scholarly journals Factors Affecting Splicing Strength of Yeast Genes

2011 ◽  
Vol 2011 ◽  
pp. 1-13 ◽  
Author(s):  
Pinchao Ma ◽  
Xuhua Xia
Keyword(s):  
Screening Tool ◽  
Consensus Sequence ◽  
Fungal Species ◽  
Splicing Factors ◽  
Splicing Regulation ◽  
Splice Sites ◽  
Crucial Importance ◽  
Factors Affecting ◽  
Unicellular Eukaryotes ◽  
Yeast Genes

Accurate and efficient splicing is of crucial importance for highly-transcribed intron-containing genes (ICGs) in rapidly replicating unicellular eukaryotes such as the budding yeastSaccharomyces cerevisiae. We characterize the 5′ and 3′ splice sites (ss) by position weight matrix scores (PWMSs), which is the highest for the consensus sequence and the lowest for splice sites differing most from the consensus sequence and used PWMS as a proxy for splicing strength.HAC1, which is known to be spliced by a nonspliceosomal mechanism, has the most negative PWMS for both its 5′ ss and 3′ ss. Several genes under strong splicing regulation and requiring additional splicing factors for their splicing also have small or negative PWMS values. Splicing strength is higher for highly transcribed ICGs than for lowly transcribed ICGs and higher for transcripts that bind strongly to spliceosomes than those that bind weakly. The 3′ splice site features a prominent poly-U tract before the 3′AG. Our results suggest the potential of using PWMS as a screening tool for ICGs that are either spliced by a nonspliceosome mechanism or under strong splicing regulation in yeast and other fungal species.

scholarly journals Factors affecting authentic 5' splice site selection in plant nuclei.

1993 ◽  
Vol 13 (3) ◽  
pp. 1323-1331 ◽  
Author(s):  
A J McCullough ◽  
H Lou ◽  
M A Schuler
Keyword(s):  
Splice Site ◽  
Transition Point ◽  
Consensus Sequence ◽  
Point Mutations ◽  
Splice Sites ◽  
Factors Affecting ◽  
Plant Expression Vector ◽  
Normal Site ◽  
Intron Boundary

To define elements critical for 5' splice selection in dicot plant nuclei, wild-type and mutant transcripts containing the first intron of the pea rbcS3A gene were expressed in vivo by using an autonomously replicating plant expression vector. Mutations within the normal 5' splice site (+1) of this intron demonstrate that 5' splice sites at the normal exon-intron boundary having only limited agreement with a 5' splice site consensus sequence can be spliced quite effectively in dicot nuclei. Inactivation of the normal 5' splice site occurs only by point mutations of the G at position +1 of the intron (+1G) or +2U or by multiple mutations at other positions and results in the activation of three cryptic 5' splice sites in the adjacent exon and intron. cis competition of cryptic sites having consensus 5' splice site sequences with the normal 5' splice site demonstrates that cryptic splice sites in the exon, but not the intron, can compete to some extent with the normal site. Replacement of the sequences between the cryptic and normal 5' splice sites with heterologous exon or intron sequences demonstrates that the 5' boundary of this plant intron is defined by its position relative to the AU transition point between exon and intron. These results suggest that potential 5' splice sites upstream of the AU transition point are accessible for recognition by the plant pre-mRNA splicing machinery and that those downstream in the AU-rich intron are masked from recognition.

Factors affecting authentic 5' splice site selection in plant nuclei

1993 ◽  
Vol 13 (3) ◽  
pp. 1323-1331
Author(s):  
A J McCullough ◽  
H Lou ◽  
M A Schuler
Keyword(s):  
Splice Site ◽  
Transition Point ◽  
Consensus Sequence ◽  
Point Mutations ◽  
Splice Sites ◽  
Factors Affecting ◽  
Plant Expression Vector ◽  
Normal Site ◽  
Intron Boundary

