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 Acute depletion of METTL3 identifies a role for N6-methyladenosine in alternative intron/exon inclusion in the nascent transcriptome

2020 ◽  
Author(s):  
Guifeng Wei ◽  
Mafalda Almeida ◽  
Greta Pintacuda ◽  
Heather Coker ◽  
Joseph S Bowness ◽  
...  
Keyword(s):  
Stem Cells ◽  
Embryonic Stem Cells ◽  
Histone Modification ◽  
Splice Site ◽  
Rna Processing ◽  
Binding Sites ◽  
Rna Binding ◽  
Embryonic Stem ◽  
Splice Sites ◽  
Rna Regulation

AbstractRNA N6-methyladenosine (m6A) modification plays important roles in multiple aspects of RNA regulation. m6A is installed co-transcriptionally by the METTL3/14 complex, but its direct roles in RNA processing remain unclear. Here we investigate the presence of m6A in nascent RNA of mouse embryonic stem cells (mESCs). We find that around 10% m6A peaks are in introns, often close to 5’-splice sites. RNA m6A peaks significantly overlap with RBM15 RNA binding sites and the histone modification H3K36me3. Interestingly, acute dTAG depletion of METTL3 reveals that inclusion of m6A-bearing alternative introns/exons in the nascent transcriptome is disrupted. For terminal or variable-length exons, m6A peaks are generally located upstream of a repressed 5’-splice site, and downstream of an enhanced 5’-splice site. Intriguingly, genes with the most immediate effects on splicing include several components of the m6A pathway, suggesting an autoregulatory function. Our findings demonstrate a direct crosstalk between m6A machinery and the regulation of RNA processing.

scholarly journals ssHMM: Extracting intuitive sequence-structure motifs from high-throughput RNA-binding protein data

2016 ◽  
Author(s):  
David Heller ◽  
Martin Vingron ◽  
Ralf Krestel ◽  
Uwe Ohler ◽  
Annalisa Marsico
Keyword(s):  
High Throughput ◽  
Rna Structure ◽  
Rna Binding ◽  
Rna Binding Proteins ◽  
Synthetic Data ◽  
Sequence Motif ◽  
Sequence Motifs ◽  
Sequence Structure ◽  
Rna Motif ◽  
Post Transcriptional Regulation

AbstractRNA-binding proteins (RBPs) play important roles in RNA post-transcriptional regulation and recognize target RNAs via sequence-structure motifs. To which extent RNA structure influences protein binding in the presence or absence of a sequence motif is still poorly understood. Existing RNA motif finders which produce informative motifs and simultaneously capture the relationship between primary sequence and different RNA secondary structures are missing. We developed ssHMM, an RNA motif finder that combines a hidden Markov model (HMM) with Gibbs sampling to learn the joint sequence and structure binding preferences of RBPs from high-throughput data, such as CLIP-Seq sequences, and visualizes them as a graph. Evaluations on synthetic data showed that ssHMM reliably recovers fuzzy sequence motifs in 80 to 100% of the cases. It produces motifs with higher information content than existing tools and is faster than other methods on large datasets. Examples of new sequence-structure motifs identified by ssHMM for uncharacterized RBPs are also discussed. ssHMM is freely available on Github at https://github.molgen.mpg.de/heller/ssHMM.

scholarly journals Genetic enhancement of RNA-processing defects by a dominant mutation in B52, the Drosophila gene for an SR protein splicing factor.

1995 ◽  
Vol 15 (11) ◽  
pp. 6273-6282 ◽  
Author(s):  
X Peng ◽  
S M Mount
Keyword(s):  
Splice Site ◽  
Rna Processing ◽  
Rna Binding ◽  
Critical Role ◽  
Mrna Splicing ◽  
Genetic Enhancement ◽  
X Rays ◽  
Loss Of Function ◽  
Sr Protein ◽  
Processing Defects

