Widespread separation of the polypyrimidine tract from 3’ AG by G tracts in association with alternative exons in metazoa and plants

Mapping Intimacies ◽

10.1101/363804 ◽

2018 ◽

Author(s):

Hai Nguyen ◽

Jiuyong Xie

Keyword(s):

Alternative Splicing ◽

Branch Point ◽

Intron Retention ◽

Regulatory Elements ◽

Protein Isoforms ◽

Model Organisms ◽

Branch Points ◽

Splice Sites ◽

Polypyrimidine Tract ◽

Whole Genome Analysis

SummaryAt the end of introns, the polypyrimidine tract (Py) is often close to the 3’ AG in a consensus (Y)20NCAGgt in humans. Interestingly, we have found that they could also be separated by purine-rich elements including G tracts in thousands of human genes. These regulatory elements between the Py and 3’AG (REPA) mainly regulate alternative 3’ splice sites (3’SS) and intron retention. Here we show their widespread distribution and special properties across kingdoms. The purine-rich 3’SS are found in up to about 60% of the introns among more than 1000 species/lineages by whole genome analysis, and up to 18% of these introns contain the REPA G tracts in about 2.4 millions of 3’SS in total. In particular, they are significantly enriched over their 3’SS and genome backgrounds in metazoa and plants, and highly associated with alternative splicing of genes in diverse functional clusters. They are also highly enriched (3-6 folds) in the canonical as well as aberrantly used 3’ splice sites in cancer patients carrying mutations of the branch point factor SF3B1 or the 3’AG binding factor U2AF35. Moreover, the REPA G tract-harbouring 3’SS have significantly reduced occurrences of branch point (BP) motifs between the −24 and −4 positions, in particular absent from the −7 - −5 positions in several model organisms examined. The more distant branch points are associated with increased occurrences of alternative splicing in human and zebrafish. The branch points, REPA G tracts and associated 3’SS motifs appear to have emerged differentially in a phylum- or species-specific way during evolution. Thus, there is widespread separation of the Py and 3’AG by REPA G tracts, likely evolved among different species or branches of life. This special 3’SS arrangement contributes to the generation of diverse transcript or protein isoforms in biological functions or diseases through alternative or aberrant splicing.

Exon definition facilitates reliable control of alternative splicing in the RON proto-oncogene

10.1101/714022 ◽

2019 ◽

Author(s):

M. Enculescu ◽

S. Braun ◽

S. T. Setty ◽

K. Zarnack ◽

J. König ◽

...

Keyword(s):

Alternative Splicing ◽

Epithelial To Mesenchymal Transition ◽

Intron Retention ◽

Regulatory Elements ◽

Protein Isoforms ◽

Splicing Regulation ◽

Exon Definition ◽

Mesenchymal Transition ◽

Mrna Maturation ◽

Exon 11

ABSTRACTAlternative splicing is a key step in eukaryotic gene expression that allows the production of multiple protein isoforms from the same gene. Even though splicing is perturbed in many diseases, we currently lack insights into regulatory mechanisms promoting its precision and efficiency. We analyse high-throughput mutagenesis data obtained for an alternatively spliced exon in the proto-oncogene RON and determine the functional units that control this splicing event. Using mathematical modeling of distinct splicing mechanisms, we show that alternative splicing is based in RON on a so-called ‘exon definition’ mechanism. Here, the recognition of the adjacent exons by the spliceosome is required for removal of an intron. We use our model to analyze the differences between the exon and intron definition scenarios and find that exon definition is crucial to prevent the accumulation of deleterious, partially spliced retention products during alternative splicing regulation. Furthermore, it modularizes splicing control, as multiple regulatory inputs are integrated into a common net input, irrespective of the location and nature of the corresponding cis-regulatory elements in the pre-mRNA. Our analysis suggests that exon definition promotes robust and reliable splicing outcomes in RON splicing.SIGNIFICANCEDuring mRNA maturation, pieces of the pre-mRNA (introns) are removed during splicing, and remaining parts (exons) are joined together. In alternative splicing, certain exons are either included or excluded, resulting in different splice products. Inclusion of RON alternative exon 11 leads to a functional receptor tyrosine kinase, while skipping results in a constitutively active receptor that promotes epithelial-to-mesenchymal transition and contributes to tumour invasiveness. Intron retention results in to deleterious isoforms that cannot be translated properly. Using kinetic modeling, we investigate the combinatorial regulation of this important splicing decision, and find that the experimental data supports a so-called exon definition mechanism. We show that this mechanism enhances the precision of alternative splicing regulation and prevents the retention of introns in the mature mRNA.

