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1.
Nat Commun ; 15(1): 4272, 2024 May 20.
Article in English | MEDLINE | ID: mdl-38769321

ABSTRACT

The mitoribosome translates mitochondrial mRNAs and regulates energy conversion that is a signature of aerobic life forms. We present a 2.2 Å resolution structure of human mitoribosome together with validated mitoribosomal RNA (rRNA) modifications, including aminoacylated CP-tRNAVal. The structure shows how mitoribosomal proteins stabilise binding of mRNA and tRNA helping to align it in the decoding center, whereas the GDP-bound mS29 stabilizes intersubunit communication. Comparison between different states, with respect to tRNA position, allowed us to characterize a non-canonical L1 stalk, and molecular dynamics simulations revealed how it facilitates tRNA transitions in a way that does not require interactions with rRNA. We also report functionally important polyamines that are depleted when cells are subjected to an antibiotic treatment. The structural, biochemical, and computational data illuminate the principal functional components of the translation mechanism in mitochondria and provide a description of the structure and function of the human mitoribosome.


Subject(s)
Mitochondrial Ribosomes , RNA, Transfer , Humans , RNA, Transfer/metabolism , RNA, Transfer/chemistry , RNA, Transfer/genetics , Mitochondrial Ribosomes/metabolism , Mitochondrial Ribosomes/chemistry , Ligands , Molecular Dynamics Simulation , RNA, Messenger/metabolism , RNA, Messenger/genetics , Mitochondria/metabolism , RNA, Ribosomal/metabolism , RNA, Ribosomal/chemistry , Ribosomal Proteins/metabolism , Ribosomal Proteins/chemistry , Guanosine Diphosphate/metabolism , Polyamines/metabolism , Polyamines/chemistry , Protein Binding
2.
bioRxiv ; 2023 Jul 15.
Article in English | MEDLINE | ID: mdl-37503168

ABSTRACT

The mitoribosome translates mitochondrial mRNAs and regulates energy conversion that is a signature of aerobic life forms. We present a 2.2 Å resolution structure of human mitoribosome together with validated mitoribosomal RNA (rRNA) modifications, including aminoacylated CP-tRNA Val . The structure shows how mitoribosomal proteins stabilise binding of mRNA and tRNA helping to align it in the decoding center, whereas the GDP-bound mS29 stabilizes intersubunit communication. Comparison between different states, with respect to tRNA position, allowed to characterize a non-canonical L1 stalk, and molecular dynamics simulations revealed how it facilitates tRNA transition in a way that does not require interactions with rRNA. We also report functionally important polyamines that are depleted when cells are subjected to an antibiotic treatment. The structural, biochemical, and computational data illuminate the principal functional components of the translation mechanism in mitochondria and provide the most complete description so far of the structure and function of the human mitoribosome.

3.
Sci Rep ; 12(1): 7988, 2022 05 14.
Article in English | MEDLINE | ID: mdl-35568729

ABSTRACT

Dyslipidemia is considered an essential component of the pathological process of amyotrophic lateral sclerosis (ALS), a fatal motor neuron disease. Although TAR DNA Binding Protein 43 kDa (TDP-43) links both familial and sporadic forms of ALS and cytoplasmic aggregates are a hallmark of most cases of ALS, the molecular mechanism and the in vivo relation of ALS dyslipidemia with TDP-43 have been unclear. To analyze the dyslipidemia-related gene expression by TDP-43, we performed expression microarray and RNA deep sequencing (RNA-Seq) using cell lines expressing high levels of TDP-43 and identified 434 significantly altered genes including sterol regulatory element-binding protein 2 (SREBP2), a master regulator of cholesterol homeostasis and its downstream genes. Elevated TDP-43 impaired SREBP2 transcriptional activity, leading to inhibition of cholesterol biosynthesis. The amount of cholesterol was significantly decreased in the spinal cords of TDP-43-overexpressed ALS model mice and in the cerebrospinal fluids of ALS patients. These results suggested that TDP-43 could play an essential role in cholesterol biosynthesis in relation to ALS dyslipidemia.


