Patterns of exon-intron architecture variation of genes in eukaryotic genomes

Zhu, Liucun; Zhang, Ying; Zhang, Wen; Yang, Sihai; Chen, Jian-Qun; Tian, Dacheng

doi:10.1186/1471-2164-10-47

Cited by 147 publications

(156 citation statements)

References 28 publications

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“…Simultaneously, the percentage of intronic mapped reads increased from 7% in oocytes to 30% in blastocysts. Introns are known to contain a higher proportion of repetitive elements than exons, which has been shown to reduce the mappability of intron-derived reads and thus could explain the decreased number of uniquely mapped reads (20). If multiple mapped reads were allowed in the alignments, we observed an increased portion of reads mapping to repetitive sequences after genome activation.…”

Section: Discussionmentioning

confidence: 81%

Fine mapping of genome activation in bovine embryos by RNA sequencing

Graf

Krebs

Zakhartchenko³

et al. 2014

Proc. Natl. Acad. Sci. U.S.A.

280

300

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During maternal-to-embryonic transition control of embryonic development gradually switches from maternal RNAs and proteins stored in the oocyte to gene products generated after embryonic genome activation (EGA). Detailed insight into the onset of embryonic transcription is obscured by the presence of maternal transcripts. Using the bovine model system, we established by RNA sequencing a comprehensive catalogue of transcripts in germinal vesicle and metaphase II oocytes, and in embryos at the four-cell, eight-cell, 16-cell, and blastocyst stages. These were produced by in vitro fertilization of Bos taurus taurus oocytes with sperm from a Bos taurus indicus bull to facilitate parent-specific transcriptome analysis. Transcripts from 12.4 to 13.7 × 10 3 different genes were detected in the various developmental stages. EGA was analyzed by (i) detection of embryonic transcripts, which are not present in oocytes; (ii) detection of transcripts from the paternal allele; and (iii) detection of primary transcripts with intronic sequences. These strategies revealed (i) 220, (ii) 937, and (iii) 6,848 genes to be activated from the four-cell to the blastocyst stage. The largest proportion of gene activation [i.e., (i) 59%, (ii) 42%, and (iii) 58%] was found in eight-cell embryos, indicating major EGA at this stage. Gene ontology analysis of genes activated at the four-cell stage identified categories related to RNA processing, translation, and transport, consistent with preparation for major EGA. Our study provides the largest transcriptome data set of bovine oocyte maturation and early embryonic development and detailed insight into the timing of embryonic activation of specific genes.

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Section: Discussionmentioning

confidence: 81%

Fine mapping of genome activation in bovine embryos by RNA sequencing

Graf

Krebs

Zakhartchenko³

et al. 2014

Proc. Natl. Acad. Sci. U.S.A.

280

300

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“…The GC content of analyzed ICP27-targeted host gene introns and exons near the impacted splice site averaged 64.5% and 68.0%, respectively, similar to that of HSV genes and much higher than that of typical human introns (46%) and exons (51%) ( Fig. S5A; ref. 27). No example of a consensus 5′ or 3′ splice site was observed in an ICP27-targeted intron, suggesting that, although the average strength for both 5′ and 3′ splice sites was comparable to that of typical splice sites in human genes (Fig.…”

Section: Significancementioning

confidence: 92%

Herpes simplex virus ICP27 regulates alternative pre-mRNA polyadenylation and splicing in a sequence-dependent manner

Tang

Patel

Krause

2016

Proc. Natl. Acad. Sci. U.S.A.