To define elements critical for 5' splice selection in dicot plant nuclei, wild-type and mutant transcripts containing the first intron of the pea rbcS3A gene were expressed in vivo by using an autonomously replicating plant expression vector. Mutations within the normal 5' splice site (+1) of this intron demonstrate that 5' splice sites at the normal exon-intron boundary having only limited agreement with a 5' splice site consensus sequence can be spliced quite effectively in dicot nuclei. Inactivation of the normal 5' splice site occurs only by point mutations of the G at position +1 of the intron (+1G) or +2U or by multiple mutations at other positions and results in the activation of three cryptic 5' splice sites in the adjacent exon and intron. cis competition of cryptic sites having consensus 5' splice site sequences with the normal 5' splice site demonstrates that cryptic splice sites in the exon, but not the intron, can compete to some extent with the normal site. Replacement of the sequences between the cryptic and normal 5' splice sites with heterologous exon or intron sequences demonstrates that the 5' boundary of this plant intron is defined by its position relative to the AU transition point between exon and intron. These results suggest that potential 5' splice sites upstream of the AU transition point are accessible for recognition by the plant pre-mRNA splicing machinery and that those downstream in the AU-rich intron are masked from recognition.

scholarly journals Regulation of RNA Splicing: Aberrant Splicing Regulation and Therapeutic Targets in Cancer

Cells ◽  
2021 ◽  
Vol 10 (4) ◽  
pp. 923
Author(s):  
Koji Kitamura ◽  
Keisuke Nimura
Keyword(s):  
Dna Sequences ◽  
Rna Splicing ◽  
Splicing Factors ◽  
Splicing Regulation ◽  
Aberrant Splicing ◽  
Aberrant Expression ◽  
Non Coding Rnas ◽  
Precursor Mrna ◽  
Splicing Enhancer ◽  
Small Nuclear Ribonucleoproteins

RNA splicing is a critical step in the maturation of precursor mRNA (pre-mRNA) by removing introns and exons. The combination of inclusion and exclusion of introns and exons in pre-mRNA can generate vast diversity in mature mRNA from a limited number of genes. Cancer cells acquire cancer-specific mechanisms through aberrant splicing regulation to acquire resistance to treatment and to promote malignancy. Splicing regulation involves many factors, such as proteins, non-coding RNAs, and DNA sequences at many steps. Thus, the dysregulation of splicing is caused by many factors, including mutations in RNA splicing factors, aberrant expression levels of RNA splicing factors, small nuclear ribonucleoproteins biogenesis, mutations in snRNA, or genomic sequences that are involved in the regulation of splicing, such as 5’ and 3’ splice sites, branch point site, splicing enhancer/silencer, and changes in the chromatin status that affect the splicing profile. This review focuses on the dysregulation of RNA splicing related to cancer and the associated therapeutic methods.

scholarly journals Structural disruption of exonic stem–loops immediately upstream of the intron regulates mammalian splicing

2020 ◽  
Vol 48 (11) ◽  
pp. 6294-6309 ◽  
Author(s):  
Kaushik Saha ◽  
Whitney England ◽  
Mike Minh Fernandez ◽  
Tapan Biswas ◽  
Robert C Spitale ◽  
...  
Keyword(s):  
Structural Information ◽  
Structural Features ◽  
Splicing Factors ◽  
Splice Sites ◽  
Exonic Splicing Enhancer ◽  
Stem Loop ◽  
The Core ◽  
Retained Introns ◽  
Splicing Enhancer ◽  
Structural Disruption

Abstract Recognition of highly degenerate mammalian splice sites by the core spliceosomal machinery is regulated by several protein factors that predominantly bind exonic splicing motifs. These are postulated to be single-stranded in order to be functional, yet knowledge of secondary structural features that regulate the exposure of exonic splicing motifs across the transcriptome is not currently available. Using transcriptome-wide RNA structural information we show that retained introns in mouse are commonly flanked by a short (≲70 nucleotide), highly base-paired segment upstream and a predominantly single-stranded exonic segment downstream. Splicing assays with select pre-mRNA substrates demonstrate that loops immediately upstream of the introns contain pre-mRNA-specific splicing enhancers, the substitution or hybridization of which impedes splicing. Additionally, the exonic segments flanking the retained introns appeared to be more enriched in a previously identified set of hexameric exonic splicing enhancer (ESE) sequences compared to their spliced counterparts, suggesting that base-pairing in the exonic segments upstream of retained introns could be a means for occlusion of ESEs. The upstream exonic loops of the test substrate promoted recruitment of splicing factors and consequent pre-mRNA structural remodeling, leading up to assembly of the early spliceosome. These results suggest that disruption of exonic stem–loop structures immediately upstream (but not downstream) of the introns regulate alternative splicing events, likely through modulating accessibility of splicing factors.

