scholarly journals Human 5p-tailed Mirtrons are Processed by RNaseP

2021 ◽  
Author(s):  
M. Farid Zia ◽  
Jacob Peter ◽  
Johnathan Hoover ◽  
kuan-hui E Chen ◽  
Alex Sutton Flynt
Keyword(s):  
Human Genome ◽  
Splice Site ◽  
Strong Correlation ◽  
Sequence Motifs ◽  
Rna Turnover ◽  
High Confidence ◽  
Trna Processing ◽  
Canonical Pathways ◽  
Necessary And Sufficient ◽  
Hairpin Precursor

Approximately a thousand microRNAs (miRNAs) are documented from human cells. A third appear to transit non-canonical pathways that typically bypass processing by Drosha, the dedicated nuclear miRNA producing enzyme. The largest class of non-canonical miRNAs are mirtrons which eschew Drosha to mature through spliceosome activity. While mirtrons are found in several configurations, the vast majority of human mirtron species are 5p-tailed. For these mirtrons, a 3p splice site defines the 3p end of their hairpin precursor while a tail of variable length separates the 5p base of the hairpin from the nearest splice site. How this tail is removed is not understood. Here we examine sequence motifs in 5p-tailed mirtrons and interactions with RNA turnover processes to characterize biogenesis processes. Through studying the high confidence 5p-tailed mirtron, hsa-miR-5010, we identify RNaseP as necessary and sufficient for severing the 5p tail of this mirtron. Further, depletion of RNaseP activity globally decreased 5p-tailed mirtron expression implicating this endoribonuclease in biogenesis of the entire class. Moreover, as 5p-tailed mirtron biogenesis appears to be connected to tRNA processing we found a strong correlation between accumulation of tRNA fragments (tRFs) and 5p-tailed mirtron abundance. This suggests that dysregulation of tRNA processing seen in cancers may also impact expression of the ~400 5p-tailed mirtrons encoded in the human genome.

scholarly journals The transcriptionally competent U2 gene is necessary and sufficient for adenovirus type 12 induction of the fragile site at 17q21-22.

1995 ◽  
Vol 15 (11) ◽  
pp. 6256-6261 ◽  
Author(s):  
S Gargano ◽  
P Wang ◽  
E Rusanganwa ◽  
S Bacchetti
Keyword(s):  
Human Genome ◽  
Tandem Repeats ◽  
Fragile Site ◽  
Adenovirus Type ◽  
Fragile Sites ◽  
Human Cells ◽  
Necessary And Sufficient

Adenovirus type 12 induces four fragile sites upon infection of human cells. The U2 locus, consisting of up to 20 tandem repeats of a 5.8-kbp monomer, maps at the most sensitive of these sites at 17q21-22. We have previously shown that an artificial U2 locus integrated into the human genome generates a new virus-induced fragile site. To determine which elements within the U2 monomer are responsible for fragility, we constructed loci consisting of tandem repeats of subfragments of the U2 monomer. With this approach, we demonstrate that a transcriptionally competent U2 gene is necessary and sufficient for virus-induced fragility and that no other element within the 5.8-kbp monomer contributes to this effect.

scholarly journals Multiple Splicing Defects in an Intronic False Exon

2000 ◽  
Vol 20 (17) ◽  
pp. 6414-6425 ◽  
Author(s):  
Hanzhen Sun ◽  
Lawrence A. Chasin
Keyword(s):  
Splice Site ◽  
Negative Influence ◽  
Splice Sites ◽  
Polypyrimidine Tract ◽  
Exon Definition ◽  
Exon 2 ◽  
Vast Number ◽  
Consensus Sequences ◽  
Splice Site Sequence ◽  
Necessary And Sufficient

ABSTRACT Splice site consensus sequences alone are insufficient to dictate the recognition of real constitutive splice sites within the typically large transcripts of higher eukaryotes, and large numbers of pseudoexons flanked by pseudosplice sites with good matches to the consensus sequences can be easily designated. In an attempt to identify elements that prevent pseudoexon splicing, we have systematically altered known splicing signals, as well as immediately adjacent flanking sequences, of an arbitrarily chosen pseudoexon from intron 1 of the human hprt gene. The substitution of a 5′ splice site that perfectly matches the 5′ consensus combined with mutation to match the CAG/G sequence of the 3′ consensus failed to get this model pseudoexon included as the central exon in a dhfr minigene context. Provision of a real 3′ splice site and a consensus 5′ splice site and removal of an upstream inhibitory sequence were necessary and sufficient to confer splicing on the pseudoexon. This activated context also supported the splicing of a second pseudoexon sequence containing no apparent enhancer. Thus, both the 5′ splice site sequence and the polypyrimidine tract of the pseudoexon are defective despite their good agreement with the consensus. On the other hand, the pseudoexon body did not exert a negative influence on splicing. The introduction into the pseudoexon of a sequence selected for binding to ASF/SF2 or its replacement with β-globin exon 2 only partially reversed the effect of the upstream negative element and the defective polypyrimidine tract. These results support the idea that exon-bridging enhancers are not a prerequisite for constitutive exon definition and suggest that intrinsically defective splice sites and negative elements play important roles in distinguishing the real splicing signal from the vast number of false splicing signals.