Subject(s)
Amyotrophic Lateral Sclerosis , DNA-Binding Proteins , Motor Neuron Disease , Sterol Regulatory Element Binding Protein 2 , Amyotrophic Lateral Sclerosis/metabolism , Animals , DNA-Binding Proteins/genetics , Humans , Mice , Sterol Regulatory Element Binding Protein 2/genetics , Sterols
4.
Nucleic Acids Res ; 47(19): 10357-10372, 2019 11 04.
Article in English | MEDLINE | ID: mdl-31504794

ABSTRACT

Activation of ribosomal RNA (rRNA) synthesis is pivotal during cell growth and proliferation, but its aberrant upregulation may promote tumorigenesis. Here, we demonstrate that the candidate oncoprotein, LYAR, enhances ribosomal DNA (rDNA) transcription. Our data reveal that LYAR binds the histone-associated protein BRD2 without involvement of acetyl-lysine-binding bromodomains and recruits BRD2 to the rDNA promoter and transcribed regions via association with upstream binding factor. We show that BRD2 is required for the recruitment of the MYST-type acetyltransferase KAT7 to rDNA loci, resulting in enhanced local acetylation of histone H4. In addition, LYAR binds a complex of BRD4 and KAT7, which is then recruited to rDNA independently of the BRD2-KAT7 complex to accelerate the local acetylation of both H4 and H3. BRD2 also helps recruit BRD4 to rDNA. By contrast, LYAR has no effect on rDNA methylation or the binding of RNA polymerase I subunits to rDNA. These data suggest that LYAR promotes the association of the BRD2-KAT7 and BRD4-KAT7 complexes with transcription-competent rDNA loci but not to transcriptionally silent rDNA loci, thereby increasing rRNA synthesis by altering the local acetylation status of histone H3 and H4.


Subject(s)
Cell Cycle Proteins/genetics , DNA-Binding Proteins/genetics , Histone Acetyltransferases/genetics , Nuclear Proteins/genetics , Transcription Factors/genetics , Acetylation , Carcinogenesis/genetics , Chromatin/genetics , DNA Methylation/genetics , DNA, Ribosomal/genetics , Histones/genetics , Humans , RNA Polymerase I/genetics , RNA, Ribosomal/biosynthesis , RNA, Ribosomal/genetics , Transcription, Genetic
5.
Nucleic Acids Res ; 47(5): 2487-2505, 2019 03 18.
Article in English | MEDLINE | ID: mdl-30759234

ABSTRACT

TDP-43 regulates cellular levels of Cajal bodies (CBs) that provide platforms for the assembly and RNA modifications of small nuclear ribonucleoproteins (snRNPs) involved in pre-mRNA splicing. Alterations in these snRNPs may be linked to pathogenesis of amyotrophic lateral sclerosis. However, specific roles for TDP-43 in CBs remain unknown. Here, we demonstrate that TDP-43 regulates the CB localization of four UG-rich motif-bearing C/D-box-containing small Cajal body-specific RNAs (C/D scaRNAs; i.e. scaRNA2, 7, 9 and 28) through the direct binding to these scaRNAs. TDP-43 enhances binding of a CB-localizing protein, WD40-repeat protein 79 (WDR79), to a subpopulation of scaRNA2 and scaRNA28; the remaining population of the four C/D scaRNAs was localized to CB-like structures even with WDR79 depletion. Depletion of TDP-43, in contrast, shifted the localization of these C/D scaRNAs, mainly into the nucleolus, as well as destabilizing scaRNA2, and reduced the site-specific 2'-O-methylation of U1 and U2 snRNAs, including at 70A in U1 snRNA and, 19G, 25G, 47U and 61C in U2 snRNA. Collectively, we suggest that TDP-43 and WDR79 have separate roles in determining CB localization of subsets of C/D and H/ACA scaRNAs.


Subject(s)
Amyotrophic Lateral Sclerosis/genetics , Coiled Bodies/genetics , DNA-Binding Proteins/genetics , Proteins/genetics , Amyotrophic Lateral Sclerosis/pathology , Cell Nucleolus/genetics , Coiled Bodies/metabolism , Cytidine/analogs & derivatives , Cytidine/genetics , HeLa Cells , Humans , Molecular Chaperones , RNA, Guide, Kinetoplastida/genetics , RNA, Small Nuclear/genetics , Ribonucleoproteins, Small Nuclear/genetics , Telomerase
6.
PLoS One ; 14(1): e0210003, 2019.
Article in English | MEDLINE | ID: mdl-30608951

