Hybridization-proximity labeling reveals spatially ordered interactions of nuclear RNA compartments

MAC5 is a component of the conserved MOS4-associated complex. It plays critical roles in development and immunity. Here we report that MAC5 is required for microRNA (miRNA) biogenesis. MAC5 interacts with Serrate (SE), which is a core component of the microprocessor that processes primary miRNA transcripts (pri-miRNAs) into miRNAs and binds the stem-loop region of pri-miRNAs. MAC5 is essential for both the efficient processing and the stability of pri-miRNAs. Interestingly, the reduction of pri-miRNA levels inmac5is partially caused by XRN2/XRN3, the nuclear-localized 5′-to-3′ exoribonucleases, and depends on SE. These results reveal that MAC5 plays a dual role in promoting pri-miRNA processing and stability through its interaction with SE and/or pri-miRNAs. This study also uncovers that pri-miRNAs need to be protected from nuclear RNA decay machinery, which is connected to the microprocessor.

Download Full-text

Nuclear RNA purification by flow cytometry to study nuclear processes in plants

STAR Protocols ◽

10.1016/j.xpro.2021.100320 ◽

2021 ◽

Vol 2 (1) ◽

pp. 100320

Author(s):

Belén Moro ◽

Malgorzata Kisielow ◽

Veronica Barragan Borrero ◽

Antoine Bouet ◽

Christopher A. Brosnan ◽

...

Keyword(s):

Flow Cytometry ◽

Rna Purification ◽

Nuclear Rna ◽

Nuclear Processes

Download Full-text

Characterization of the nuclear and cytosolic transcriptomes in human brain tissue reveals new insights into the subcellular distribution of RNA transcripts

Scientific Reports ◽

10.1038/s41598-021-83541-1 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Ammar Zaghlool ◽

Adnan Niazi ◽

Åsa K. Björklund ◽

Jakub Orzechowski Westholm ◽

Adam Ameur ◽

...

Keyword(s):

Human Brain ◽

Expression Analysis ◽

Differential Expression Analysis ◽

Adult Brain ◽

Sequencing Data ◽

Human Brain Tissue ◽

Protein Coding ◽

Rna Transcripts ◽

Nuclear Rna ◽

The Impact

AbstractTranscriptome analysis has mainly relied on analyzing RNA sequencing data from whole cells, overlooking the impact of subcellular RNA localization and its influence on our understanding of gene function, and interpretation of gene expression signatures in cells. Here, we separated cytosolic and nuclear RNA from human fetal and adult brain samples and performed a comprehensive analysis of cytosolic and nuclear transcriptomes. There are significant differences in RNA expression for protein-coding and lncRNA genes between cytosol and nucleus. We show that transcripts encoding the nuclear-encoded mitochondrial proteins are significantly enriched in the cytosol compared to the rest of protein-coding genes. Differential expression analysis between fetal and adult frontal cortex show that results obtained from the cytosolic RNA differ from results using nuclear RNA both at the level of transcript types and the number of differentially expressed genes. Our data provide a resource for the subcellular localization of thousands of RNA transcripts in the human brain and highlight differences in using the cytosolic or the nuclear transcriptomes for expression analysis.

Download Full-text

7SK small nuclear RNA inhibits cancer cell proliferation through apoptosis induction

Tumor Biology ◽

10.1007/s13277-014-2907-8 ◽

2014 ◽

Vol 36 (4) ◽

pp. 2809-2814 ◽

Cited By ~ 9

Author(s):

Farid Keramati ◽

Ehsan Seyedjafari ◽

Parviz Fallah ◽

Masoud Soleimani ◽

Hossein Ghanbarian

Keyword(s):

Cell Proliferation ◽

Cancer Cell ◽

Cancer Cell Proliferation ◽

Small Nuclear Rna ◽

Apoptosis Induction ◽

Nuclear Rna

Download Full-text

Upregulation of Vitamin C Transporter Functional Expression in 5xFAD Mouse Intestine

Nutrients ◽

10.3390/nu13020617 ◽

2021 ◽

Vol 13 (2) ◽

pp. 617

Author(s):

Trevor Teafatiller ◽

Christopher W. Heskett ◽

Anshu Agrawal ◽

Jonathan S. Marchant ◽

Janet E. Baulch ◽

...