Polypyrimidine Tract Binding Protein Functions as a Repressor To Regulate Alternative Splicing of α-Actinin Mutally Exclusive Exons

Molecular and Cellular Biology ◽

10.1128/mcb.19.4.2699 ◽

1999 ◽

Vol 19 (4) ◽

pp. 2699-2711 ◽

Cited By ~ 88

Author(s):

Justine Southby ◽

Clare Gooding ◽

Christopher W. J. Smith

Keyword(s):

Branch Point ◽

Splice Site ◽

Binding Protein ◽

Regulatory Elements ◽

Regulatory Sequences ◽

Branch Points ◽

Polypyrimidine Tract ◽

Polypyrimidine Tract Binding ◽

Polypyrimidine Tract Binding Protein

ABSTRACT The smooth muscle (SM) and nonmuscle (NM) isoforms of α-actinin are produced by mutually exclusive splicing of an upstream NM exon and a downstream SM-specific exon. A rat α-actinin genomic clone encompassing the mutually exclusive exons was isolated and sequenced. The SM exon was found to utilize two branch points located 382 and 386 nucleotides (nt) upstream of the 3′ splice site, while the NM exon used a single branch point 191 nt upstream. Mutually exclusive splicing arises from the proximity of the SM branch points to the NM 5′ splice site, and this steric repression could be relieved in part by the insertion of spacer elements. In addition, the SM exon is repressed in non-SM cells and extracts. In vitro splicing of spacer-containing transcripts could be activated by (i) truncation of the transcript between the SM polypyrimidine tract and exon, (ii) addition of competitor RNAs containing the 3′ end of the actinin intron or regulatory sequences from α-tropomyosin (TM), and (iii) depletion of the splicing extract by using biotinylated α-TM RNAs. A number of lines of evidence point to polypyrimidine tract binding protein (PTB) as the trans-acting factor responsible for repression. PTB was the only nuclear protein observed to cross-link to the actinin RNA, and the ability of various competitor RNAs to activate splicing correlated with their ability to bind PTB. Furthermore, repression of α-actinin splicing in the nuclear extracts depleted of PTB by using biotinylated RNA could be specifically restored by the addition of recombinant PTB. Thus, α-actinin mutually exclusive splicing is enforced by the unusual location of the SM branch point, while constitutive repression of the SM exon is conferred by regulatory elements between the branch point and 3′ splice site and by PTB.

Control of BEK and K-SAM splice sites in alternative splicing of the fibroblast growth factor receptor 2 pre-mRNA

Molecular and Cellular Biology ◽

10.1128/mcb.13.9.5461-5468.1993 ◽

1993 ◽

Vol 13 (9) ◽

pp. 5461-5468

Author(s):

E Gilbert ◽

F Del Gatto ◽

P Champion-Arnaud ◽

M C Gesnel ◽

R Breathnach

Keyword(s):

Alternative Splicing ◽

Growth Factor ◽

Fibroblast Growth Factor ◽

Fibroblast Growth Factor Receptor ◽

Growth Factor Receptor ◽

Fibroblast Growth ◽

Splice Sites ◽

Polypyrimidine Tract ◽

Profound Influence ◽

In Cells

The fibroblast growth factor receptor 2 gene pre-mRNA can be spliced by using either the K-SAM exon or the BEK exon. The exon chosen has a profound influence on the ligand-binding specificity of the receptor obtained. Cells make a choice between the two alternative exons by controlling use of both exons. Using fibroblast growth factor receptor 2 minigenes, we have shown that in cells normally using the K-SAM exon, the BEK exon is not used efficiently even in the absence of the K-SAM exon. This is because these cells apparently express a titratable repressor of BEK exon use. In cells normally using the BEK exon, the K-SAM exon is not used efficiently even in the absence of a functional BEK exon. Three purines in the K-SAM polypyrimidine tract are at least in part responsible for this, as their mutation to pyrimidines leads to efficient use of the K-SAM exon, while mutating the BEK polypyrimidine tract to include these purines stops BEK exon use.