ABSTRACT

Extracellular vesicle (EV) microRNAs are of major interest as potential diagnostic biomarkers in all cancer types. This study aims to identify miRNA profiles of shed microvesicles (sMVs) and exosomes (Exos) secreted from the isogenic colorectal cancer (CRC) cell lines SW480 and SW620 and evaluate their ability to predict CRC. Deep sequencing of miRNAs in parental cell lysates (CLs) and highly-purified sMVs and Exos was performed. We focused on miRNAs enriched in EVs and dysregulated miRNAs in metastatic cells (SW620) relative to primary cancer cells (SW480). We investigated the ability of EV miRNA signatures to predict CRC tumours using 594 tumours (representing different pathological stages) and 11 normal samples obtained from TCGA. In SW480 and SW620 cells we identified 345 miRNAs, of which 61 and 73 were upregulated and downregulated in SW620-CLs compared to SW480-CLs, respectively. Selective distribution of cellular miRNAs into EVs results in distinct miRNA signatures for sMVs and Exos in each cell line. Cross cell line comparisons of EV miRNA profiles reveal a subset of miRNAs critical in CRC progression from primary carcinoma to metastasis. Many miRNAs non-detectable (<5 TPM) in CLs were significantly enriched (>1000 TPM) in secreted EVs. Strikingly, miR-7641 which is non-detectable in SW480-CL but upregulated in SW620-CL is highly enriched in EVs secreted from both cell lines. Pearson correlation analysis demonstrated that EV miRNA profiles can be used to predict CRC tumours with ~96% accuracy. Our findings suggest that EV miRNA profiles from CRC cell lines may allow prediction of CRC tumours, and that miR-7641 may serve as an attractive candidate for the specific, non-invasive diagnosis and prognosis of CRC.


Subject(s)
Colorectal Neoplasms/genetics , Exosomes/genetics , MicroRNAs/genetics , Blotting, Western , Cell Line , Colorectal Neoplasms/metabolism , Cryoelectron Microscopy , Exosomes/metabolism , Gene Expression Regulation, Neoplastic/genetics , Humans , MicroRNAs/metabolism
7.
Nucleic Acids Res ; 46(18): 9289-9298, 2018 10 12.
Article in English | MEDLINE | ID: mdl-30202881

ABSTRACT

During ribosome biogenesis, ribosomal RNAs acquire various chemical modifications that ensure the fidelity of translation, and dysregulation of the modification processes can cause proteome changes as observed in cancer and inherited human disorders. Here, we report the complete chemical modifications of all RNAs of the human 80S ribosome as determined with quantitative mass spectrometry. We assigned 228 sites with 14 different post-transcriptional modifications, most of which are located in functional regions of the ribosome. All modifications detected are typical of eukaryotic ribosomal RNAs, and no human-specific modifications were observed, in contrast to a recently reported cryo-electron microscopy analysis. While human ribosomal RNAs appeared to have little polymorphism regarding the post-transcriptional modifications, we found that pseudouridylation at two specific sites in 28S ribosomal RNA are significantly reduced in ribosomes of patients with familial dyskeratosis congenita, a genetic disease caused by a point mutation in the pseudouridine synthase gene DKC1. The landscape of the entire epitranscriptomic ribosomal RNA modifications provides a firm basis for understanding ribosome function and dysfunction associated with human disease.


Subject(s)
RNA Processing, Post-Transcriptional , RNA, Ribosomal, 28S/genetics , RNA/genetics , Ribosomes/genetics , Cell Cycle Proteins/genetics , Cell Cycle Proteins/metabolism , Cell Line, Transformed , Cryoelectron Microscopy , Dyskeratosis Congenita/genetics , HeLa Cells , Humans , Mutation , Nuclear Proteins/genetics , Nuclear Proteins/metabolism , Protein Biosynthesis , Pseudouridine/metabolism , RNA/chemistry , RNA/metabolism , RNA, Ribosomal, 28S/chemistry , RNA, Ribosomal, 28S/metabolism , Ribosomes/metabolism , Ribosomes/ultrastructure
8.
RNA Biol ; 15(7): 849-855, 2018.
Article in English | MEDLINE | ID: mdl-29683372

ABSTRACT

Chtop binds competitively to the arginine methyltransferases PRMT1 and PRMT5, thereby promoting the asymmetric or symmetric methylation of arginine residues, respectively. In cooperation with PRMT1, Chtop activates transcription of certain gene groups, such as the estrogen-inducible genes in breast cancer cells, the 5-hydroxymethylcytosine-modified genes involved in glioblastomagenesis, or the Zbp-89-dependent genes in erythroleukemia cells. Chtop also represses expression of the fetal γ-globin gene. In addition, Chtop is a component of the TREX complex that links transcription elongation to mRNA export. The regulation of Chtop expression is, therefore, a key process during the expression of certain gene groups and pathogenesis of certain diseases. Our recent study revealed that cellular levels of Chtop are strictly autoregulated by a mechanism involving intron retention and nonsense-mediated mRNA decay. Here, we summarize roles of Chtop in gene-specific expression and highlight our recent findings concerning the autoregulation of Chtop.


