT1 and miR-409-5p together with LEF1 and miR-409-5p was detected by dual luciferase assay. Results showed that the expression of BIRC5 and PVT1 were significantly increased in hepatoma cells and was highest in PLC/PRF5 compared with other hepatoma cells. Knockdown of PVT1 obviously reduced the ability of PLC/PRF5 cell proliferation and colony formation, whereas enhanced cell apoptosis. The protein expression of BIRC5 and LEF1 was also decreased after PVT1 was knockdown. Moreover, miR-409-5p level was increased after PVT1 silencing and it can interact with both PVT1 and LEF1. In conclusion, lncRNA PVT1 may exert its accelerative effect on HCC by targeting LEF1 in Hippo signaling pathway through miR-409-5p, thereby enhancing the expression of apoptosis inhibitor BIRC5.

scholarly journals FBXL19-AS1 promotes cell proliferation and inhibits cell apoptosis via miR-876-5p/FOXM1 axis in breast cancer

2019 ◽  
Author(s):  
Guolei Dong ◽  
Teng Pan ◽  
Dongdong Zhou ◽  
Chunyan Li ◽  
Jingjing Liu ◽  
...  
Keyword(s):  
Breast Cancer ◽  
Cell Proliferation ◽  
Cell Apoptosis ◽  
Loss Of Function ◽  
Forkhead Box ◽  
Forkhead Box M1 ◽  
Non Coding Rna ◽  
High Level ◽  
Long Non Coding Rna

Abstract As the most common cancer and one of the leading causes of cancer-associated mortality, breast cancer continues to need more key molecules to regulate its progression. F-box and leucine-rich repeat protein 19 antisense RNA 1 (known as FBXL19-AS1) is a long non-coding RNA (lncRNA) which has been reported as an oncogene in several types of human cancers. However, the specific downstream targets of FBXL19-AS1 remain unknown. In this study, we set out to find more reliable downstream molecules of FBXL19-AS1 in breast cancer. FBXL19-AS1 was expressed at a high level in breast cancer cells. Loss-of-function experiments revealed that silencing FBXL19-AS1 could impair cell proliferation and induce cell apoptosis in breast cancer. In addition, the location of FBXL19-AS1 in the cytoplasm was detected by fluorescent in situ hybridization assay, while FBXL19-AS1 regulated the expression of Forkhead box M1 (FOXM1) by directly absorbing miR-876-5p. Through rescue assays, it was observed that FOXM1 overexpression recovered the inhibited tumor growth caused by FBXL19-AS1 downregulation. We affirmed the function of FBXL19-AS1 in breast cancer and described the mechanism of the FBXL19-AS1/miR-876-5p/FOXM1 axis. The current work presents the molecular mechanism which underlies FBXL19-AS1 in breast cancer and suggests a comprehensive, feasible FBXL19-AS1-mediated therapeutic approach for treating breast cancer.

Long non-coding RNA chromogenic in situ hybridisation signal pattern correlation with breast tumour pathology

2015 ◽  
Vol 69 (1) ◽  
pp. 76-81 ◽  
Author(s):  
Zhouwei Zhang ◽  
Donald L Weaver ◽  
Daniel Olsen ◽  
James deKay ◽  
Zhihua Peng ◽  
...  
Keyword(s):  
In Situ Hybridisation ◽  
Breast Tumour ◽  
Signal Pattern ◽  
Non Coding Rna ◽  
Pattern Correlation ◽  
Tumour Pathology ◽  
Hybridisation Signal ◽  
Long Non Coding Rna

scholarly journals Silencing of HuR Inhibits Osteosarcoma Cell Epithelial-Mesenchymal Transition via AGO2 in Association With Long Non-Coding RNA XIST

2021 ◽  
Vol 11 ◽  
Author(s):  
Yongming Liu ◽  
Yuan Zhang ◽  
Jinxue Zhang ◽  
Jingchang Ma ◽  
Xuexue Xu ◽  
...  
Keyword(s):  
Cell Proliferation ◽  
Western Blotting ◽  
Epithelial Mesenchymal Transition ◽  
Osteosarcoma Cell ◽  
Mesenchymal Transition ◽  
Non Coding Rna ◽  
Lncrna Xist ◽  
Rna Immunoprecipitation ◽  
Long Non Coding Rna

BackgroundOsteosarcoma (OS) is a highly malignant and aggressive bone tumor. This study was performed to explore the mechanisms of HuR (human antigen R) in the progression of OS.MethodsHuR expression levels in OS tissues and cells were detected by immunohistochemistry and western blotting. HuR siRNA was transfected into SJSA-1 OS cells to downregulate HuR expression, and then cell proliferation, migration, and epithelial-mesenchymal transition (EMT) were evaluated. RNA immunoprecipitation was performed to determine the association of the long non-coding RNA (lncRNA) XIST and argonaute RISC catalytic component (AGO) 2 with HuR. Fluorescence in situ hybridization analysis was performed to detect the expression of lncRNA XIST. Western blotting and immunofluorescence assays were performed to observe AGO2 expression after HuR or/and lncRNA XIST knockdown.ResultsKnockdown of HuR repressed OS cell migration and EMT. AGO2 was identified as a target of HuR and silencing of HuR decreased AGO2 expression. The lncRNA XIST was associated with HuR-mediated AGO2 suppression. Moreover, knockdown of AGO2 significantly inhibited cell proliferation, migration, and EMT in OS.ConclusionOur findings indicate that HuR knockdown suppresses OS cell EMT by regulating lncRNA XIST/AGO2 signaling.

