scholarly journals Forced isoform switching of Neat1_1 to Neat1_2 leads to the loss of Neat1_1 and the hyperformation of paraspeckles but does not affect the development and growth of mice

2019 ◽  
Author(s):  
Momo Isobe ◽  
Hikaru Toya ◽  
Mari Mito ◽  
Tomoki Chiba ◽  
Hiroshi Asahara ◽  
...  
Keyword(s):  
Long Noncoding Rna ◽  
Noncoding Rna ◽  
Gene Locus ◽  
Cell Types ◽  
Small Population ◽  
Nuclear Bodies ◽  
Mutant Mice ◽  
Isoform Switching ◽  
Tip Cells ◽  
Normal Laboratory

AbstractNeat1 is a long noncoding RNA (lncRNA) that serves as an architectural component of the nuclear bodies known as paraspeckles. Two isoforms of Neat1, the short isoform Neat1_1 and the long isoform Neat1_2, are generated from the same gene locus by alternative 3’ processing. Neat1_1 is the most abundant and the best conserved isoform expressed in various cell types, whereas Neat1_2 is expressed in a small population of particular cell types, including the tip cells of the intestinal epithelium. To investigate the physiological significance of isoform switching, we created mutant mice that solely expressed Neat1_2 by deleting the upstream polyadenylation (poly-A) signal (PAS) required for the production of Neat1_1. We observed the loss of Neat1_1 and strong upregulation of Neat1_2 in various tissues and cells and the subsequent hyperformation of paraspeckles, especially in cells that normally express Neat1_2. However, the mutant mice were born at the expected Mendelian ratios and did not exhibit obvious external and histological abnormalities. These observations suggested that the hyperformation of paraspeckles does not interfere with the development and growth of these animals under normal laboratory conditions.

scholarly journals Myeloid leukemia vulnerabilities at CTCF-enriched long noncoding RNA loci

2021 ◽  
Author(s):  
Michelle Ng ◽  
Lonneke Verboon ◽  
Hasan Issa ◽  
Raj Bhayadia ◽  
Oriol Alejo-Valle ◽  
...  
Keyword(s):  
Long Noncoding Rna ◽  
Myeloid Leukemia ◽  
Noncoding Rna ◽  
K562 Cells ◽  
Cell Types ◽  
Clinical Aspects ◽  
Hematopoietic Stem ◽  
Regulatory Effects

Abstract The noncoding genome presents a largely untapped source of biological insights, including thousands of long noncoding RNA (lncRNA) loci. While some produce bona fide lncRNAs, others exert transcript-independent cis-regulatory effects, and the lack of predictive features renders mechanistic dissection challenging. Here, we describe CTCF-enriched lncRNA loci (C-LNC) as a subclass of functional genetic elements exemplified by MYNRL15, a pan-myeloid leukemia dependency identified by an lncRNA-based CRISPRi screen. MYNRL15 perturbation selectively impairs acute myeloid leukemia (AML) cells over hematopoietic stem / progenitor cells in vitro, and depletes AML xenografts in vivo. Mechanistically, we show that crucial DNA elements in the locus mediate its phenotype, triggering chromatin reorganization and downregulation of cancer dependency genes upon perturbation. Elevated CTCF density distinguishes MYNRL15 and 531 other lncRNA loci in K562 cells, of which 43-54% associate with clinical aspects of AML and 18.4% are functionally required for leukemia maintenance. Curated C-LNC catalogs in other cell types will help refine the search for noncoding oncogenic vulnerabilities in AML and other malignancies.

scholarly journals Identification of heat-inducible long noncoding RNA MALAT1-containing novel nuclear (HiNoCo) body

2021 ◽  
Author(s):  
Rena Onoguchi-Mizutani ◽  
Yoshitaka Kirikae ◽  
Yoko Ogura ◽  
Tony Gutschner ◽  
Sven Diederichs ◽  
...  
Keyword(s):  
Heat Shock ◽  
Heat Shock Response ◽  
Long Noncoding Rna ◽  
Mammalian Cells ◽  
Noncoding Rna ◽  
Heat Shock Factor ◽  
Nuclear Bodies ◽  
Cajal Body ◽  
Heat Shock Factor 1 ◽  
Shock Response