Keyword(s):

Mouse Model ◽

Functional Expression ◽

Specific Protein ◽

Glutathione Peroxidase 1 ◽

Stress Response Genes ◽

Nuclear Rna ◽

The Status ◽

5Xfad Mouse ◽

Mouse Intestine ◽

5Xfad Mice

The process of obtaining ascorbic acid (AA) via intestinal absorption and blood circulation is carrier-mediated utilizing the AA transporters SVCT1 and SVCT2, which are expressed in the intestine and brain (SVCT2 in abundance). AA concentration is decreased in Alzheimer’s disease (AD), but information regarding the status of intestinal AA uptake in the AD is still lacking. We aimed here to understand how AA homeostasis is modulated in a transgenic mouse model (5xFAD) of AD. AA levels in serum from 5xFAD mice were markedly lower than controls. Expression of oxidative stress response genes (glutathione peroxidase 1 (GPX1) and superoxide dismutase 1 (SOD1)) were significantly increased in AD mice jejunum, and this increase was mitigated by AA supplementation. Uptake of AA in the jejunum was upregulated. This increased AA transport was caused by a marked increase in SVCT1 and SVCT2 protein, mRNA, and heterogeneous nuclear RNA (hnRNA) expression. A significant increase in the expression of HNF1α and specific protein 1 (Sp1), which drive SLC23A1 and SLC23A2 promoter activity, respectively, was observed. Expression of hSVCT interacting proteins GRHPR and CLSTN3 were also increased. SVCT2 protein and mRNA expression in the hippocampus of 5xFAD mice was not altered. Together, these investigations reveal adaptive up-regulation of intestinal AA uptake in the 5xFAD mouse model.

Download Full-text

Studies on the effects of chemicals on the processing of nuclear RNA

Biochemical Pharmacology ◽

10.1016/0006-2952(71)90330-3 ◽

1971 ◽

Vol 20 (5) ◽

pp. 1029-1033 ◽

Cited By ~ 4

Author(s):

Michael B. Sporn

Keyword(s):

Nuclear Rna

Download Full-text

Effect of 5-bromodeoxyuridine on heterogeneous nuclear RNA in rat hepatoma cells

Nucleic Acids Research ◽

10.1093/nar/6.4.1731 ◽

1979 ◽

Vol 6 (4) ◽

pp. 1731-1746

Author(s):

Heather W. Weber ◽

Robert H. Stellwagen

Keyword(s):

Hepatoma Cells ◽

Nuclear Rna ◽

Rat Hepatoma ◽

Rat Hepatoma Cells

Download Full-text

INHIBITING EFFECT OF THE NEW CYTOTOXIC ANTIBIOTIC DAUNOMYCIN ON NUCLEIC ACIDS AND MITOTIC ACTIVITY OF HELA CELLS

The Journal of Cell Biology ◽

10.1083/jcb.27.3.545 ◽

1965 ◽

Vol 27 (3) ◽

pp. 545-550 ◽

Cited By ~ 64

Author(s):

A. Di Marco ◽

R. Silvestrini ◽

S. Di Marco ◽

T. Dasdia

Keyword(s):

Mitotic Activity ◽

Rna Synthesis ◽

Thymidine Incorporation ◽

Acid Synthesis ◽

Acetyl Derivative ◽

Total Inhibition ◽

Nuclear Rna ◽

Nucleolar Rna ◽

Higher Doses

The effect has been studied of Actinomycin D, Daunomycin (Da.), and Da. N acetyl derivative on mitotic activity and on the nucleic acid synthesis of in vitro HeLa cell cultures. The experiments were carried out by means of the radioautographic technique using stripping films. The relative uptake of thymidine-H3 and uridine-H3 was determined by means of the reduced silver grain count present in the nuclei of controls and treated cells. The mitotic activity and thymidine incorporation were noticeably reduced by Daunomycin and Actinomycin, whereas both processes appeared less affected by Da. N acetyl derivative. As regards nuclear RNA synthesis, all three antibiotics at low doses chiefly inhibit nucleolar RNA synthesis. On the other hand, whilst Actinomycin at higher doses causes an almost total inhibition of the synthesis of the whole nuclear RNA, in Daunomycin- and Da. N acetyl derivative-treated cells extranucleolar RNA synthesis is less susceptible to inhibition.

Download Full-text