The intronic branch point sequence is under strong evolutionary constraint in the bovine and human genome

AbstractThe branch point sequence is a cis-acting intronic motif required for mRNA splicing. Despite their functional importance, branch point sequences are not routinely annotated. Here we predict branch point sequences in 179,476 bovine introns and investigate their variability using a catalogue of 29.4 million variants detected in 266 cattle genomes. We localize the bovine branch point within a degenerate heptamer “nnyTrAy”. An adenine residue at position 6, that acts as branch point, and a thymine residue at position 4 of the heptamer are more strongly depleted for mutations than coding sequences suggesting extreme purifying selection. We provide evidence that mutations affecting these evolutionarily constrained residues lead to alternative splicing. We confirm evolutionary constraints on branch point sequences using a catalogue of 115 million SNPs established from 3,942 human genomes of the gnomAD database.

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Quantification of the evolutionary constraint on intronic branch point sequences in the bovine and human genome

10.1101/2021.03.26.437175 ◽

2021 ◽

Author(s):

Naveen Kumar Kadri ◽

Hubert Pausch

Keyword(s):

Human Genome ◽

Branch Point ◽

Purifying Selection ◽

Splice Acceptor Site ◽

Evolutionary Constraint ◽

Sequence Motif ◽

Acceptor Site ◽

Sequence Motifs ◽

Branch Point Sequence ◽

Nucleotide Resolution

We predict the branch point sequence in 180,892 bovine introns and investigate the variability of this cis-acting splicing element at nucleotide resolution. A degenerate heptamer "nnyTrAy" with conserved thymine and adenine residues at positions 4 and 6 constitutes the bovine branch point sequence. This motif is located between 18 and 37 bp upstream of the 3′ splice acceptor site. More than 90% of the introns contain canonical branch point sequence motifs with thymine and adenine residues at positions 4 and 6. Using a catalogue of 29.4 million variants detected in 266 cattle, we show that the conserved thymine and adenine residues are strongly depleted for mutations. These two intronic residues harbor 39% and 41% less variants than coding sequences suggesting extreme purifying selection. The evolutionary constraint is higher at the thymine residue than the branch point adenine itself in heptamers with a canonical branch point sequence motif. We replicate these observations in human branch point sequences with a catalogue of more than 115 million SNPs detected in 3,942 genomes from the gnomAD database. Our study suggests that the evolutionary constraint is stronger on intronic branch point sequences than coding regions in the bovine and human genome.

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Emergence of SARS-CoV-2 through recombination and strong purifying selection

Science Advances ◽

10.1126/sciadv.abb9153 ◽

2020 ◽

Vol 6 (27) ◽

pp. eabb9153 ◽

Cited By ~ 49

Author(s):

Xiaojun Li ◽

Elena E. Giorgi ◽

Manukumar Honnayakanahalli Marichannegowda ◽

Brian Foley ◽

Chuan Xiao ◽

...

Keyword(s):

Host Species ◽

Purifying Selection ◽

New Drugs ◽

Evolutionary Constraints ◽

Binding Motif ◽

The Novel ◽

Global Pandemic ◽

Show Evidence ◽

Human Coronaviruses ◽

Novel Coronavirus

COVID-19 has become a global pandemic caused by the novel coronavirus SARS-CoV-2. Understanding the origins of SARS-CoV-2 is critical for deterring future zoonosis, discovering new drugs, and developing a vaccine. We show evidence of strong purifying selection around the receptor binding motif (RBM) in the spike and other genes among bat, pangolin, and human coronaviruses, suggesting similar evolutionary constraints in different host species. We also demonstrate that SARS-CoV-2’s entire RBM was introduced through recombination with coronaviruses from pangolins, possibly a critical step in the evolution of SARS-CoV-2’s ability to infect humans. Similar purifying selection in different host species, together with frequent recombination among coronaviruses, suggests a common evolutionary mechanism that could lead to new emerging human coronaviruses.