The heat shock response is critical for the survival of all organisms. Metastasis-associated long adenocarcinoma transcript 1 (MALAT1) is a long noncoding RNA localized in nuclear speckles, but its physiological role remains elusive. Here, we show that heat shock induces translocation of MALAT1 to a distinct nuclear body named heat shock-inducible noncoding RNA-containing nuclear (HiNoCo) body in mammalian cells. The MALAT1 knockout A549 cells showed reduced proliferation after heat shock. The HiNoCo body, formed by a nearby nuclear speckle, is distinct from any other known nuclear bodies, including the nuclear stress body, Cajal body, germs, paraspeckles, nucleoli, and promyelocytic leukemia body. The formation of HiNoCo body is reversible and independent of heat shock factor 1, the master transcription regulator of the heat shock response. Our results suggest the HiNoCo body participates in heat shock factor 1-independent heat shock responses in mammalian cells.

scholarly journals Myeloid leukemia vulnerabilities at CTCF-enriched long noncoding RNA loci

2021 ◽  
Author(s):  
Michelle Ng ◽  
Lonneke Verboon ◽  
Hasan Issa ◽  
Raj Bhayadia ◽  
Oriol Alejo-Valle ◽  
...  
Keyword(s):  
Long Noncoding Rna ◽  
Myeloid Leukemia ◽  
Noncoding Rna ◽  
Transcriptome Profiling ◽  
Cell Types ◽  
Chromatin Interaction ◽  
Hematopoietic Stem ◽  
Regulatory Effects

Abstract The noncoding genome presents a largely untapped source of biological insights, including thousands of long noncoding RNA (lncRNA) loci. While some produce bona fide lncRNAs, others exert transcript-independent cis-regulatory effects, and a lack of predictive features renders mechanistic dissection challenging. Here, we describe MYNRL15, a CTCF-enriched lncRNA locus and pan-myeloid leukemia dependency initially identified by expression-guided CRISPR interference screens. We show that accessibility and integrity of the MYNRL15 locus is required for myeloid leukemia maintenance; its perturbation selectively impairs acute myeloid leukemia (AML) cells compared to hematopoietic stem and progenitor cells in vitro, and depletes AML xenografts in vivo. While the MYNRL15 transcript and neighboring protein-coding genes appear dispensable, dense CRISPR tiling of the locus revealed two crucial candidate cis-regulatory DNA elements which drive the perturbation phenotype. Disruption of these elements triggers the formation of a tumor-suppressive, long-range chromatin interaction. By integrating transcriptome profiling with a CRISPR-Cas9 knockout screen of genes from the gained interaction region, we pinpointed two downregulated, potent cancer dependency genes as effectors of MYNRL15 disruption: WDR61 and IMP3. Finally, guided by distinctive features of the MYNRL15 locus, we find that elevated CTCF density characterizes a set of lncRNA loci enriched in leukemia vulnerabilities (22.6-24.2% essentiality rate). A catalog of CTCF-enriched lncRNA loci (C-LNCs) in 18 cell types representing different cancer entities and tissues is provided with this study, towards refining the search for noncoding oncogenic vulnerabilities in leukemia and other malignancies.

Editing of Long Noncoding RNA DANCR Gene Locus Using Genetic Engineering Tools

2017 ◽  
Author(s):  
Gulin Baran ◽  
Burcu Talug ◽  
Nazli Keskin ◽  
Zeynep Tokcaer Keskin ◽  
Batu Erman ◽  
...  
Keyword(s):  
Genetic Engineering ◽  
Long Noncoding Rna ◽  
Noncoding Rna ◽  
Gene Locus

scholarly journals Hypoxia drives glucose transporter 3 expression through hypoxia-inducible transcription factor (HIF)–mediated induction of the long noncoding RNA NICI

2019 ◽  
Vol 295 (13) ◽  
pp. 4065-4078 ◽  
Author(s):  
Victoria Lauer ◽  
Steffen Grampp ◽  
James Platt ◽  
Veronique Lafleur ◽  
Olivia Lombardi ◽  
...  
Keyword(s):  
Transcriptional Activation ◽  
Long Noncoding Rna ◽  
Noncoding Rna ◽  
Glucose Transporter ◽  
Glucose Consumption ◽  
Cell Types ◽  
Cell Renal Cell Carcinoma ◽  
Protein Coding ◽  
Von Hippel Lindau ◽  
Patient Prognosis

