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 Whole transcriptome analysis reveals correlation of long noncoding RNA ZEB1-AS1 with invasive profile in melanoma

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Ádamo Davi Diógenes Siena ◽  
Jéssica Rodrigues Plaça ◽  
Luiza Ferreira Araújo ◽  
Isabela Ichihara de Barros ◽  
Kamila Peronni ◽  
...  
Keyword(s):  
Transcriptome Analysis ◽  
Long Noncoding Rna ◽  
Noncoding Rna ◽  
Whole Transcriptome Analysis ◽  
Whole Transcriptome

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 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 NEAT1 long noncoding RNA regulates transcription via protein sequestration within subnuclear bodies

2014 ◽  
Vol 25 (1) ◽  
pp. 169-183 ◽  
Author(s):  
Tetsuro Hirose ◽  
Giorgio Virnicchi ◽  
Akie Tanigawa ◽  
Takao Naganuma ◽  
Ruohan Li ◽  
...  
Keyword(s):  
Cell Death ◽  
Long Noncoding Rna ◽  
Noncoding Rna ◽  
Proteasome Inhibition ◽  
Nuclear Bodies ◽  
Cell Death Pathway ◽  
Immuno Electron Microscopy ◽  
Concomitant Reduction ◽  
Protein Sequestration ◽  
Target Gene Transcription

Paraspeckles are subnuclear structures formed around nuclear paraspeckle assembly transcript 1 (NEAT1)/MENε/β long noncoding RNA (lncRNA). Here we show that paraspeckles become dramatically enlarged after proteasome inhibition. This enlargement is mainly caused by NEAT1 transcriptional up-regulation rather than accumulation of undegraded paraspeckle proteins. Of interest, however, using immuno–electron microscopy, we find that key paraspeckle proteins become effectively depleted from the nucleoplasm by 50% when paraspeckle assembly is enhanced, suggesting a sequestration mechanism. We also perform microarrays from NEAT1-knockdown cells and find that NEAT1 represses transcription of several genes, including the RNA-specific adenosine deaminase B2 (ADARB2) gene. In contrast, the NEAT1-binding paraspeckle protein splicing factor proline/glutamine-rich (SFPQ) is required for ADARB2 transcription. This leads us to hypothesize that ADARB2 expression is controlled by NEAT1-dependent sequestration of SFPQ. Accordingly, we find that ADARB2 expression is strongly reduced upon enhanced SFPQ sequestration by proteasome inhibition, with concomitant reduction in SFPQ binding to the ADARB2 promoter. Finally, NEAT1−/− fibroblasts are more sensitive to proteasome inhibition, which triggers cell death, suggesting that paraspeckles/NEAT1 attenuates the cell death pathway. These data further confirm that paraspeckles are stress-responsive nuclear bodies and provide a model in which induced NEAT1 controls target gene transcription by protein sequestration into paraspeckles.

scholarly journals Dynamic paraspeckle component localisation during spermatogenesis

Reproduction ◽  
2019 ◽  
Vol 158 (3) ◽  
pp. 267-280
Author(s):  
Andrew T Major ◽  
Cathryn A Hogarth ◽  
Julia C Young ◽  
Yasuyuki Kurihara ◽  
David A Jans ◽  
...  
Keyword(s):  
Stress Responses ◽  
Sertoli Cells ◽  
Noncoding Rna ◽  
Adult Mouse ◽  
Expression Profiles ◽  
Adult Life ◽  
Cell Nuclei ◽  
Developmentally Regulated ◽  
Nuclear Retention ◽  
Related Proteins