scholarly journals Aberrant RNA Splicing in Cancer

2019 ◽  
Vol 3 (1) ◽  
pp. 167-185 ◽  
Author(s):  
Luisa Escobar-Hoyos ◽  
Katherine Knorr ◽  
Omar Abdel-Wahab
Keyword(s):  
Small Molecules ◽  
Rna Splicing ◽  
Clinical Development ◽  
Splicing Factors ◽  
Global Changes ◽  
Splicing Regulation ◽  
Enzymatic Process ◽  
Patients With Cancer ◽  
Aberrant Rna

RNA splicing, the enzymatic process of removing segments of premature RNA to produce mature RNA, is a key mediator of proteome diversity and regulator of gene expression. Increased systematic sequencing of the genome and transcriptome of cancers has identified a variety of means by which RNA splicing is altered in cancer relative to normal cells. These findings, in combination with the discovery of recurrent change-of-function mutations in splicing factors in a variety of cancers, suggest that alterations in splicing are drivers of tumorigenesis. Greater characterization of altered splicing in cancer parallels increasing efforts to pharmacologically perturb splicing and early-phase clinical development of small molecules that disrupt splicing in patients with cancer. Here we review recent studies of global changes in splicing in cancer, splicing regulation of mitogenic pathways critical in cancer transformation, and efforts to therapeutically target splicing in cancer.

scholarly journals Saccharomyces cerevisiae and Schizosaccharomyces pombe contain a homologue to the 54-kD subunit of the signal recognition particle that in S. cerevisiae is essential for growth.

1989 ◽  
Vol 109 (6) ◽  
pp. 3223-3230 ◽  
Author(s):  
B C Hann ◽  
M A Poritz ◽  
P Walter
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Schizosaccharomyces Pombe ◽  
Dna Sequences ◽  
Consensus Sequence ◽  
Signal Recognition Particle ◽  
Signal Recognition ◽  
Protein Subunit ◽  
Reading Frame ◽  
Conserved Sequence ◽  
Yeast Genes

We have isolated and sequenced genes from Saccharomyces cerevisiae (SRP54SC) and Schizosaccharomyces pombe (SRP54sp) encoding proteins homologous to both the 54-kD protein subunit (SRP54mam) of the mammalian signal recognition particle (SRP) and the product of a gene of unknown function in Escherichia coli, ffh (Römisch, K., J. Webb, J. Herz, S. Prehn, R. Frank, M. Vingron, and B. Dobberstein. 1989. Nature (Lond.). 340:478-482; Bernstein H. D., M. A. Poritz, K. Strub, P. J. Hoben, S. Brenner, P. Walter. 1989. Nature (Lond.). 340:482-486). To accomplish this we took advantage of short stretches of conserved sequence between ffh and SRP54mam and used the polymerase chain reaction (PCR) to amplify fragments of the homologous yeast genes. The DNA sequences predict proteins for SRP54sc and SRP54sp that are 47% and 52% identical to SRP54mam, respectively. Like SRP54mam and ffh, both predicted yeast proteins contain a GTP binding consensus sequence in their NH2-terminal half (G-domain), and methionine-rich sequences in their COOH-terminal half (M-domain). In contrast to SRP54mam and ffh the yeast proteins contain additional Met-rich sequences inserted at the COOH-terminal portion of the M-domain. SRP54sp contains a 480-nucleotide intron located 78 nucleotides from the 5' end of the open reading frame. Although the function of the yeast homologues is unknown, gene disruption experiments in S. cerevisiae show that the gene is essential for growth. The identification of SRP54sc and SRP54sp provides the first evidence for SRP related proteins in yeast.

CHARACTERIZATION OF THE SPLICE SITES IN GT–AG AND GC–AG INTRONS IN HIGHER EUKARYOTES USING FULL-LENGTH cDNAs

2004 ◽  
Vol 02 (02) ◽  
pp. 309-331 ◽  
Author(s):  
SUMIE KITAMURA–ABE ◽  
HITOMI ITOH ◽  
TAKANORI WASHIO ◽  
AKIHIRO TSUTSUMI ◽  
MASARU TOMITA
Keyword(s):  
Alternative Splice ◽  
Splice Site ◽  
Consensus Sequence ◽  
Full Length ◽  
Splice Sites ◽  
Consensus Sequences ◽  
Full Length Cdna ◽  
Strong Consensus ◽  
Higher Eukaryotes