Subject(s)
Glioblastoma/metabolism , Nuclear Proteins/metabolism , Protein-Arginine N-Methyltransferases/metabolism , RNA, Messenger/metabolism , Repressor Proteins/metabolism , Transcription Factors/metabolism , Transcription, Genetic , Animals , Arginine/metabolism , Humans , Introns , Methylation , Mice , Nonsense Mediated mRNA Decay , Nuclear Proteins/genetics , Protein-Arginine N-Methyltransferases/genetics , RNA Splicing , RNA, Messenger/genetics , Repressor Proteins/genetics , Transcription Factors/genetics , beta-Thalassemia/metabolism
9.
RNA Biol ; 15(2): 261-268, 2018 02 01.
Article in English | MEDLINE | ID: mdl-29168419

ABSTRACT

During the biogenesis of U1 small nuclear ribonucleoprotein, a small population of U1 snRNA molecules acquires an extra methylation at the first transcribed nucleotide and a nucleolytic cleavage to remove the 3' structured region including the Sm protein-binding site and stem-loop 4. These modifications occur before hypermethylation of the monomethylated 5' cap, whereby producing truncated forms of U1 snRNA (U1-tfs) that are diverted from the normal pathway to a processing body-associated degradation pathway. Here, we demonstrate that a small population of U2 snRNA molecules receives post-transcriptional modifications similar to those of U1 to yield U2-tfs. Like U1-tfs, U2-tfs molecules were produced from transcripts of the U2 snRNA gene having all cis-elements or lacking the 3' box. Unlike U1-tfs, however, a portion of U2-tfs received additional uridylylation of up to 5 nucleotides in length at position 87 (designated as U2-tfs-polyU) and formed an Sm protein-binding site-like structure that was stabilized by the small nuclear ribonucleoprotein SmB/B' probably as a part of heptameric Sm core complex that associates to the RNA. Both U2-tfs and U2-tfs-polyU were degraded by a nuclease distinct from the canonical Dis3L2 by a process catalyzed by terminal uridylyltransferase 7. Collectively, our data suggest that U2 snRNA biogenesis is regulated, at least in part, by a novel degradation pathway to ensure that defective U2 molecules are not incorporated into the spliceosome.


Subject(s)
RNA, Small Nuclear/chemistry , RNA, Small Nuclear/metabolism , Cell Line , Humans , Models, Molecular , Nucleic Acid Conformation , RNA Processing, Post-Transcriptional , RNA, Small Nuclear/genetics , Ribonucleoproteins, Small Nuclear/genetics
10.
Sci Rep ; 7(1): 7709, 2017 08 09.
Article in English | MEDLINE | ID: mdl-28794432

ABSTRACT

The 43-kDa trans-activating response region DNA-binding protein 43 (TDP-43) is a product of a causative gene for amyotrophic lateral sclerosis (ALS). Despite of accumulating evidence that mitochondrial dysfunction underlies the pathogenesis of TDP-43-related ALS, the roles of wild-type TDP-43 in mitochondria are unknown. Here, we show that the small TDP-43 population present in mitochondria binds directly to a subset of mitochondrial tRNAs and precursor RNA encoded in L-strand mtDNA. Upregulated expression of TDP-43 stabilised the processing intermediates of mitochondrial polycistronic transcripts and their products including the components of electron transport and 16S mt-rRNA, similar to the phenotype observed in cells deficient for mitochondrial RNase P. Conversely, TDP-43 deficiency reduced the population of processing intermediates and impaired mitochondrial function. We propose that TDP-43 has a novel role in maintaining mitochondrial homeostasis by regulating the processing of mitochondrial transcripts.


Subject(s)
DNA-Binding Proteins/metabolism , Genes, Mitochondrial , Mitochondria/genetics , Mitochondria/metabolism , RNA Processing, Post-Transcriptional , Transcription, Genetic , Cell Line , DNA-Binding Proteins/genetics , Gene Expression , Humans , Mitochondria/ultrastructure , Protein Binding , Protein Transport , RNA Stability , RNA, Transfer/genetics
11.
Nucleic Acids Res ; 45(6): 3437-3447, 2017 04 07.
Article in English | MEDLINE | ID: mdl-27899605