scholarly journals Homolog of ELAC2 is a central regulator of the mitochondrial unfolded protein response

2021 ◽  
Author(s):  
James P Held ◽  
Benjamin R Saunders ◽  
Claudia V Pereria ◽  
Maulik R Patel
Keyword(s):  
Transcription Factors ◽  
Stress Response ◽  
Unfolded Protein Response ◽  
Negative Regulation ◽  
Mitochondrial Stress ◽  
Trna Processing ◽  
Unfolded Protein ◽  
Necessary And Sufficient ◽  
Protein Response ◽  
Mitochondrial Unfolded Protein Response

The mitochondrial unfolded protein response (UPRmt) has emerged as a predominant mechanism that preserves mitochondrial function. Consequently, multiple pathways likely exist to modulate UPRmt. We unexpectedly discovered that the tRNA processing enzyme, homolog of ELAC2 (HOE-1), is central to UPRmt regulation in Caenorhabditis elegans. We find that nuclear HOE-1 is necessary and sufficient to robustly activate UPRmt. We show that HOE-1 acts via transcription factors ATFS-1 and DVE-1 that are crucial for UPRmt. Mechanistically, we show that HOE-1 likely mediates its effects via tRNAs, as blocking tRNA export prevents HOE-1-induced UPRmt. Interestingly, we find that HOE-1 does not act via the integrated stress response, which can be activated by uncharged tRNAs, pointing towards its reliance on a new mechanism. Finally, we show that the subcellular localization of HOE-1 is responsive to mitochondrial stress and is subject to negative regulation via ATFS-1. Together, we have discovered a novel RNA-based cellular pathway that modulates UPRmt.

scholarly journals Intronic tRNAs of mitochondrial origin regulate constitutive and alternative splicing

2020 ◽  
Vol 21 (1) ◽  
Author(s):  
Simon M. Hoser ◽  
Anne Hoffmann ◽  
Andreas Meindl ◽  
Maximilian Gamper ◽  
Jörg Fallmann ◽  
...  
Keyword(s):  
Alternative Splicing ◽  
Human Genome ◽  
Splice Site ◽  
Mutational Analysis ◽  
Mitochondrial Protein ◽  
Regulatory Elements ◽  
Trna Genes ◽  
Mitochondrial Trna ◽  
Mobility Shift ◽  
Cloverleaf Structure

Abstract Background The presence of nuclear mitochondrial DNA (numtDNA) has been reported within several nuclear genomes. Next to mitochondrial protein-coding genes, numtDNA sequences also encode for mitochondrial tRNA genes. However, the biological roles of numtDNA remain elusive. Results Employing in silico analysis, we identify 281 mitochondrial tRNA homologs in the human genome, which we term nimtRNAs (nuclear intronic mitochondrial-derived tRNAs), being contained within introns of 76 nuclear host genes. Despite base changes in nimtRNAs when compared to their mtRNA homologs, a canonical tRNA cloverleaf structure is maintained. To address potential functions of intronic nimtRNAs, we insert them into introns of constitutive and alternative splicing reporters and demonstrate that nimtRNAs promote pre-mRNA splicing, dependent on the number and positioning of nimtRNA genes and splice site recognition efficiency. A mutational analysis reveals that the nimtRNA cloverleaf structure is required for the observed splicing increase. Utilizing a CRISPR/Cas9 approach, we show that a partial deletion of a single endogenous nimtRNALys within intron 28 of the PPFIBP1 gene decreases inclusion of the downstream-located exon 29 of the PPFIBP1 mRNA. By employing a pull-down approach followed by mass spectrometry, a 3′-splice site-associated protein network is identified, including KHDRBS1, which we show directly interacts with nimtRNATyr by an electrophoretic mobility shift assay. Conclusions We propose that nimtRNAs, along with associated protein factors, can act as a novel class of intronic splicing regulatory elements in the human genome by participating in the regulation of splicing.

scholarly journals U1 snRNP-Dependent Function of TIAR in the Regulation of Alternative RNA Processing of the Human Calcitonin/CGRP Pre-mRNA

2003 ◽  
Vol 23 (17) ◽  
pp. 5959-5971 ◽  
Author(s):  
Hui Zhu ◽  
Robert A. Hasman ◽  
Katherine M. Young ◽  
Nancy L. Kedersha ◽  
Hua Lou
Keyword(s):  
Splice Site ◽  
Rna Processing ◽  
Rna Binding ◽  
Sequence Motif ◽  
Human Calcitonin ◽  
Sequence Motifs ◽  
Multiple Sequence ◽  
Enhancer Element ◽  
Binding Domains ◽  
U6 Snrna