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

Evolutionarily Conserved Coupling of Transcription and Alternative Splicing in the Protein 4.1R and 4.1B Genes Regulates N-Terminal Protein Structure.

Blood ◽

10.1182/blood.v106.11.1664.1664 ◽

2005 ◽

Vol 106 (11) ◽

pp. 1664-1664

Author(s):

Jeff Tan ◽

Marilyn K. Parra ◽

Narla Mohandas ◽

John G. Conboy

Keyword(s):

Alternative Splicing ◽

Rna Processing ◽

Regulatory Elements ◽

Protein Isoforms ◽

Tissue Type ◽

Translation Initiation Site ◽

Acceptor Site ◽

Exon 2 ◽

Evolutionarily Conserved ◽

Protein 4.1R

Abstract The protein 4.1R gene is regulated by complex pre-mRNA processing events that facilitate the synthesis of protein isoforms with different structure, function, and subcellular localization in red cells and various nucleated cell types. One of these events involves the stage-specific activation of exon 16 inclusion in erythroblasts, which mechanically stabilizes the membrane skeleton by increasing the protein’s affinity for spectrin and actin. Some of the splicing factor proteins and RNA regulatory elements responsible for this tissue-specific alternative splicing event have been defined. Here we focus on another RNA processing event, in the 5′ end of the transcript that can affect the structure and function of the membrane binding domain of protein 4.1R. We have shown that 4.1R transcripts originating at three far upstream alternative promoters/first exons splice differentially to alternative acceptor sites in exon 2′/2 in a manner that suggests strict coupling between transcription and alternative splicing events. A precisely analogous gene organization and RNA processing pattern has also been shown to occur in the paralogous 4.1B gene. Now we demonstrate that this coupling is evolutionarily conserved among several vertebrate classes from fish to mammals. The 4.1R and 4.1B genes from fish, bird, amphibian, and mammal genomes exhibit shared features including alternative first exons and differential splice acceptors in exon 2. In all cases, the 5′-most exon (exon 1A) splices exclusively to a weaker internal acceptor site in exon 2, skipping a short sequence designated as exon 2′ (17-33nt). Conversely, alternative first exons 1B and/or 1C always splice to the stronger first acceptor site, retaining exon 2′. These correlations are independent of tissue type or species of origin. Since exon 2′ contains a translation initiation site, this regulated splicing event generate protein isoforms with distinct N-termini. We propose that these 4.1 genes represent a physiologically relevant model system for mechanistic analysis of transcription-coupled alternative splicing. We have recently constructed a 9kb “minigene” that successfully reproduces the differential splicing patterns of exons 1A and 1B to exon 2′/2 in transfected cells. This minigene will facilitate identification of the determinants that guide coupling. Current experiments are testing the importance for proper splicing of the transcriptional promoter, first exon sequences, length and sequence of the intron, and sequence of a conserved element within exon 2′. Ultimately these studies should provide new insights into the mechanisms of coupling between far upstream, transcription-related processes and downstream alternative splicing.

Alternative splicing takes charge of interleukin-22 and interferon lambda 4 signaling

10.31237/osf.io/sca8k ◽

2018 ◽

Author(s):

Chrissie Lim

Keyword(s):