Expression profiles and subcellular localisations of core Drosophila behaviour/human splicing (DBHS) proteins (PSPC1, SFPQ and NONO) and NEAT1, a long noncoding RNA (lncRNA), are investigated in developing and adult mouse testes. Core DBHS proteins are markers for the distinct subnuclear domain termed paraspeckles, while a long NEAT1 isoform scaffold facilitates paraspeckle nucleation. Paraspeckles contain many proteins (>40) and are broadly involved in RNA metabolism, including transcriptional regulation by protein sequestration, nuclear retention of A-to-I edited RNA transcripts to regulate translation and promoting survival during cellular stress. Immunohistochemistry reveals cell-specific profiles for core DBHS paraspeckle protein expression, indicating their functional diversity. PSPC1 is an androgen receptor co-activator, and it is detected in differentiating Sertoli cell nuclei from day 15 onwards, as they develop androgen responsiveness. PSPC1 is nuclear in the most mature male germ cell type present at each age, from foetal to adult life. In adult mouse testes, PSPC1 and SFPQ are present in Sertoli cells, spermatocytes and round spermatids, while the NEAT1 lncRNA appears in the punctate nuclear foci delineating paraspeckles only within Leydig cells. Identification of NEAT1 in the cytoplasm of spermatogonia and spermatocytes must reflect non-paraspeckle-related functions. NONO was absent from germ cells but nuclear in Sertoli cells. Reciprocal nuclear profiles of PSPC1 and γ-H2AX in spermatogenic cells suggest that each performs developmentally regulated roles in stress responses. These findings demonstrate paraspeckles and paraspeckle-related proteins contribute to diverse functions during testis development and spermatogenesis.

Mechanisms of Long Noncoding RNA Nuclear Retention

2020 ◽  
Vol 45 (11) ◽  
pp. 947-960
Author(s):  
Chun-Jie Guo ◽  
Guang Xu ◽  
Ling-Ling Chen
Keyword(s):  
Long Noncoding Rna ◽  
Noncoding Rna ◽  
Nuclear Retention

Gene expression analysis in modeling Parkinson’s disease

2020 ◽  
pp. 103-104
Author(s):  
М.М. Руденок ◽  
А.Х. Алиева ◽  
А.А. Колачева ◽  
М.В. Угрюмов ◽  
П.А. Сломинский ◽  
...  
Keyword(s):  
Parkinson’S Disease ◽  
Parkinson's Disease ◽  
Early Stage ◽  
Systemic Disease ◽  
Molecular Genetic ◽  
Presymptomatic Stage ◽  
Whole Transcriptome Analysis ◽  
Whole Transcriptome ◽  
The Brain ◽  
Transcriptome Level

Несмотря на очевидный прогресс, достигнутый в изучении молекулярно-генетических факторов и механизмов патогенеза болезни Паркинсона (БП), в настоящее время стало ясно, что нарушения в структуре ДНК не описывают весь спектр патологических изменений, наблюдаемых при развитии заболевания. В настоящее время показано, что существенное влияние на патогенез БП могут оказывать изменения на уровне транскриптома. В работе были использованы мышиные модели досимптомной стадии БП, поздней досимптомной и ранней симптомной (РСС) стадиями БП. Для полнотранскриптомного анализа пулов РНК тканей черной субстанции и стриатума мозга мышей использовались микрочипы MouseRef-8 v2.0 Expression BeadChip Kit («Illumina», США). Полученные данные указывают на последовательное вовлечение транскриптома в патогенез БП, а также на то, что изменения на транскриптомном уровне процессов транспорта и митохондриального биогенеза могут играть важную роль в нейродегенерации при БП уже на самых ранних этапах. Parkinson’s disease (PD) is a complex systemic disease, mainly associated with the death of dopaminergic neurons. Despite the obvious progress made in the study of molecular genetic factors and mechanisms of PD pathogenesis, it has now become clear that violations in the DNA structure do not describe the entire spectrum of pathological changes observed during the development of the disease. It has now been shown that changes at the transcriptome level can have a significant effect on the pathogenesis of PD. The authors used models of the presymptomatic stage of PD with mice decapitation after 6 hours (6 h-PSS), presymptomatic stage with decapitation after 24 hours (24 h-PSS), advanced presymptomatic (Adv-PSS) and early symptomatic (ESS) stages of PD. For whole transcriptome analysis of RNA pools of the substantia nigra and mouse striatum, the MouseRef-8 v2.0 Expression BeadChip Kit microchips (Illumina, USA) were used. As a result of the analysis of whole transcriptome data, it was shown that, there are a greater number of statistically significant changes in the tissues of the brain and peripheral blood of mice with Adv-PSS and ESS models of PD compared to 6 h-PSS and 24 h-PSS models. In general, the obtained data indicate the sequential involvement of the transcriptome in the pathogenesis of PD, as well as the fact that changes at the transcriptome level of the processes of transport and mitochondrial biogenesis can play an important role in neurodegeneration in PD at an early stage.

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