ABSTRACT Alternative RNA processing of human calcitonin/CGRP pre-mRNA is regulated by an intronic enhancer element. Previous studies have demonstrated that multiple sequence motifs within the enhancer and a number of trans-acting factors play critical roles in the regulation. Here, we report the identification of TIAR as a novel player in the regulation of human calcitonin/CGRP alternative RNA processing. TIAR binds to the U tract sequence motif downstream of a pseudo 5′ splice site within the previously characterized intron enhancer element. Binding of TIAR promotes inclusion of the alternative 3′-terminal exon located more than 200 nucleotides upstream from the U tract. In cells that preferentially include this exon, overexpression of a mutant TIAR that lacks the RNA binding domains suppressed inclusion of this exon. In this report, we also demonstrate an unusual novel interaction between U6 snRNA and the pseudo 5′ splice site, which was shown previously to bind U1 snRNA. Interestingly, TIAR binding to the U tract sequence depends on the interaction of not only U1 but also U6 snRNA with the pseudo 5′ splice site. Conversely, TIAR binding promotes U6 snRNA binding to its target. The synergistic relationship between TIAR and U6 snRNA strongly suggests a novel role of U6 snRNP in regulated alternative RNA processing.

scholarly journals Sequences homologous to 5' splice sites are required for the inhibitory activity of papillomavirus late 3' untranslated regions

1994 ◽  
Vol 14 (8) ◽  
pp. 5278-5289 ◽  
Author(s):  
P A Furth ◽  
W T Choe ◽  
J H Rex ◽  
J C Byrne ◽  
C C Baker
Keyword(s):  
Human Papillomavirus ◽  
Splice Site ◽  
Inhibitory Activity ◽  
Site Directed Mutagenesis ◽  
Untranslated Regions ◽  
Sequence Motifs ◽  
Splice Sites ◽  
Late Gene Expression ◽  
Human Papillomavirus Type 16 ◽  
Cytoplasmic Rna

Expression of bovine papillomavirus type 1 (BPV-1) late genes is limited to terminally differentiated keratinocytes in an infected epithelium. We have previously shown that although the BPV-1 late polyadenylation site is functional in nonpermissive cells, a 53-nucleotide (nt) fragment of the late 3' untranslated region acts posttranscriptionally to reduce polyadenylated cytoplasmic RNA levels. This 53-nt fragment does not appear to function by destabilizing polyadenylated cytoplasmic RNA (P. A. Furth and C. C. Baker, J. Virol. 65:5806-5812, 1991). In this study, we used site-directed mutagenesis and deletion analysis to demonstrate that the sequence AAG/GUAAGU, which is identical to the consensus 5' splice site sequence, was both necessary and sufficient for the inhibitory activity of the 53-nt fragment. Furthermore, base pairing between the 5' end of the U1 small nuclear RNA and this 5' splice site-like sequence was shown to be required for the inhibitory activity in vivo. We have also further mapped the human papillomavirus type 16 late 3' inhibitory element (I. M. Kennedy, J. K. Haddow, and J. B. Clements, J. Virol. 65:2093-2097, 1991) to a 51-nt region containing four overlapping sequence motifs with partial homology to 5' splice sites. Mutation of each of these motifs demonstrated that only one of these motifs is required for the inhibitory activity. However, the presence of the other motifs may contribute to the full inhibitory activity of the element. No BPV-1 or human papillomavirus type 16 mRNAs which are spliced by using the potential 5' splice sites present in the viral late 3' untranslated regions have been identified. This suggests that the primary function of these 5' splice site-like sequences is the inhibition of late gene expression. The most likely mechanism of action of these elements is reduction of polyadenylation efficiency, perhaps through interference with 3'-terminal exon definition.

scholarly journals dbNSFP v4: a comprehensive database of transcript-specific functional predictions and annotations for human nonsynonymous and splice-site SNVs

2020 ◽  
Vol 12 (1) ◽  
Author(s):  
Xiaoming Liu ◽  
Chang Li ◽  
Chengcheng Mou ◽  
Yibo Dong ◽  
Yicheng Tu
Keyword(s):  
Web Service ◽  
Human Genome ◽  
Exome Sequencing ◽  
Splice Site ◽  
Human Disease ◽  
Functional Annotation ◽  
Current Version ◽  
Functional Annotations ◽  
Whole Exome ◽  
Gene Level

AbstractWhole exome sequencing has been increasingly used in human disease studies. Prioritization based on appropriate functional annotations has been used as an indispensable step to select candidate variants. Here we present the latest updates to dbNSFP (version 4.1), a database designed to facilitate this step by providing deleteriousness prediction and functional annotation for all potential nonsynonymous and splice-site SNVs (a total of 84,013,093) in the human genome. The current version compiled 36 deleteriousness prediction scores, including 12 transcript-specific scores, and other variant and gene-level functional annotations. The database is available at http://database.liulab.science/dbNSFP with a downloadable version and a web-service.

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