Hypoxia-inducible transcription factors (HIFs) directly dictate the expression of multiple RNA species including novel and as yet uncharacterized long noncoding transcripts with unknown function. We used pan-genomic HIF-binding and transcriptomic data to identify a novel long noncoding RNA Noncoding Intergenic Co-Induced transcript (NICI) on chromosome 12p13.31 which is regulated by hypoxia via HIF-1 promoter-binding in multiple cell types. CRISPR/Cas9-mediated deletion of the hypoxia-response element revealed co-regulation of NICI and the neighboring protein-coding gene, solute carrier family 2 member 3 (SLC2A3) which encodes the high-affinity glucose transporter 3 (GLUT3). Knockdown or knockout of NICI attenuated hypoxic induction of SLC2A3, indicating a direct regulatory role of NICI in SLC2A3 expression, which was further evidenced by CRISPR/Cas9-VPR–mediated activation of NICI expression. We also demonstrate that regulation of SLC2A3 is mediated through transcriptional activation rather than posttranscriptional mechanisms because knockout of NICI leads to reduced recruitment of RNA polymerase 2 to the SLC2A3 promoter. Consistent with this we observe NICI-dependent regulation of glucose consumption and cell proliferation. Furthermore, NICI expression is regulated by the von Hippel–Lindau (VHL) tumor suppressor and is highly expressed in clear cell renal cell carcinoma (ccRCC), where SLC2A3 expression is associated with patient prognosis, implying an important role for the HIF/NICI/SLC2A3 axis in this malignancy.

scholarly journals Paraspeckles: nuclear bodies built on long noncoding RNA

2009 ◽  
Vol 186 (5) ◽  
pp. 637-644 ◽  
Author(s):  
Charles S. Bond ◽  
Archa H. Fox
Keyword(s):  
Long Noncoding Rna ◽  
Noncoding Rna ◽  
Nuclear Bodies ◽  
Cell Nuclei ◽  
Nuclear Retention ◽  
Differentiated Cells ◽  
Large Numbers ◽  
Whole Transcriptome Analysis ◽  
Interchromatin Space ◽  
Whole Transcriptome

Paraspeckles are ribonucleoprotein bodies found in the interchromatin space of mammalian cell nuclei. These structures play a role in regulating the expression of certain genes in differentiated cells by nuclear retention of RNA. The core paraspeckle proteins (PSF/SFPQ, P54NRB/NONO, and PSPC1 [paraspeckle protein 1]) are members of the DBHS (Drosophila melanogaster behavior, human splicing) family. These proteins, together with the long nonprotein-coding RNA NEAT1 (MEN-ε/β), associate to form paraspeckles and maintain their integrity. Given the large numbers of long noncoding transcripts currently being discovered through whole transcriptome analysis, paraspeckles may be a paradigm for a class of subnuclear bodies formed around long noncoding RNA.

scholarly journals Ancient exapted transposable elements promote nuclear enrichment of human long noncoding RNAs

2017 ◽  
Author(s):  
Joana Carlevaro-Fita ◽  
Taisia Polidori ◽  
Monalisa Das ◽  
Carmen Navarro ◽  
Tatjana I. Zoller ◽  
...  
Keyword(s):  
Transposable Elements ◽  
Long Noncoding Rna ◽  
Noncoding Rna ◽  
Cell Types ◽  
Subcellular Localisation ◽  
Evolutionary Selection ◽  
Dependent Relationship ◽  
Evolutionarily Conserved ◽  
Show Evidence ◽  
Multiple Cell

AbstractThe sequence domains underlying long noncoding RNA (lncRNA) activities, including their characteristic nuclear enrichment, remain largely unknown. It has been proposed that these domains can originate from neofunctionalised fragments of transposable elements (TEs), otherwise known as RIDLs (Repeat Insertion Domains of Long Noncoding RNA), although just a handful have been identified. It is challenging to distinguish functional RIDL instances against a numerous genomic background of neutrally-evolving TEs. We here show evidence that a subset of TE types experience evolutionary selection in the context of lncRNA exons. Together these comprise an enrichment group of 5374 TE fragments in 3566 loci. Their host lncRNAs tend to be functionally validated and associated with disease. This RIDL group was used to explore the relationship between TEs and lncRNA subcellular localisation. Using global localisation data from ten human cell lines, we uncover a dose-dependent relationship between nuclear/cytoplasmic distribution, and evolutionarily-conserved L2b, MIRb and MIRc elements. This is observed in multiple cell types, and is unaffected by confounders of transcript length or expression. Experimental validation with engineered transgenes shows that these TEs drive nuclear enrichment in a natural sequence context. Together these data reveal a role for TEs in regulating the subcellular localisation of lncRNAs.

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