SR proteins are essential for pre-mRNA splicing in vitro, act early in the splicing pathway, and can influence alternative splice site choice. Here we describe the isolation of both dominant and loss-of-function alleles of B52, the gene for a Drosophila SR protein. The allele B52ED was identified as a dominant second-site enhancer of white-apricot (wa), a retrotransposon insertion in the second intron of the eye pigmentation gene white with a complex RNA-processing defect. B52ED also exaggerates the mutant phenotype of a distinct white allele carrying a 5' splice site mutation (wDR18), and alters the pattern of sex-specific splicing at doublesex under sensitized conditions, so that the male-specific splice is favored. In addition to being a dominant enhancer of these RNA-processing defects, B52ED is a recessive lethal allele that fails to complement other lethal alleles of B52. Comparison of B52ED with the B52+ allele from which it was derived revealed a single change in a conserved amino acid in the beta 4 strand of the first RNA-binding domain of B52, which suggests that altered RNA binding is responsible for the dominant phenotype. Reversion of the B52ED dominant allele with X rays led to the isolation of a B52 null allele. Together, these results indicate a critical role for the SR protein B52 in pre-mRNA splicing in vivo.

scholarly journals The zinc fingers of the SR-like protein ZRANB2 are single-stranded RNA-binding domains that recognize 5' splice site-like sequences

2009 ◽  
Vol 106 (14) ◽  
pp. 5581-5586 ◽  
Author(s):  
F. E. Loughlin ◽  
R. E. Mansfield ◽  
P. M. Vaz ◽  
A. P. McGrath ◽  
S. Setiyaputra ◽  
...  
Keyword(s):  
Splice Site ◽  
Rna Binding ◽  
Zinc Fingers ◽  
Binding Domains ◽  
Rna Binding Domains

scholarly journals Searching for ncRNAs in eukaryotic genomes: Maximizing biological input with RNAmotif

2004 ◽  
Vol 1 (1) ◽  
pp. 64-79 ◽  
Author(s):  
Lesley J. Collins ◽  
Thomas J. Macke ◽  
David Penny
Keyword(s):  
Secondary Structure ◽  
Rna Binding ◽  
Genomic Sequence ◽  
Biological Information ◽  
Biological Knowledge ◽  
Sequence Motif ◽  
Sequence Motifs ◽  
Ncrna Gene ◽  
Ribonucleoprotein Complexes ◽  
Eukaryotic Genomes

Summary Non-coding RNAs (ncRNAs) contain both characteristic secondary-structure and short sequence motifs. However, “complex” ncRNAs (RNA bound to proteins in ribonucleoprotein complexes) can be hard to identify in genomic sequence data. Programs able to search for ncRNAs were previously limited to ncRNA molecules that either align very well or have highly conserved secondary-structure. The RNAmotif program uses additional information to find ncRNA gene candidates through the design of an appropriate “descriptor” to model sequence motifs, secondary-structure and protein/RNA binding information. This enables searches of those ncRNAs that contain variable secondary-structure and limited sequence motif information. Applying the biologically-based concept of “positive and negative controls” to the RNAmotif search technique, we can now go beyond the testing phase to successfully search real genomes, complete with their background noise and related molecules. Descriptors are designed for two “complex” ncRNAs, the U5snRNA (from the spliceosome) and RNaseP RNA, which successfully uncover these sequences from some eukaryotic genomes. We include explanations about the construction of the input “descriptors” from known biological information, to allow searches for other ncRNAs. RNAmotif maximizes the input of biological knowledge into a search for an ncRNA gene and now allows the investigation of some of the hardest-to-find, yet important, genes in some very interesting eukaryotic organisms.

scholarly journals An intron enhancer containing a 5' splice site sequence in the human calcitonin/calcitonin gene-related peptide gene.

