Non-hominid TP63 lacks retroviral LTRs but contains a novel conserved upstream exon

Nkx2-5 marks the earliest recognizable cardiac progenitor cells, and is activated in response to inductive signals involved in lineage specification. Nkx2-5 is also expressed in the developing foregut, thyroid, spleen, stomach and tongue. One approach to elucidate the signals involved in cardiogenesis was to examine the transcriptional regulation of early lineage markers such as Nkx2-5. We generated F0 transgenic mice, which carry Nkx2-5 flanking sequences linked to a lacZ reporter gene. We identified multiple regulatory regions located within the proximal 10.7 kb of the Nkx2-5 gene. In addition to a proximal promoter, we identified a second promoter and a novel upstream exon that could participate in the regulation of Nkx2-5 transcription. Although used rarely in normal development, this novel exon could be spliced into the Nkx2-5 coding region in several ways, thereby potentially creating novel Nkx2-5 protein isoforms, whose transcriptional activity is greatly diminished as compared to wild-type Nkx2-5. An enhancer that directs expression in pharynx, spleen, thyroid and stomach was identified within 3.5 kb of exon 1 between the coding exon 1 and the novel upstream exon 1a. Two or more enhancers upstream of exon 1a were capable of driving expression in the cardiac crescent, throughout the myocardium of the early heart tube, then in the outflow tract and right ventricle of the looped heart tube. A negative element was also located upstream of exon1a, which interacted in complex ways with enhancers to direct correct spatial expression. In addition, potential autoregulatory elements can be cooperatively stimulated by Nkx2-5 and GATA-4. Our results demonstrate that a complex suite of interacting regulatory domains regulate Nkx2-5 transcription. Dissection of these elements should reveal essential features of cardiac induction and positive and negative signaling within the cardiac field.

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An additional 5'-upstream exon exists in the human pleiotrophin-encoding gene

Gene ◽

10.1016/0378-1119(94)00674-h ◽

1995 ◽

Vol 153 (2) ◽

pp. 301-302 ◽

Cited By ~ 7

Author(s):

Shoupeng Lai ◽

Anke M. Schulte ◽

Anton Wellstein ◽

Anna Tate Riegel

Keyword(s):

Encoding Gene ◽

Upstream Exon

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In vivo recognition of a vertebrate mini-exon as an exon-intron-exon unit.

Molecular and Cellular Biology ◽

10.1128/mcb.13.5.2677 ◽

1993 ◽

Vol 13 (5) ◽

pp. 2677-2687 ◽

Cited By ~ 40

Author(s):

D A Sterner ◽

S M Berget

Keyword(s):

Splice Site ◽

Rna Splicing ◽

Troponin I ◽

Exon Skipping ◽

Splice Sites ◽

Small Vertebrate ◽

Upstream Exon ◽

I Gene

Very small vertebrate exons are problematic for RNA splicing because of the proximity of their 3' and 5' splice sites. In this study, we investigated the recognition of a constitutive 7-nucleotide mini-exon from the troponin I gene that resides quite close to the adjacent upstream exon. The mini-exon failed to be included in spliced RNA when placed in a heterologous gene unless accompanied by the upstream exon. The requirement for the upstream exon disappeared when the mini-exon was internally expanded, suggesting that the splice sites bordering the mini-exon are compatible with those of other constitutive vertebrate exons and that the small size of the exon impaired inclusion. Mutation of the 5' splice site of the natural upstream exon did not result in either exon skipping or activation of a cryptic 5' splice site, the normal vertebrate phenotypes for such mutants. Instead, a spliced RNA accumulated that still contained the upstream intron. In vitro, the mini-exon failed to assemble into spliceosome complexes unless either internally expanded or accompanied by the upstream exon. Thus, impaired usage of the mini-exon in vivo was accompanied by impaired recognition in vitro, and recognition of the mini-exon was facilitated by the presence of the upstream exon in vivo and in vitro. Cumulatively, the atypical in vivo and in vitro properties of the troponin exons suggest a mechanism for the recognition of this mini-exon in which initial recognition of an exon-intron-exon unit is followed by subsequent recognition of the intron.

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A novel splicing silencer generated by DMD exon 45 deletion junction could explain upstream exon 44 skipping that modifies dystrophinopathy

Journal of Human Genetics ◽

10.1038/jhg.2014.36 ◽

2014 ◽

Vol 59 (8) ◽

pp. 423-429 ◽

Cited By ~ 13

Author(s):

Ery Kus Dwianingsih ◽

Rusdy Ghazali Malueka ◽

Atsushi Nishida ◽

Kyoko Itoh ◽

Tomoko Lee ◽

...

Keyword(s):

Splicing Silencer ◽

Upstream Exon ◽

Deletion Junction

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The self-splicing intron in theNeurosporaapocytochrome b gene contains a long reading frame in frame with the upstream exon

Nucleic Acids Research ◽

10.1093/nar/16.3.1125 ◽

1988 ◽

Vol 16 (3) ◽

pp. 1125-1134 ◽

Cited By ~ 16

Author(s):

Richard A. Collins ◽

Catherine A. Reynolds ◽

Joan Olive

Keyword(s):

The Self ◽

Reading Frame ◽

Self Splicing ◽

Upstream Exon

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Self-Splicing of the Bacteriophage T4 Group I Introns Requires Efficient Translation of the Pre-mRNA In Vivo and Correlates with the Growth State of the Infected Bacterium

Journal of Bacteriology ◽

10.1128/jb.01287-06 ◽

2006 ◽

Vol 189 (3) ◽

pp. 980-990 ◽

Cited By ~ 16

Author(s):