ABSTRACT

Ribosome biogenesis occurs successively in the nucleolus, nucleoplasm, and cytoplasm. Maturation of the ribosomal small subunit is completed in the cytoplasm by incorporation of a particular class of ribosomal proteins and final cleavage of 18S-E pre-rRNA (18S-E). Here, we show that poly(A)-specific ribonuclease (PARN) participates in steps leading to 18S-E maturation in human cells. We found PARN as a novel component of the pre-40S particle pulled down with the pre-ribosome factor LTV1 or Bystin. Reverse pull-down analysis revealed that PARN is a constitutive component of the Bystin-associated pre-40S particle. Knockdown of PARN or exogenous expression of an enzyme-dead PARN mutant (D28A) accumulated 18S-E in both the cytoplasm and nucleus. Moreover, expression of D28A accumulated 18S-E in Bystin-associated pre-40S particles, suggesting that the enzymatic activity of PARN is necessary for the release of 18S-E from Bystin-associated pre-40S particles. Finally, RNase H-based fragmentation analysis and 3΄-sequence analysis of 18S-E species present in cells expressing wild-type PARN or D28A suggested that PARN degrades the extended regions encompassing nucleotides 5-44 at the 3΄ end of mature 18S rRNA. Our results reveal a novel role for PARN in ribosome biogenesis in human cells.


Subject(s)
Exoribonucleases/physiology , RNA Precursors/metabolism , RNA Processing, Post-Transcriptional , RNA, Ribosomal, 18S/metabolism , Ribosome Subunits, Small, Eukaryotic/metabolism , Cell Adhesion Molecules/analysis , Exoribonucleases/analysis , Exoribonucleases/genetics , Exoribonucleases/metabolism , HeLa Cells , Humans , Mutation , Ribosomal Proteins/analysis , Ribosome Subunits, Small, Eukaryotic/chemistry
12.
Sci Rep ; 6: 38397, 2016 12 05.
Article in English | MEDLINE | ID: mdl-27917920

ABSTRACT

Previously we reported that LIM1863 colorectal cancer (CRC) cells secrete three distinct extracellular vesicle subtypes - two subpopulations of exosomes (apical EpCAM-Exos and basolateral A33-Exos) and shed microvesicles (sMVs) - with distinct protein and miRNA signatures. Here, we extend our omics approach to understand the fundamental role of LIM1863-derived EVs by performing a comprehensive analysis of their mRNAs and long non-coding RNAs (lncRNAs) using RNA-Seq. We show that 2,389 mRNAs, 317 pseudogene transcripts, 1,028 lncRNAs and 206 short non-coding RNAs selectively distributed to (i.e., are enriched in) LIM1863 EVs, relative to the parent cell. An Ensembl/UniProtKB analysis revealed 1,937 mRNAs encode canonical proteins, 348 isoforms (including splice-variant proteins), and 119 'missing proteins' (i.e., annotated in Ensembl but not UniProtKB). Further dissection of our protein/RNA data revealed that 6/151 observed RNA binding proteins have the potential to interact with ~75% of EV-enriched RNAs. Intriguingly, the co-existence of U1 and U2 ribonucleoproteins and their cognate snRNAs in LIM1863 EVs suggests a possible association of CRC EVs with recipient cell splicing events. Our data reveal several potential lncRNA CRC biomarkers and novel splicing/fusion genes that, collectively, will advance our understanding of EV biology in CRC and accelerate the development of EV-based diagnostics and therapeutics.


Subject(s)
Biomarkers, Tumor/genetics , Colonic Neoplasms/diagnosis , Colonic Neoplasms/genetics , Gene Expression Regulation, Neoplastic , RNA, Long Noncoding/genetics , RNA, Neoplasm/genetics , Transcriptome , Biomarkers, Tumor/metabolism , Cell Line, Tumor , Cell-Derived Microparticles/chemistry , Cell-Derived Microparticles/metabolism , Colonic Neoplasms/pathology , Databases, Factual , Exosomes/chemistry , Exosomes/metabolism , Gene Ontology , Humans , MicroRNAs/genetics , MicroRNAs/metabolism , Molecular Sequence Annotation , RNA, Long Noncoding/metabolism , RNA, Neoplasm/metabolism , Ribonucleoprotein, U1 Small Nuclear/genetics , Ribonucleoprotein, U1 Small Nuclear/metabolism , Ribonucleoprotein, U2 Small Nuclear/genetics , Ribonucleoprotein, U2 Small Nuclear/metabolism
13.
Genes Dev ; 30(21): 2376-2390, 2016 11 01.
Article in English | MEDLINE | ID: mdl-27881600