Alternative Splicing ◽

Intron Retention ◽

Protein Isoforms ◽

Functional Domain ◽

Type I ◽

Protein Coding ◽

Interleukin 22 ◽

Interferon Lambda ◽

Type Iii Ifn ◽

Overexpression System

Immune responses require the tight control of dose, location, strength and duration through genetic, epigenetic or biochemical regulation. Of these, the generation of alternatively-spliced constructs increases transcriptional and proteomic diversity in post-transcriptional modification, localization and functional domain integrity. Specifically, this thesis explores how splice variation engenders profound differences in the biological functions of interleukin-22 (IL-22) binding protein (IL-22BP) and interferon lambda 4 (IFNλ4), which are both central components of distinct cytokine pathways in mucosal immunity and inflammation. IL-22BP is a soluble receptor for IL-22 that is expressed as three isoforms in humans, though the physiological relevance of the three human isoforms has remained a mystery due to the absence of this variation in mice. We present novel findings that IL-22BPi1 is inactive due to intracellular retention by its unique exon, while IL-22BPi3 is also an antagonist but with differential activity from IL-22BPi2. Importantly, while IL-22BPi3 has widespread expression in steady-state homeostatic conditions, IL-22BPi2 is the only isoform induced by inflammatory TLR2/retinoic acid stimulation, highlighting important spatiotemporal control of the two isoforms that exploit their differential activities. IFNλ4 presents a different mystery in which the protein-coding variant is genetically associated with poorer clearance, but the mechanism for this association remains unclear. We investigated several non-canonical functions proposed by the field, including intrinsic differences in activity of the three protein isoforms and their interference with antiviral activites of other type I or III interferons. Establishing an overexpression system and purifying recombinant proteins, we found that only the full-length isoform is active and exhibits similar effects to canonical type III IFN IFNλ3, without any blockade of other IFN signaling. Simultaneously, functional IFNλ4 expression is suppressed in hepatocytes and dendritic cells through preferential splicing to increase intron retention and expression of inactive isoforms. Therefore, alternative splicing in IFNλ4 is an important mechanism to control IFNλ4 bioactivity. The divergent manners in which alternative splice forms impact the activity of both IL-22BP and IFNλ4 highlight the important contributions of this process to cytokine biology and bigger implications that escape detection by genomic analyses.

Novel Form of Alternative Splicing of NFKB1. Its Role in Polycythemia and Adaptation to High Altitude in Andean Aymara

Blood ◽

10.1182/blood-2018-99-117463 ◽

2018 ◽

Vol 132 (Supplement 1) ◽

pp. 2316-2316

Author(s):

Jihyun Song ◽

Seonggyun Han ◽

Ricardo Amaru ◽

Teddy Quispe ◽

Dongwook Kim ◽

...

Keyword(s):

Alternative Splicing ◽

High Altitude ◽

Cell Activation ◽

Conflicts Of Interest ◽

Intron Retention ◽

Exon Skipping ◽

Cardiovascular Development ◽

Splice Sites ◽

Inflammatory Pathways ◽

Exon 4

Abstract Evolutionary adaptations to high altitude in Tibetans, Ethiopians, and Andean populations of South America have shown that Tibetans and Ethiopians have normal hemoglobin %, while most of Aymara and Quechua of the Andean highlands are polycythemic. Whole genome sequencing (WGS) in Quechua identified enriched SENP1 and ANP32D genes correlating with polycythemia (Zhou et al, Am J Hum Genet. 2013 Sep 5; 93(3): 452-462) but these genes were neither enriched nor segregated with polycythemia in Aymara. Instead, we identified that genes enriched in Aymara are related to regulation of cardiovascular development in high-altitude adapted Andeans, BRINP3, NOS2, and TBX5 (Crawford et al, Am J Hum Genet. 2017 Nov 2;101(5):752-767). To further search for Aymara propensity to polycythemia, we analyzed transcriptomes from Aymara and Europeans living in La Paz, Bolivia (3,639-4,150m) from limited amount of peripheral blood reticulocytes, platelets and granulocytes, but only granulocyte RNA was adequate for unbiased whole transcriptome analyses. In Aymaras, 2,585 genes were upregulated and 365 genes were downregulated (Adjp<0.05, fold difference <-2.0, and >2.0). Many of these modulated genes are involved in inflammatory pathways including B-cell activation (FDR=0.005) and NF-κB signaling pathway (FDR=0.011). We then analyzed differential exon usage in the transcriptome and identified 2,475 genes with alternative splicing events, comprising 1,568 exon skipping, 485 intron retention, 175 alternative 3' splice sites, 144 alternative 5' splice sites, and 902 mutually exclusive exons. These alternative spliced genes were also overrepresented in inflammatory pathways (TNF receptor, IL-1 and IL-23 mediated signaling, and NF-κB signaling). Notably we detected the previously unreported NFKB1 alternate transcripts skipping exon 4 or 5, which lead to the out-of-framed NFKB1 mRNA, generating the truncated nonfunctional NF-κB protein (Figure). Inflammation is a potent suppressor of erythropoiesis and the NF-κB is transcriptional regulator of plethora of inflammatory genes. Further, NF-κB also interacts with erythropoiesis-regulators, hypoxia-inducible factors (HIFs). By the integrative analysis of the Aymara transcriptome and WGS, we identified 46 NFKB1 splicing quantitative trait loci (sQTLs). Among these 46 sQTLs, five single nucleotide polymorphisms (SNP) were in high linkage disequilibrium, and two (rs230511 and rs230504) were more enriched in Aymara (allele frequency: 0.878) (Figure) and within a genomic region where Andeans are genetically differentiated from lowland Native Americans (peak FST = 0.37, peak PBSn1 = 0.31). These sQTLs rs230511 and rs230504 were corelated with two functionally important exon skipping (exon 4 and 5) in NFKB1 as described above. Furthermore, these two SNPs were correlated with higher hemoglobin levels and lower leukocytes; the wild-type NFKB1 transcript inversely correlated with hemoglobin%. We report Aymara have differentially expressed and alternatively spliced transcripts of genes modulating inflammation, particularly NFKB1. This Aymara enriched NFKB1 haplotype variant stands out as a major cause of Aymara adaptation to high altitude, as this truncated nonfunctional NF-κB variant peptide correlates with higher hemoglobin, lower leukocytes and suppresses inflammation. These data indicate that NFKB1 SNPs enriched in Aymara are associated with alternative spliced NFKB1 transcripts which contribute to polycythemia in Aymara. Further evaluation of NF-κB and HIFs' transcriptional activity and their correlation with inflammatory makers, hepcidin and erythroferrone in Aymara and Europeans living at the same high altitude is under way. JS and SH contributed equally to this work. YL and JTP act as equivalent co-senior authors. Figure. Figure. Disclosures No relevant conflicts of interest to declare.