scholarly journals Integrative analysis of the 3D genome structure reveals that CTCF maintains the properties of mouse female germline stem cells

2022 ◽  
Vol 79 (1) ◽  
Author(s):  
Geng G. Tian ◽  
Xinyan Zhao ◽  
Changliang Hou ◽  
Wenhai Xie ◽  
Xiaoyong Li ◽  
...  
Keyword(s):  
Stem Cells ◽  
Chromatin Structure ◽  
Three Dimensional ◽  
High Order ◽  
Chromatin Organization ◽  
Germline Stem Cells ◽  
High Order Chromatin Structure ◽  
Female Germline ◽  
High Order Chromatin

AbstractThe three-dimensional configuration of the genome ensures cell type-specific gene expression profiles by placing genes and regulatory elements in close spatial proximity. Here, we used in situ high-throughput chromosome conformation (in situ Hi-C), RNA sequencing (RNA-seq) and chromatin immunoprecipitation sequencing (ChIP-seq) to characterize the high-order chromatin structure signature of female germline stem cells (FGSCs) and identify its regulating key factor based on the data-driven of multiple omics data. By comparison with pluripotent stem cells (PSCs), adult stem cells (ASCs), and somatic cells at three major levels of chromatin architecture, A/B compartments, topologically associating domains, and chromatin loops, the chromatin architecture of FGSCs was most similar to that of other ASCs and largely different from that of PSCs and somatic cells. After integrative analysis of the three-dimensional chromatin structure, active compartment-associating loops (aCALs) were identified as a signature of high-order chromatin organization in FGSCs, which revealed that CCCTC-binding factor was a major factor to maintain the properties of FGSCs through regulation of aCALs. We found FGSCs belong to ASCs at chromatin structure level and characterized aCALs as the high-order chromatin structure signature of FGSCs. Furthermore, CTCF was identified to play a key role in regulating aCALS to maintain the biological functions of FGSCs. These data provide a valuable resource for future studies of the features of chromatin organization in mammalian stem cells and further understanding of the fundamental characteristics of FGSCs.

scholarly journals Evaluation of fluorescence in situ hybridization techniques to study long non-coding RNA expression in cultured cells

2017 ◽  
Vol 46 (1) ◽  
pp. e4-e4 ◽  
Author(s):  
Ricardo J Soares ◽  
Giulia Maglieri ◽  
Tony Gutschner ◽  
Sven Diederichs ◽  
Anders H Lund ◽  
...  
Keyword(s):  
In Situ Hybridization ◽  
Fluorescence In Situ Hybridization ◽  
Cultured Cells ◽  
Rna Expression ◽  
Non Coding Rna ◽  
Long Non Coding Rna

scholarly journals MALAT1 Long Non-coding RNA Expression in Thyroid Tissues: Analysis by In Situ Hybridization and Real-Time PCR

2016 ◽  
Vol 28 (1) ◽  
pp. 7-12 ◽  
Author(s):  
Ranran Zhang ◽  
Heather Hardin ◽  
Wei Huang ◽  
Jidong Chen ◽  
Sofia Asioli ◽  
...  
Keyword(s):  
In Situ Hybridization ◽  
Real Time ◽  
Real Time Pcr ◽  
Rna Expression ◽  
Non Coding Rna ◽  
Long Non Coding Rna

The making of a Barr body: the mosaic of factors that eXIST on the mammalian inactive X chromosome

2016 ◽  
Vol 94 (1) ◽  
pp. 56-70 ◽  
Author(s):  
Thomas Dixon-McDougall ◽  
Carolyn Brown
Keyword(s):  
Gene Expression ◽  
X Chromosome ◽  
Current Knowledge ◽  
Pericentric Heterochromatin ◽  
Barr Body ◽  
Facultative Heterochromatin ◽  
Inactive X Chromosome ◽  
Non Coding Rna ◽  
Stable Maintenance ◽  
Long Non Coding Rna

During X-chromosome inactivation (XCI), nearly an entire X chromosome is permanently silenced and converted into a Barr body, providing dosage compensation for eutherians between the sexes. XCI is facilitated by the upregulation of the long non-coding RNA gene, XIST, which coats its chromosome of origin, recruits heterochromatin factors, and silences gene expression. During XCI, at least two distinct types of heterochromatin are established, and in this review we discuss the enrichment of facultative heterochromatin marks such as H3K27me3, H2AK119ub, and macroH2A as well as pericentric heterochromatin marks such as HP1, H3K9me3, and H4K20me3. The extremely stable maintenance of silencing is a product of reinforcing interactions within and between these domains. This paper “Xplores” the current knowledge of the pathways involved in XCI, how the pathways interact, and the gaps in our understanding that need to be filled.

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