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The herpes simplex virus (HSV) infected cell culture polypeptide 27 (ICP27) protein is essential for virus infection of cells. Recent studies suggested that ICP27 inhibits splicing in a gene-specific manner via an unknown mechanism. Here, RNA-sequencing revealed that ICP27 not only inhibits splicing of certain introns in <1% of cellular genes, but also can promote use of alternative 5′ splice sites. In addition, ICP27 induced expression of pre-mRNAs prematurely cleaved and polyadenylated from cryptic polyadenylation signals (PAS) located in intron 1 or 2 of ∼1% of cellular genes. These previously undescribed prematurely cleaved and polyadenylated pre-mRNAs, some of which contain novel ORFs, were typically intronless, <2 Kb in length, expressed early during viral infection, and efficiently exported to cytoplasm. Sequence analysis revealed that ICP27-targeted genes are GC-rich (as are HSV genes), contain cytosine-rich sequences near the 5′ splice site, and have suboptimal splice sites in the impacted intron, suggesting that a common mechanism is shared between ICP27-mediated alternative polyadenylation and splicing. Optimization of splice site sequences or mutation of nearby cytosines eliminated ICP27-mediated splicing inhibition, and introduction of C-rich sequences to an ICP27-insensitive splicing reporter conferred this phenotype, supporting the inference that specific gene sequences confer susceptibility to ICP27. Although HSV is the first virus and ICP27 is the first viral protein shown to activate cryptic PASs in introns, we suspect that other viruses and cellular genes also encode this function. (ICP27), an immediate early (IE) gene (among those first expressed after virus enters the cells) that is required for expression of some early and late viral genes as well as for virus growth, is highly conserved between HSV-1 and -2, two closely related neurotropic herpesviruses (1). ICP27 has a role in transcriptional regulation through association with the C-terminal domain of RNA polymerase II (2, 3), forms homodimers (4, 5), interacts with U1 small nuclear ribonucleoprotein (snRNP) through its C-terminal domain, and colocalizes with U1 and U2 snRNPs (6, 7). It also interacts with splicing factors such as SRSF3, SRSF1, SRSF7, and SRSF2 (8-11), and is involved in nuclear export of some viral transcripts (12, 13). The role of ICP27 in regulating pre-mRNA splicing remains controversial. Early studies indicated that, in an in vitro pre-mRNA splicing system, ICP27 may nonspecifically inhibit host pre-mRNA splicing, impairing spliceosome assembly as a result of interaction with SR protein kinase 1 (SRPK1) through ICP27's N-terminal RGG RNA-binding motif and/or interaction with spliceosome-association protein 145 (SAP145 or SF3B2) through ICP27's C-terminal domain (8, 11). A recent communication reported that HSV-1 does not inhibit cotranscriptional splicing and proposed that previous reports of ICP27-induced splicing inhibition were artifacts, due to misinterpretation of run-on transcription (14). Indeed, splicing of ...

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“…These results correlate with the longer size of P2X 3 introns in a gene that is not as widely expressed by neural cell types and does not need high efficiency transcription rates. Intron I is often referred to contain expression enhancers and other regulatory elements in mammals [30]- [32], this is the case of the purine nucleoside phosphorylase, where short portions of the intron 1 (around 170 bp) provided enhanced transcription in mammalian cell culture expression systems. In P2X orthologs (Figures 1(b)-(h)), intron I size and sequence it's also conserved, possibly pointing to unidentified regulatory elements in P2X genes.…”

Section: Genomic Organization Of P2x Genes Of the Mousementioning

confidence: 99%

Genomic Organization of Purinergic P2X Receptors

Loera-Valencia¹,

Jaramillo-Polanco²,

Liñán-Rico³

et al. 2015

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Purinergic P2X receptors are a family of ligand-gated cationic channels activated by extracellular ATP. P2X subunit protein sequences are highly conserved between vertebrate species. However, they can generate a great diversity of coding splicing variants to fulfill several roles in mammalian physiology. Despite intensive research in P2X expression in both central and peripheral nervous system, there is little information about their homology, genomic structure and other key features that can help to develop selective drugs or regulatory strategies of pharmacological value which are lacking today. In order to obtain clues on mammalian P2X diversity, we have performed a bioinformatics analysis of the coding regions and introns of the seven P2X subunits present in human, simian, dog, mouse, rat and zebrafish. Here we report the arrangements of exon and intron sequences, considering its number, size, phase and placement; proposing some ideas about the gain and loss of exons and retention of introns. Taken together, these evidences show traits that can be used to gain insight into the evolutionary history of vertebrate P2X receptors and better understand the diversity of subunits coding the purinergic signaling in mammals.

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Patterns of exon-intron architecture variation of genes in eukaryotic genomes

Cited by 147 publications

References 28 publications

Fine mapping of genome activation in bovine embryos by RNA sequencing

Fine mapping of genome activation in bovine embryos by RNA sequencing

Herpes simplex virus ICP27 regulates alternative pre-mRNA polyadenylation and splicing in a sequence-dependent manner

Genomic Organization of Purinergic P2X Receptors

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