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Novel start codons introduce novel coding sequences in the human genomes

10.1101/2020.11.04.368936 ◽

2020 ◽

Author(s):

He Zhang ◽

Yang Xie

Keyword(s):

Translation Initiation ◽

Genomic Analysis ◽

Comparative Genomic ◽

Human Populations ◽

The Novel ◽

Coding Sequences ◽

Human Genomes ◽

High Level ◽

Selection Signal ◽

Human Specific

AbstractStart-gain mutations can introduce novel start codons and generate novel coding sequences that may affect the function of genes. In this study, we systematically investigated the novel start codons that were either polymorphic or fixed in the human genomes. 829 polymorphic start-gain SNVs were identified in the human populations, and the novel start codons introduced by these SNVs have significantly higher activity in translation initiation. Some of these start-gain SNVs were reported to be associated with phenotypes and diseases in previous studies. By comparative genomic analysis, we found 26 human-specific start codons that were fixed after the divergence between the human and chimpanzee, and high-level translation initiation activity was observed on them. The negative selection signal was detected in the novel coding sequences introduced by these human-specific start codons, indicating the important function of these novel coding sequences. This study reveals start-gain mutations are keeping appearing in the human genomes during the evolution and may be important sources altering the function of genes which may further affect the phenotypes or cause diseases.

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Genome-Wide Identification and Characterization of the RCI2 Gene Family in Allotetraploid Brassica napus Compared with Its Diploid Progenitors

International Journal of Molecular Sciences ◽

10.3390/ijms23020614 ◽

2022 ◽

Vol 23 (2) ◽

pp. 614

Author(s):

Weiqi Sun ◽

Mengdi Li ◽

Jianbo Wang

Keyword(s):

Brassica Napus ◽

Gene Family ◽

Gene Structure ◽

Stress Responses ◽

Stress Protein ◽

Purifying Selection ◽

Cis Acting ◽

Genome Wide ◽

Duplication Events

Brassica napus and its diploid progenitors (B. rapa and B. oleracea) are suitable for studying the problems associated with polyploidization. As an important anti-stress protein, RCI2 proteins widely exist in various tissues of plants, and are crucial to plant growth, development, and stress response. In this study, the RCI2 gene family was comprehensively identified and analyzed, and 9, 9, and 24 RCI2 genes were identified in B. rapa, B. oleracea, and B. napus, respectively. Phylogenetic analysis showed that all of the identified RCI2 genes were divided into two groups, and further divided into three subgroups. Ka/Ks analysis showed that most of the identified RCI2 genes underwent a purifying selection after the duplication events. Moreover, gene structure analysis showed that the structure of RCI2 genes is largely conserved during polyploidization. The promoters of the RCI2 genes in B. napus contained more cis-acting elements, which were mainly involved in plant development and growth, plant hormone response, and stress responses. Thus, B. napus might have potential advantages in some biological aspects. In addition, the changes of RCI2 genes during polyploidization were also discussed from the aspects of gene number, gene structure, gene relative location, and gene expression, which can provide reference for future polyploidization analysis.

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Assessment of branch point prediction tools to predict physiological branch points and their alteration by variants

10.21203/rs.2.12748/v2 ◽

2019 ◽

Author(s):

Raphael Leman ◽

Hélène Tubeuf ◽

Sabine Raad ◽

Isabelle Tournier ◽

Céline Derambure ◽

...

Keyword(s):

Branch Point ◽

Mrna Splicing ◽

Large Set ◽

Branch Points ◽

Splice Sites ◽

Prediction Tools ◽

Mature Mrna ◽

Bioinformatics Tools ◽

The Impact

Abstract Background: Branch points (BPs) map within short motifs upstream of acceptor splice sites (3’ss) and are essential for splicing of pre-mature mRNA. Several BP-dedicated bioinformatics tools, including HSF, SVM-BPfinder, BPP, Branchpointer, LaBranchoR and RNABPS were developed during the last decade. Here, we evaluated their capability to detect the position of BPs, and also to predict the impact on splicing of variants occurring upstream of 3’ss. Results: We used a large set of constitutive and alternative human 3’ss collected from Ensembl (n = 264,787 3’ss) and from in-house RNAseq experiments (n = 51,986 3’ss). We also gathered an unprecedented collection of functional splicing data for 120 variants (62 unpublished) occurring in BP areas of disease-causing genes. Branchpointer showed the best performance to detect the relevant BPs upstream of constitutive and alternative 3’ss (99.48 % and 65.84 % accuracies, respectively). For variants occurring in a BP area, BPP emerged as having the best performance to predict effects on mRNA splicing, with an accuracy of 89.17 %. Conclusions: Our investigations revealed that Branchpointer was optimal to detect BPs upstream of 3’ss, and that BPP was most relevant to predict splicing alteration due to variants in the BP area. Keywords: Branch Point, Prediction, RNA, Benchmark, HSF, SVM-BPfinder, BPP, Branchpointer, LaBranchoR, RNABPS, Variants