In Vivo Analysis of Erythroid Protein 4.1 Pre-mRNA Splicing Mechanisms: Use of Antisense Morpholinos to Assay Function of Deep Intron Regulatory Elements

Blood ◽

10.1182/blood.v116.21.815.815 ◽

2010 ◽

Vol 116 (21) ◽

pp. 815-815

Author(s):

Marilyn Parra ◽

Xiuli An ◽

Narla Mohandas ◽

John G. Conboy

Keyword(s):

Alternative Splicing ◽

Splice Site ◽

Cultured Cells ◽

Conflicts Of Interest ◽

Regulatory Elements ◽

Protein Isoforms ◽

Start Codon ◽

Exon 2 ◽

Mouse Tissues

Abstract Abstract 815 Erythroid stage-specific alternative splicing plays an essential role in the expression of protein 4.1R isoforms that interact with other skeletal proteins to strengthen the membrane. In late erythroblasts, 4.1R mRNA is processed from pre-mRNA that initiates transcription at alternative first exon 1A (E1A) and splices exclusively to the more distal of two alternative 3' splice sites at exon 2 (E2dis), ~100kb downstream. This splicing event is important because it is required to generate the shorter N-terminal domain characteristic of 80kDa isoforms of 4.1R protein in red cells. We have reported that E1A splicing to E2dis requires two nested intrasplicing events mediated by an essential deep intron element originally annotated as exon 1B. However, these studies employed small minigenes transfected into cultured cells, an artificial system that may not correctly reflect in vivo mechanisms. Here we used an antisense RNA strategy to explore splicing of endogenous full length 4.1R pre-mRNA in tissues of live mice and in primary erythroblasts. Chemically modified oligonucleotides known as vivo-morpholinos (vMOs), introduced via tail vein injection and internalized into selected organs, can base pair with complementary cellular RNA sequences and block function of candidate regulatory motifs. Importantly, two independent vMOs directed against the 4.1R intraexon regulatory element both substantially abrogated intrasplicing in several mouse tissues, robustly switching E1A splicing from E2dis to the proximal 3' splice site in E2 (E2prox). This switch results in inclusion of start codon AUG1 in mature 4.1R mRNA and synthesis of larger isoforms of 4.1R protein. These results were highly sequence-specific, since negative control vMOs directed against other genes did not alter E1A splicing to E2dis. Interestingly, we have recently used vMOs to confirm the existence of a similar deep intron element required for analogous E1A-E2dis splicing in the paralogous 4.1B gene. Together these findings strongly support the in vivo physiological function of deep intron elements in the control of intrasplicing in both 4.1R and 4.1B pre-mRNAs. To test whether the 4.1R intrasplicing mechanism is also active in erythroid cells, we incubated mouse splenic erythroblasts isolated from FVA-treated animals with morpholinos directed against the intraexon. Two independent morpholinos against its 5' splice site and branch point both induced a concentration-dependent switch in E1A splicing from E2dis to E2prox. Control morpholinos had no effect on E1A splicing. Because the splicing switch results in inclusion of alternative translation initiation codon AUG1, it was predicted to induce synthesis of larger isoforms of 4.1R including the N-terminal headpiece known to influence 4.1R binding affinities for other skeletal proteins. Western blot analysis of erythroblast proteins confirmed a switch to expression of larger 4.1R protein isoforms that are not present in normal late stage erythroblasts. Intrasplicing is mediated by deep intron elements, and is essential for accurate physiological splicing of natural 4.1R pre-mRNA in erythroid and other cells. Antisense morpholinos represent a new tool for alternative splicing studies in vivo or in cultured erythroblasts. Disclosures: No relevant conflicts of interest to declare.