ABSTRACT

In cytoplasm, the survival of motor neuron (SMN) complex delivers pre-small nuclear RNAs (pre-snRNAs) to the heptameric Sm ring for the assembly of the ring complex on pre-snRNAs at the conserved Sm site [A(U)4-6G]. Gemin5, a WD40 protein component of the SMN complex, is responsible for recognizing pre-snRNAs. In addition, Gemin5 has been reported to specifically bind to the m7G cap. In this study, we show that the WD40 domain of Gemin5 is both necessary and sufficient for binding the Sm site of pre-snRNAs by isothermal titration calorimetry (ITC) and mutagenesis assays. We further determined the crystal structures of the WD40 domain of Gemin5 in complex with the Sm site or m7G cap of pre-snRNA, which reveal that the WD40 domain of Gemin5 recognizes the Sm site and m7G cap of pre-snRNAs via two distinct binding sites by respective base-specific interactions. In addition, we also uncovered a novel role of Gemin5 in escorting the truncated forms of U1 pre-snRNAs for proper disposal. Overall, the elucidated Gemin5 structures will contribute to a better understanding of Gemin5 in small nuclear ribonucleic protein (snRNP) biogenesis as well as, potentially, other cellular activities.


Subject(s)
Models, Molecular , RNA Precursors/metabolism , Ribonucleoproteins, Small Nuclear/metabolism , SMN Complex Proteins/chemistry , SMN Complex Proteins/metabolism , Binding Sites , Cell Line , Crystallization , HEK293 Cells , Humans , Point Mutation , Protein Binding , Protein Domains/genetics , Protein Structure, Tertiary , Protein Transport , RNA Precursors/chemistry , Ribonucleoproteins, Small Nuclear/biosynthesis , SMN Complex Proteins/genetics
14.
PLoS One ; 11(10): e0164773, 2016.
Article in English | MEDLINE | ID: mdl-27776129

ABSTRACT

Scd6, a yeast homologue of human RAP55, is a component of messenger ribonucleoproteins (mRNPs) that repress translation by binding to translation initiation factors, and also is a decapping activator along with the binding partners Edc3 and Dhh1. Herein, we report that Scd6 is a substrate of the intrinsic protein arginine methyltransferase, Hmt1, in budding yeast Saccharomyces cerevisiae. Mass spectrometric analysis revealed that several arginine residues within the Scd6 RGG motif, which is important for mRNA binding, were methylated in Hmt1 dependent manner. Under stress conditions such as glucose starvation, Scd6 localized to cytoplasmic processing bodies (P-bodies) wherein translationally repressed mRNPs and untranslated mRNAs accumulate. Localization of Scd6 to P-bodies was impaired in hmt1 deletion mutant and in the presence of methylation-deficient substitution of Scd6. In addition, deletion of scd6 and dhh1 led to severe synthetic growth defect at high temperature. Methylation-deficient mutation of Scd6 suppressed the phenotypic defects of scd6 dhh1 double mutant, whereas methylation-mimic mutation did not, suggesting that the arginine methylation might negatively regulate Scd6 function relating to Dhh1. Therefore, the present data suggest that Hmt1-based arginine methylation is required for Scd6 localization and function.


Subject(s)
Cytoplasm/metabolism , Protein-Arginine N-Methyltransferases/metabolism , Repressor Proteins/metabolism , Ribonucleoproteins/metabolism , Saccharomyces cerevisiae Proteins/metabolism , Saccharomyces cerevisiae/growth & development , Arginine/metabolism , Binding Sites , Gene Expression Regulation, Fungal , Methylation , Protein Binding , RNA, Fungal/metabolism , RNA, Messenger/metabolism , Ribonucleoproteins/chemistry , Saccharomyces cerevisiae/genetics , Saccharomyces cerevisiae/metabolism , Saccharomyces cerevisiae Proteins/chemistry
15.
Nucleic Acids Res ; 44(20): 9847-9859, 2016 Nov 16.
Article in English | MEDLINE | ID: mdl-27683223

ABSTRACT

Chtop (chromatin target of Prmt1) regulates various aspects of gene expression including transcription and mRNA export. Despite these important functions, the regulatory mechanism underlying Chtop expression remains undetermined. Using Chtop-expressing human cell lines, we demonstrate that Chtop expression is controlled via an autoregulatory negative feedback loop whereby Chtop binds its own mRNA to retain intron 2 during splicing; a premature termination codon present at the 5' end of intron 2 leads to nonsense-mediated decay of the mRNA. We also show that Chtop interacts with exon 2 of Chtop mRNA via its arginine-glycine-rich (RG) domain, and with intron 2 via its N-terminal (N1) domain; both are required for retention of intron 2. In addition, we show that hnRNP H accelerates intron 2 splicing of Chtop mRNA in a manner dependent on Chtop expression level, suggesting that Chtop and hnRNP H regulate intron 2 retention of Chtop mRNA antagonistically. Thus, the present study provides a novel molecular mechanism by which mRNA and protein levels are constitutively regulated by intron retention.