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Exploitation of a thermosensitive splicing event to study pre-mRNA splicing in vivo

Molecular and Cellular Biology ◽

10.1128/mcb.8.4.1558-1569.1988 ◽

1988 ◽

Vol 8 (4) ◽

pp. 1558-1569

Author(s):

P E Cizdziel ◽

M de Mars ◽

E C Murphy

Keyword(s):

Splice Site ◽

Rna Splicing ◽

Mrna Splicing ◽

Viral Rna ◽

Temperature Sensitive ◽

Exon Ligation ◽

Branch Point Sequence ◽

Infected Cells ◽

Low Efficiency

The spliced form of MuSVts110 viral RNA is approximately 20-fold more abundant at growth temperatures of 33 degrees C or lower than at 37 to 41 degrees C. This difference is due to changes in the efficiency of MuSVts110 RNA splicing rather than selective thermolability of the spliced species at 37 to 41 degrees C or general thermosensitivity of RNA splicing in MuSVts110-infected cells. Moreover, RNA transcribed from MuSVts110 DNA introduced into a variety of cell lines is spliced in a temperature-sensitive fashion, suggesting that the structure of the viral RNA controls the efficiency of the event. We exploited this novel splicing event to study the cleavage and ligation events during splicing in vivo. No spliced viral mRNA or splicing intermediates were observed in MuSVts110-infected cells (6m2 cells) at 39 degrees C. However, after a short (about 30-min) lag following a shift to 33 degrees C, viral pre-mRNA cleaved at the 5' splice site began to accumulate. Ligated exons were not detected until about 60 min following the initial detection of cleavage at the 5' splice site, suggesting that these two splicing reactions did not occur concurrently. Splicing of viral RNA in the MuSVts110 revertant 54-5A4, which lacks the sequence -AG/TGT- at the usual 3' splice site, was studied. Cleavage at the 5' splice site in the revertant viral RNA proceeded in a temperature-sensitive fashion. No novel cryptic 3' splice sites were activated; however, splicing at an alternate upstream 3' splice site used at low efficiency in normal MuSVts110 RNA was increased to a level close to that of 5'-splice-site cleavage in the revertant viral RNA. Increased splicing at this site in 54-5A4 viral RNA is probably driven by the unavailability of the usual 3' splice site for exon ligation. The thermosensitivity of this alternate splice event suggests that the sequences governing the thermodependence of MuSVts110 RNA splicing do not involve any particular 3' splice site or branch point sequence, but rather lie near the 5' end of the intron.

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Branch point sequence

The Dictionary of Genomics, Transcriptomics and Proteomics ◽

10.1002/9783527678679.dg01185 ◽

2015 ◽

pp. 1-1

Keyword(s):

Branch Point ◽

Branch Point Sequence

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Cloning and Sequencing of Defective Particles Derived from the Autonomous Parvovirus Minute Virus of Mice for the Construction of Vectors with Minimal cis-Acting Sequences

Journal of Virology ◽

10.1128/jvi.75.3.1284-1293.2001 ◽

2001 ◽

Vol 75 (3) ◽

pp. 1284-1293 ◽

Cited By ~ 7

Author(s):

Nathalie Clément ◽

Bernard Avalosse ◽

Karim El Bakkouri ◽

Thierry Velu ◽

Annick Brandenburger

Keyword(s):

Virus Production ◽

Dna Amplification ◽

Wild Type ◽

Nonstructural Proteins ◽

Helper Plasmid ◽

Minute Virus Of Mice ◽

Coding Sequences ◽

Cis Acting ◽

Minute Virus ◽

Helper Plasmids

ABSTRACT The production of wild-type-free stocks of recombinant parvovirus minute virus of mice [MVM(p)] is difficult due to the presence of homologous sequences in vector and helper genomes that cannot easily be eliminated from the overlapping coding sequences. We have therefore cloned and sequenced spontaneously occurring defective particles of MVM(p) with very small genomes to identify the minimalcis-acting sequences required for DNA amplification and virus production. One of them has lost all capsid-coding sequences but is still able to replicate in permissive cells when nonstructural proteins are provided in trans by a helper plasmid. Vectors derived from this particle produce stocks with no detectable wild-type MVM after cotransfection with new, matched, helper plasmids that present no homology downstream from the transgene.

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