For the purpose of analyzing the relation between the splice sites and the order of introns, we conducted the following analysis for the GT–AG and GC–AG splice site groups. First, the pre-mRNAs of H. sapiens, M. musculus, D. melanogaster, A. thaliana and O. sativa were sampled by mapping the full-length cDNA to the genomes. Next, the consensus sequences at different regions of pre-mRNAs were analyzed in the five species. We also investigated the mononucleotide and dinucleotide frequencies in the extensive regions around the 5' splice sites (5'ss) and 3' splice sites (3'ss). As a result, differential frequencies of nucleotides at the first 5'ss in both the GT–AG and GC–AG splice site groups were observed in A. thaliana and O. sativa pre-mRNAs. The trend, which indicates that GC 5'ss possess strong consensus sequences, was observed not only in mammalian pre-mRNAs but also in the pre-mRNAs of D. melanogaster, A. thaliana and O. sativa. Furthermore, we examined the consensus sequences of the constitutive and alternative splice sites. It was suggested that in the case of the alternative GC–AG introns, the tendency to have a weak consensus sequence at 5'ss is different between H. sapiens and M. musculus pre-mRNAs.

scholarly journals Can analytical shading be art?

2015 ◽  
Vol 47 (3) ◽  
pp. 121-135
Author(s):  
Jerzy Siwek ◽  
Wojciech Wacławik
Keyword(s):  
Experimental Studies ◽  
Digital Terrain Model ◽  
Crucial Importance ◽  
Significant Similarity ◽  
Basic Principles ◽  
Factors Affecting ◽  
Terrain Model ◽  
Digital Terrain ◽  
Proper Generalization

Abstract Despite numerous theoretical and experimental studies of analytical relief shading, devised about half a century ago, its quality has not yet reached the excellence of traditional (manual) shading. The paper discusses its basic principles and the main factors affecting the quality of shading. It also stresses the crucial importance of the digital terrain model used as the basis for shading as well as the proper generalization of the relief. Experiments with shading modules of ArcGIS and Surfer, aiming to explore the functionality of algorithms they employ, have demonstrated significant similarity of the results. In conclusion, the authors attempt to answer the question posted in the title of the article. In their view, analytical shading is not art because shading algorithms are incapable of producing the visually beautiful effects that an experienced cartographer with artistic talents can create.

scholarly journals Potential G-quadruplex forming sequences and N6-methyladenosine colocalize at human pre-mRNA intron splice sites

2020 ◽  
Author(s):  
Manuel Jara-Espejo ◽  
Aaron M. Fleming ◽  
Cynthia J. Burrows
Keyword(s):  
Bioinformatic Analysis ◽  
Mrna Splicing ◽  
Published Data ◽  
Splicing Factors ◽  
Splice Sites ◽  
Sequence Context ◽  
Intron Splice ◽  
Alternative Mrna Splicing ◽  
G Quadruplex ◽  
Splice Junctions

ABSTRACTUsing bioinformatic analysis of published data, we identify in human mRNA that potential G-quadruplex forming sequences (PQSs) colocalize with the epitranscriptomic modifications N6-methyladenosine (m6A), pseudouridine (Ψ), and inosine (I). A deeper analysis of the colocalized m6A and PQSs found them intronic in pre-mRNA near 5′ and 3′ splice sites. The loop lengths and sequence context of the m6A-bearing PQSs found short loops most commonly comprised of A nucleotides. This observation is consistent with literature reports of intronic m6A found in SAG (S = C or G) consensus motifs that are also recognized by splicing factors. The localization of m6A and PQSs in pre-mRNA at intron splice junctions suggests that these features could be involved in alternative mRNA splicing. A similar analysis for PQSs around sites of Ψ installation or A-to-I editing in mRNA also found a colocalization; however, the frequency was less than that observed with m6A.TOC Graphic

scholarly journals Deoxynivalenol globally affects the selection of 3’ splice sites in human cells by suppressing the splicing factors, U2AF1 and SF1

RNA Biology ◽  
2020 ◽  
Vol 17 (4) ◽  
pp. 584-595
Author(s):  
Zhangsheng Hu ◽  
Yu Sun ◽  
Jiongjie Chen ◽  
Yurong Zhao ◽  
Han Qiao ◽  
...  
Keyword(s):  
Human Cells ◽  
Splicing Factors ◽  
Splice Sites ◽  
Selection Of
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