Dataset Information

Identification of a novel circularized transcript of the AML1 gene.

ABSTRACT: The AML1 gene is an essential transcription factor regulating the differentiation of hematopoietic stem cells into mature blood cells. Though at least 12 different alternatively spliced AML1 mRNAs are generated, three splice variants (AML1a, AML1b and AML1c) have been characterized. Here, using the reverse transcription-polymerase chain reaction with outward-facing primers, we identified a novel non-polyadenylated transcript from the AML1 gene, with exons 5 and 6 scrambled. The novel transcript resisted RNase R digestion, indicating it is a circular RNA structure that may originate from products of mRNA alternative splicing. The expression of the novel transcript in different cells or cell lines of human and a number of other species matched those of the canonical transcripts. The discovery provides additional evidence that circular RNA could stably exist in vivo in human, and may also help to understand the mechanism of the regulation of the AML1 gene transcription.

SUBMITTER: Xu AN

PROVIDER: S-EPMC4133869 | biostudies-literature | 2013 Mar

REPOSITORIES: biostudies-literature

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Identification of a novel circularized transcript of the AML1 gene.

Xu Ai-ning AN Chen Xiu-hua XH Tan Yan-hong YH Qi Xi-ling XL Xu Zhi-fang ZF Zhang Lin-lin LL Ren Fang-gang FG Bian Si-cheng SC Chen Yi Y Wang Hong-wei HW

BMB reports 20130301 3

The AML1 gene is an essential transcription factor regulating the differentiation of hematopoietic stem cells into mature blood cells. Though at least 12 different alternatively spliced AML1 mRNAs are generated, three splice variants (AML1a, AML1b and AML1c) have been characterized. Here, using the reverse transcription-polymerase chain reaction with outward-facing primers, we identified a novel non-polyadenylated transcript from the AML1 gene, with exons 5 and 6 scrambled. The novel transcript ...[more]

PMID: 23527860

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Project description:BackgroundThe inference of splicing orthology relationships between gene transcripts is a basic step for the prediction of transcripts and the annotation of gene structures in genomes. The splicing structure of a sequence refers to the exon extremity information in a CDS or the exon-intron extremity information in a gene sequence. Splicing orthologous CDS are pairs of CDS with similar sequences and conserved splicing structures from orthologous genes. Spliced alignment that consists in aligning a spliced cDNA sequence against an unspliced genomic sequence, constitutes a promising, yet unexplored approach for the identification of splicing orthology relationships. Existing spliced alignment algorithms do not exploit the information on the splicing structure of the input sequences, namely the exon structure of the cDNA sequence and the exon-intron structure of the genomic sequences. Yet, this information is often available for coding DNA sequences (CDS) and gene sequences annotated in databases, and it can help improve the accuracy of the computed spliced alignments. To address this issue, we introduce a new spliced alignment problem and a method called SplicedFamAlign (SFA) for computing the alignment of a spliced CDS against a gene sequence while accounting for the splicing structures of the input sequences, and then the inference of transcript splicing orthology groups in a gene family based on spliced alignments.ResultsThe experimental results show that SFA outperforms existing spliced alignment methods in terms of accuracy and execution time for CDS-to-gene alignment. We also show that the performance of SFA remains high for various levels of sequence similarity between input sequences, thanks to accounting for the splicing structure of the input sequences. It is important to notice that unlike all current spliced alignment methods that are meant for cDNA-to-genome alignments and can be used for CDS-to-gene alignments, SFA is the first method specifically designed for CDS-to-gene alignments.ConclusionWe show the usefulness of SFA for the comparison of genes and transcripts within a gene family for the purpose of analyzing splicing orthologies. It can also be used for gene structure annotation and alternative splicing analyses. SplicedFamAlign was implemented in Python. Source code is freely available at https://github.com/UdeS-CoBIUS/SpliceFamAlign .

Dataset Information

Identification of a novel circularized transcript of the AML1 gene.

Publications

Identification of a novel circularized transcript of the AML1 gene.

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