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Novel transcription factor variants through RNA-sequencing: the importance of being "alternative".

Scarpato M, Federico A, Ciccodicola A, Costa V - Int J Mol Sci (2015)

Bottom Line: The highest rate of alternative splicing occurs in transcription factors encoding genes, mostly in Krüppel-associated box domains of zinc finger proteins.Through computational approaches we also predicted their novel structural and functional properties.Our findings indicate that alternative splicing is a major determinant of transcription factor diversity, confirming that accurate analysis of RNA-Sequencing data can reliably lead to the identification of novel transcripts, with potentially new functions.

View Article: PubMed Central - PubMed

Affiliation: Institute of Genetics and Biophysics "Adriano Buzzati-Traverso", National Research Council, 80131 Naples, Italy. margherita.scarpato@igb.cnr.it.

ABSTRACT
Alternative splicing is a pervasive mechanism of RNA maturation in higher eukaryotes, which increases proteomic diversity and biological complexity. It has a key regulatory role in several physiological and pathological states. The diffusion of Next Generation Sequencing, particularly of RNA-Sequencing, has exponentially empowered the identification of novel transcripts revealing that more than 95% of human genes undergo alternative splicing. The highest rate of alternative splicing occurs in transcription factors encoding genes, mostly in Krüppel-associated box domains of zinc finger proteins. Since these molecules are responsible for gene expression, alternative splicing is a crucial mechanism to "regulate the regulators". Indeed, different transcription factors isoforms may have different or even opposite functions. In this work, through a targeted re-analysis of our previously published RNA-Sequencing datasets, we identified nine novel transcripts in seven transcription factors genes. In silico analysis, combined with RT-PCR, cloning and Sanger sequencing, allowed us to experimentally validate these new variants. Through computational approaches we also predicted their novel structural and functional properties. Our findings indicate that alternative splicing is a major determinant of transcription factor diversity, confirming that accurate analysis of RNA-Sequencing data can reliably lead to the identification of novel transcripts, with potentially new functions.

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Schematic representation of newly identified TF transcripts. Newly identified transcripts encoding TFs (black)—ZNF266, SATB1, ELF2, SP140L, ARID5B, NCOA2 and IRF1—are schematically compared to known gene annotations: RefSeq (blue), AceView predictions (purple) and Gencode (red).
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ijms-16-01755-f002: Schematic representation of newly identified TF transcripts. Newly identified transcripts encoding TFs (black)—ZNF266, SATB1, ELF2, SP140L, ARID5B, NCOA2 and IRF1—are schematically compared to known gene annotations: RefSeq (blue), AceView predictions (purple) and Gencode (red).

Mentions: A schematic summary of the validated transcripts ZNF266, SATB1, ELF2, SP140L, ARID5B, NCOA2 and IRF1 genes is shown in Figure 2. These AS events were classified in (1) “exon skipping” and (2) “exon gain” with alternative AUG usage; (3) “lack of modular exons” with open reading frame (ORF) maintenance and (4) “exon skipping with frameshift and premature termination codon (PTC) formation”. As schematized in Figure 2, the new ZNF266 belongs to the first category, as it lacks part of the exon 6 and the entire exon 7 (RefSeq NM_006631.3 and NM_001271314.1). Similarly, the novel splicing event described for the SATB1 gene consists of the skipping of exon 2 (GENCODE ENST00000440737.1), which creates a potential new AUG. RNA-Seq re-analysis also indicated the presence of two new transcripts of ELF2 gene, originated by exon gain within intron 3. This event determines the usage of alternative AUG (RefSeq NM_201999.2; details are given in Figure 2).


Novel transcription factor variants through RNA-sequencing: the importance of being "alternative".

Scarpato M, Federico A, Ciccodicola A, Costa V - Int J Mol Sci (2015)

Schematic representation of newly identified TF transcripts. Newly identified transcripts encoding TFs (black)—ZNF266, SATB1, ELF2, SP140L, ARID5B, NCOA2 and IRF1—are schematically compared to known gene annotations: RefSeq (blue), AceView predictions (purple) and Gencode (red).
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4307332&req=5

ijms-16-01755-f002: Schematic representation of newly identified TF transcripts. Newly identified transcripts encoding TFs (black)—ZNF266, SATB1, ELF2, SP140L, ARID5B, NCOA2 and IRF1—are schematically compared to known gene annotations: RefSeq (blue), AceView predictions (purple) and Gencode (red).
Mentions: A schematic summary of the validated transcripts ZNF266, SATB1, ELF2, SP140L, ARID5B, NCOA2 and IRF1 genes is shown in Figure 2. These AS events were classified in (1) “exon skipping” and (2) “exon gain” with alternative AUG usage; (3) “lack of modular exons” with open reading frame (ORF) maintenance and (4) “exon skipping with frameshift and premature termination codon (PTC) formation”. As schematized in Figure 2, the new ZNF266 belongs to the first category, as it lacks part of the exon 6 and the entire exon 7 (RefSeq NM_006631.3 and NM_001271314.1). Similarly, the novel splicing event described for the SATB1 gene consists of the skipping of exon 2 (GENCODE ENST00000440737.1), which creates a potential new AUG. RNA-Seq re-analysis also indicated the presence of two new transcripts of ELF2 gene, originated by exon gain within intron 3. This event determines the usage of alternative AUG (RefSeq NM_201999.2; details are given in Figure 2).

Bottom Line: The highest rate of alternative splicing occurs in transcription factors encoding genes, mostly in Krüppel-associated box domains of zinc finger proteins.Through computational approaches we also predicted their novel structural and functional properties.Our findings indicate that alternative splicing is a major determinant of transcription factor diversity, confirming that accurate analysis of RNA-Sequencing data can reliably lead to the identification of novel transcripts, with potentially new functions.

View Article: PubMed Central - PubMed

Affiliation: Institute of Genetics and Biophysics "Adriano Buzzati-Traverso", National Research Council, 80131 Naples, Italy. margherita.scarpato@igb.cnr.it.

ABSTRACT
Alternative splicing is a pervasive mechanism of RNA maturation in higher eukaryotes, which increases proteomic diversity and biological complexity. It has a key regulatory role in several physiological and pathological states. The diffusion of Next Generation Sequencing, particularly of RNA-Sequencing, has exponentially empowered the identification of novel transcripts revealing that more than 95% of human genes undergo alternative splicing. The highest rate of alternative splicing occurs in transcription factors encoding genes, mostly in Krüppel-associated box domains of zinc finger proteins. Since these molecules are responsible for gene expression, alternative splicing is a crucial mechanism to "regulate the regulators". Indeed, different transcription factors isoforms may have different or even opposite functions. In this work, through a targeted re-analysis of our previously published RNA-Sequencing datasets, we identified nine novel transcripts in seven transcription factors genes. In silico analysis, combined with RT-PCR, cloning and Sanger sequencing, allowed us to experimentally validate these new variants. Through computational approaches we also predicted their novel structural and functional properties. Our findings indicate that alternative splicing is a major determinant of transcription factor diversity, confirming that accurate analysis of RNA-Sequencing data can reliably lead to the identification of novel transcripts, with potentially new functions.

Show MeSH