Subject(s)
Gene Expression Regulation , Homeostasis , Introns , Nonsense Mediated mRNA Decay , Nuclear Proteins/genetics , RNA Splicing , RNA, Messenger/genetics , Transcription Factors/genetics , 5' Untranslated Regions , Alternative Splicing , Cell Line , Gene Expression , Gene Order , Humans , Models, Biological , Nuclear Proteins/metabolism , Protein Binding , Protein Interaction Domains and Motifs , RNA, Messenger/metabolism , Transcription Factors/metabolism
16.
Nucleic Acids Res ; 44(6): e59, 2016 Apr 07.
Article in English | MEDLINE | ID: mdl-26673725

ABSTRACT

Pseudouridine (5-ribosyluracil, Ψ) is the only 'mass-silent' nucleoside produced by post-transcriptional RNA modification. We describe here a novel mass spectrometry (MS)-based method for direct determination of Ψ in RNA. The method assigns a Ψ-containing nucleolytic RNA fragment by an accurate measurement of a signature doubly dehydrated nucleoside anion ([C9H7N2O4](1-),m/z207.04) produced by collision-induced dissociation MS, and it determines the Ψ-containing nucleotide sequence by pseudo-MS(3), i.e. in-source fragmentation followed by MS(2) By applying this method, we identified all of the known Ψs in the canonical human spliceosomal snRNAs and, unexpectedly, found two previously unknown Ψs in the U5 and U6 snRNAs. Because the method allows direct determination of Ψ in a subpicomole quantity of RNA, it will serve as a useful tool for the structure/function studies of a wide variety of non-coding RNAs.


Subject(s)
Mass Spectrometry/methods , Pseudouridine/chemistry , RNA Processing, Post-Transcriptional , RNA, Small Nuclear/chemistry , Base Sequence , Humans , Molecular Sequence Data , Nucleic Acid Conformation , Pseudouridine/metabolism , RNA, Small Nuclear/metabolism , Spliceosomes/chemistry , Spliceosomes/metabolism
17.
Nucleic Acids Res ; 43(21): 10397-410, 2015 Dec 02.
Article in English | MEDLINE | ID: mdl-26531822

ABSTRACT

Collaborator of alternative reading frame protein (CARF) associates directly with ARF, p53, and/or human double minute 2 protein (HDM2), a ubiquitin-protein ligase, without cofactors and regulates cell proliferation by forming a negative feedback loop. Although ARF, p53, and HDM2 also participate in the regulation of ribosome biogenesis, the involvement of CARF in this process remains unexplored. In this study, we demonstrate that CARF associates with 5'-3' exoribonuclease 2 (XRN2), which plays a major role in both the maturation of rRNA and the degradation of a variety of discarded pre-rRNA species. We show that overexpression of CARF increases the localization of XRN2 in the nucleoplasm and a concomitant suppression of pre-rRNA processing that leads to accumulation of the 5' extended from of 45S/47S pre-rRNA and 5'-01, A0-1 and E-2 fragments of pre-rRNA transcript in the nucleolus. This was also observed upon XRN2 knockdown. Knockdown of CARF increased the amount of XRN2 in the nucleolar fraction as determined by cell fractionation and by immnocytochemical analysis. These observations suggest that CARF regulates early steps of pre-rRNA processing during ribosome biogenesis by controlling spatial distribution of XRN2 between the nucleoplasm and nucleolus.


Subject(s)
Apoptosis Regulatory Proteins/metabolism , Cell Nucleus/enzymology , Exoribonucleases/metabolism , RNA Processing, Post-Transcriptional , RNA, Ribosomal/metabolism , RNA-Binding Proteins/metabolism , Cell Line , Cell Nucleus/genetics , Humans , RNA Precursors/metabolism
18.
Proc Natl Acad Sci U S A ; 112(46): E6388-96, 2015 Nov 17.
Article in English | MEDLINE | ID: mdl-26540727

ABSTRACT

Plant response to drought and hyperosmosis is mediated by the phytohormone abscisic acid (ABA), a sesquiterpene compound widely distributed in various embryophyte groups. Exogenous ABA as well as hyperosmosis activates the sucrose nonfermenting 1 (SNF1)-related protein kinase2 (SnRK2), which plays a central role in cellular responses against drought and dehydration, although the details of the activation mechanism are not understood. Analysis of a mutant of the moss Physcomitrella patens with reduced ABA sensitivity and reduced hyperosmosis tolerance revealed that a protein kinase designated "ARK" (for "ABA and abiotic stress-responsive Raf-like kinase") plays an essential role in the activation of SnRK2. ARK encoded by a single gene in P. patens belongs to the family of group B3 Raf-like MAP kinase kinase kinases (B3-MAPKKKs) mediating ethylene, disease resistance, and salt and sugar responses in angiosperms. Our findings indicate that ARK, as a novel regulatory component integrating ABA and hyperosmosis signals, represents the ancestral B3-MAPKKKs, which multiplied, diversified, and came to have specific functions in angiosperms.