Linus Sandegren ◽

Britt-Marie Sjöberg

Keyword(s):

Stationary Phase ◽

De Novo ◽

Bacteriophage T4 ◽

Group I Introns ◽

Growth State ◽

Group I ◽

Splicing Efficiency ◽

Self Splicing ◽

Upstream Exon

ABSTRACT Bacteriophage T4 contains three self-splicing group I introns in genes in de novo deoxyribonucleotide biosynthesis (in td, coding for thymidylate synthase and in nrdB and nrdD, coding for ribonucleotide reductase). Their presence in these genes has fueled speculations that the introns are retained within the phage genome due to a possible regulatory role in the control of de novo deoxyribonucleotide synthesis. To study whether sequences in the upstream exon interfere with proper intron folding and splicing, we inhibited translation in T4-infected bacteria as well as in bacteria containing recombinant plasmids carrying the nrdB intron. Splicing was strongly reduced for all three T4 introns after the addition of chloramphenicol during phage infection, suggesting that the need for translating ribosomes is a general trait for unperturbed splicing. The splicing of the cloned nrdB intron was markedly reduced in the presence of chloramphenicol or when translation was hindered by stop codons inserted in the upstream exon. Several exon regions capable of forming putative interactions with nrdB intron sequences were identified, and the removal or mutation of these exon regions restored splicing efficiency in the absence of translation. Interestingly, splicing of the cloned nrdB intron was also reduced as cells entered stationary phase and splicing of all three introns was reduced upon the T4 infection of stationary-phase bacteria. Our results imply that conditions likely to be frequently encountered by natural phage populations may limit the self-splicing efficiency of group I introns. This is the first time that environmental effects on bacterial growth have been linked to the regulation of splicing of phage introns.

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Characterization of the structure and evolution of the Adh region of Drosophila hydei.

Genetics ◽

10.1093/genetics/127.2.355 ◽

1991 ◽

Vol 127 (2) ◽

pp. 355-366

Author(s):

M Menotti-Raymond ◽

W T Starmer ◽

D T Sullivan

Keyword(s):

Sequence Divergence ◽

Drosophila Hydei ◽

Repleta Group ◽

Drosophila Mulleri ◽

Duplication Events ◽

Independent Duplication ◽

The Difference ◽

Upstream Exon ◽

Complex Manner

Abstract Drosophila of the repleta group have a duplication of the gene which encodes alcohol dehydrogenase (ADH). We report the nucleotide sequence of an 8.4-kb region of genomic DNA of Drosophila hydei which includes the entire Adh region. Analysis of this sequence reveals similarity in organization to the Adh region of Drosophila mojavensis and Drosophila mulleri of the mulleri subgroup, with three genes ordered 5' to 3', Adh-psi, Adh-2, Adh-1. Deletion of a nucleotide in the second codon of each pseudogene suggests that the first Adh duplication occurred before the divergence of the hydei and mulleri subgroups. However, Adh-1 and Adh-2 of D. hydei are significantly more alike than Adh-1 and Adh-2 of D. mojavensis. Models to account for the difference in similarity between the coding genes were tested by orthologous and paralogous comparisons of the extent of sequence divergence. A model which proposes that independent duplication events generated Adh-1 and Adh-2 in the two lineages is supported by these data. The D. hydei pseudogene is transcribed and the transcript is processed in a complex manner. An intron of greater than 6.2 kb exists between the first "coding" exon and an upstream exon which is approximately 250 nucleotides in length.

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RNA processing and expression of an intron-encoded protein in yeast mitochondria: role of a conserved dodecamer sequence

Molecular and Cellular Biology ◽

10.1128/mcb.7.7.2530-2537.1987 ◽

1987 ◽

Vol 7 (7) ◽

pp. 2530-2537 ◽

Cited By ~ 1

Author(s):

H Zhu ◽

I G Macreadie ◽

R A Butow

Keyword(s):

Rna Processing ◽

Rrna Gene ◽

Yeast Mitochondria ◽

Wild Type ◽

Reading Frame ◽

Processing Activity ◽

Novel Processing ◽

Type Strains ◽

Upstream Exon

The 3' ends of most Saccharomyces cerevisiae mitochondrial mRNAs terminate at a conserved dodecamer sequence, 5'-AAUAAUAUUCUU-3', of unknown function. We have studied the consequences of mutations within a dodecamer found in an 1,143-base-pair optional intron of the mitochondrial large (21S) rRNA gene on RNA processing. The dodecamer is situated at the 3' end of an expressed open reading frame (ORF) within that intron, and the mutations are two adjacent transversions that extend the intron ORF by 51 nucleotides. The strain harboring these mutations, L5-10-1, is defective in biased intron transmission in crosses to strains that lack the intron, as are other mutants which contain nucleotide changes within the ORF (I. G. Macreadie, R. M. Scott, A. R. Zinn, and R. A. Butow, Cell 41:395-402, 1985). However, unlike these other mutants, wild-type strains, or petites which retain the intron allele, L5-10-1 is defective in processing at the intron dodecamer. In addition, L5-10-1 lacks a prominent 2.7-kilobase RNA containing both intron and exon sequences and at least two of four RNAs that correspond to various forms of the excised intron. We propose that these RNAs, missing in L5-10-1 but present in all other strains examined, arise in part by processing at the intron dodecamer. In addition, in all strains examined, we have detected a novel processing activity in which precursor 21S rRNA transcripts are cleaved in the upstream exon, about 1,500 nucleotides from the 5' end of the RNA. This activity, together with 3' intron dodecamer cleavage, probably accounts for the 2.7-kilobase RNA species, a candidate for the mRNA for the intron-encoded protein.

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