Genome-wide profiling of alternative splicing genes in hybrid poplar (P.alba×P.glandulosa cv.84K) leaves

PLoS ONE ◽

10.1371/journal.pone.0241914 ◽

2020 ◽

Vol 15 (11) ◽

pp. e0241914

Author(s):

Ruixue Wang ◽

Peng Yin ◽

Yang Ruixia ◽

Xiao Liu ◽

Lie Luo ◽

...

Keyword(s):

Alternative Splicing ◽

Inositol Phosphate ◽

Intron Retention ◽

Rna Extraction ◽

Hybrid Poplar ◽

Gc Content ◽

Plant Production ◽

Splice Sites ◽

Illumina Hiseq ◽

Poplar Leaves

Alternative splicing (AS) is a post-transcriptional process common in plants and essential for regulation of environmental fitness of plants. In the present study, we focus on the AS events in poplar leaves to understand their effects on plant growth and development. The hybrid poplar (P.alba×P.glandulosa cv.84K) leaves were collected for RNA extraction. The extracted RNA was sequenced using on an Illumina HiSeq™ 2000 platform. Using the Populus trichocarpa genome as the reference, a total of 3810 AS genes were identified (9225 AS events), which accounted for 13.51% of all the expressed genes. Intron retention was the most common AS event, accounting for 43.86% of all the AS events, followed by alternative 3′ splice sites (23.75%), alternative 5′ splice sites (23.71%), and exon skipping (8.68%). Chromosomes 10 had the most condensed AS events (33.67 events/Mb) and chromosome 19 had the least (12.42 events/Mb). Association analysis showed that AS in the poplar leaves was positively correlated with intron length, exon number, exon length, and gene expression level, and was negatively correlated with GC content. AS genes in the poplar leaves were associated mainly with inositol phosphate metabolism and phosphatidylinositol signaling system pathways that would be significant on wooden plant production.

Changes in Alternative Splicing in Apis Mellifera Bees Fed Apis Cerana Royal Jelly

Journal of Apicultural Science ◽

10.2478/jas-2014-0019 ◽

2014 ◽

Vol 58 (2) ◽

pp. 25-31 ◽

Cited By ~ 1

Author(s):

Yuan Yuan Shi ◽

Zachary Y. Huang ◽

Xiao Bo Wu ◽

Zi Long Wang ◽

Wei Yu Yan ◽

...

Keyword(s):

Alternative Splicing ◽

Apis Mellifera ◽

Honey Bee ◽

Royal Jelly ◽

Intron Retention ◽

Tricarboxylic Acid Cycle ◽

Apis Cerana ◽

Causative Factor ◽

Caste Differentiation ◽

Splice Sites

Abstract The Western honey bee (Apis mellifera) is a social insect characterized by caste differentiation in which the queen bee and worker bees display marked differences in morphology, behavior, reproduction, and longevity despite their identical genomes. The main causative factor in caste differentiation is the food fed to queen larvae, termed royal jelly (RJ). Alternative splicing (AS) is an important RNA-mediated post-transcriptional process in eukaryotes. Here we report AS changes in A. mellifera after being fed either A. mellifera RJ or A. cerana RJ. The results demonstrated that the RJ type affected 4 types of AS in adult A. mellifera: exon skipping, intron retention, alternative 5’ splice sites, and alternative 3’splice sites. After feeding with A. cerana RJ, AS occurred in many genes in adult A. mellifera that encode proteins involved in development, growth, the tricarboxylic acid cycle, and substance metabolism. This study provides the first evidence that heterospecific RJ can influence the AS of many genes related to honey bee development and growth.