1995 ◽  
Vol 15 (12) ◽  
pp. 7135-7142 ◽  
Author(s):  
H Lou ◽  
Y Yang ◽  
G J Cote ◽  
S M Berget ◽  
R F Gagel
Keyword(s):  
Splice Site ◽  
Rna Processing ◽  
Mammalian Species ◽  
Calcitonin Gene Related Peptide ◽  
Regulatory Sequences ◽  
Human Calcitonin ◽  
Terminal Exon ◽  
Related Peptide ◽  
Calcitonin Gene ◽  
Splice Site Sequence

Regulation of calcitonin (CT)/calcitonin gene-related peptide (CGRP) RNA processing involves the use of alternative 3' terminal exons. In most tissues and cell lines, the CT terminal exon is recognized. In an attempt to define regulatory sequences involved in the utilization of the CT-specific terminal exon, we performed deletion and mutation analyses of a mini-gene construct that contains the CT terminal exon and mimics the CT processing choice in vivo. These studies identified a 127-nucleotide intron enhancer located approximately 150 nucleotides downstream of the CT exon poly(A) cleavage site that is required for recognition of the exon. The enhancer contains an essential and conserved 5' splice site sequence. Mutation of the splice site resulted in diminished utilization of the CT-specific terminal exon and increased skipping of the CT exon in both the mini-gene and in the natural CT/CGRP gene. Other components of the intron enhancer modified utilization of the CT-specific terminal exon and were necessary to prevent utilization of the 5' splice site within the intron enhancer as an actual splice site directing cryptic splicing. Conservation of the intron enhancer in three mammalian species suggests an important role for this intron element in the regulation of CT/CGRP processing and an expanded role for intronic 5' splice site sequences in the regulation of RNA processing.

scholarly journals RNA Helicase A Regulates the Replication of RNA Viruses

Viruses ◽  
2021 ◽  
Vol 13 (3) ◽  
pp. 361
Author(s):  
Rui-Zhu Shi ◽  
Yuan-Qing Pan ◽  
Li Xing
Keyword(s):  
Virus Replication ◽  
Rna Binding ◽  
Rna Viruses ◽  
Rna Helicase ◽  
Rna Helicase A ◽  
Double Stranded Rna ◽  
Binding Domains ◽  
N Terminus

The RNA helicase A (RHA) is a member of DExH-box helicases and characterized by two double-stranded RNA binding domains at the N-terminus. RHA unwinds double-stranded RNA in vitro and is involved in RNA metabolisms in the cell. RHA is also hijacked by a variety of RNA viruses to facilitate virus replication. Herein, this review will provide an overview of the role of RHA in the replication of RNA viruses.

In Caenorhabditis elegans, the RNA-Binding Domains of the Cytoplasmic Polyadenylation Element Binding Protein FOG-1 Are Needed to Regulate Germ Cell Fates

Genetics ◽  
2001 ◽  
Vol 159 (4) ◽  
pp. 1617-1630
Author(s):  
Suk-Won Jin ◽  
Nancy Arno ◽  
Adam Cohen ◽  
Amy Shah ◽  
Qijin Xu ◽  
...  
Keyword(s):  
Caenorhabditis Elegans ◽  
Germ Cell ◽  
Rna Binding ◽  
Dominant Negative ◽  
Missense Mutations ◽  
Biochemical Tests ◽  
Cell Fates ◽  
Cytoplasmic Polyadenylation ◽  
Binding Domains ◽  
Rna Binding Domains

Abstract FOG-1 controls germ cell fates in the nematode Caenorhabditis elegans. Sequence analyses revealed that FOG-1 is a cytoplasmic polyadenylation element binding (CPEB) protein; similar proteins from other species have been shown to bind messenger RNAs and regulate their translation. Our analyses of fog-1 mutations indicate that each of the three RNA-binding domains of FOG-1 is essential for activity. In addition, biochemical tests show that FOG-1 is capable of binding RNA sequences in the 3′-untranslated region of its own message. Finally, genetic assays reveal that fog-1 functions zygotically, that the small fog-1 transcript has no detectable function, and that missense mutations in fog-1 cause a dominant negative phenotype. This last observation suggests that FOG-1 acts in a complex, or as a multimer, to regulate translation. On the basis of these data, we propose that FOG-1 binds RNA to regulate germ cell fates and that it does so by controlling the translation of its targets. One of these targets might be the fog-1 transcript itself.

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