Subject(s)
Bryopsida , MAP Kinase Signaling System/physiology , Osmotic Pressure/physiology , Plant Proteins , raf Kinases , Amino Acid Sequence , Bryopsida/enzymology , Bryopsida/genetics , Molecular Sequence Data , Mutation , Plant Proteins/genetics , Plant Proteins/metabolism , raf Kinases/genetics , raf Kinases/metabolism
19.
Nucleic Acids Res ; 43(11): 5524-36, 2015 Jun 23.
Article in English | MEDLINE | ID: mdl-25969445

ABSTRACT

During the early steps of ribosome biogenesis in mammals, the two ribosomal subunits 40S and 60S are produced via splitting of the large 90S pre-ribosomal particle (90S) into pre-40S and pre-60S pre-ribosomal particles (pre-40S and pre-60S). We previously proposed that replacement of fibrillarin by Nop52 (RRP1/NNP-1) for the binding to p32 (C1QBP) is a key event that drives this splitting process. However, how the replacement by RRP1 is coupled with the endo- and/or exo-ribonucleolytic cleavage of pre-rRNA remains unknown. In this study, we demonstrate that RRP1 deficiency suppressed site 2 cleavage on ITS1 of 47S/45S, 41S and 36S pre-rRNAs in human cells. RRP1 was also present in 90S and was localized in the dense fibrillar component of the nucleolus dependently on active RNA polymerase I transcription. In addition, double knockdown of XRN2 and RRP1 revealed that RRP1 accelerated the site 2 cleavage of 47S, 45S and 41S pre-rRNAs. These data suggest that RRP1 is involved not only in competitive binding with fibrillarin to C1QBP on 90S but also in site 2 cleavage in ITS1 of pre-rRNAs at early stages of human ribosome biogenesis; thus, it is likely that RRP1 integrates the cleavage of site 2 with the physical split of 90S into pre-40S and pre-60S.


Subject(s)
Nuclear Proteins/metabolism , RNA Precursors/metabolism , RNA Processing, Post-Transcriptional , RNA, Ribosomal/metabolism , Ribosomes/metabolism , Cell Line , DNA, Ribosomal Spacer , HeLa Cells , Humans , RNA Cleavage , RNA-Binding Proteins/metabolism , Ribosome Subunits, Large, Eukaryotic/metabolism
20.
Genes Cells ; 19(4): 273-86, 2014 Apr.
Article in English | MEDLINE | ID: mdl-24495227

ABSTRACT

Ribosome biogenesis is an essential process for cell growth and proliferation and is enhanced in cancer and embryonic stem cells. Mouse Ly-1 antibody reactive clone product (Lyar) is expressed at very high levels in many tumor, leukemia or embryonic stem cells; is a novel nucleolar protein with zinc-finger DNA-binding motifs and is involved in cell growth regulation. However, cellular function of Lyar remains unexplored. Here, we show that human homologue of Lyar (LYAR) accelerates ribosome biogenesis at the level of processing of preribosomal RNA (pre-rRNA). We show that LYAR is excluded from the nucleolus after actinomycin D treatment and is present in preribosomal fraction of the nuclear extract as well as in the fractions with 40S, 60S and 90S sedimentation coefficients. LYAR is required for processing of 47S/45S, 32S, 30S and 21S pre-rRNAs. In addition, we show that over-expression of LYAR increases cell proliferation without affecting the expression of c-Myc or p53. Combined, these results suggest that some rapidly growing cells enhance ribosome biogenesis by increasing the expression of LYAR.


Subject(s)
DNA-Binding Proteins/metabolism , Nuclear Proteins/metabolism , RNA Precursors/metabolism , RNA, Ribosomal/metabolism , Animals , Cell Proliferation , DNA-Binding Proteins/genetics , Dactinomycin/pharmacology , HEK293 Cells , HeLa Cells , Humans , Mice , Nuclear Proteins/genetics , Nucleic Acid Synthesis Inhibitors/pharmacology , RNA Processing, Post-Transcriptional , Structural Homology, Protein
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