Identification of a newly spliced exon in the mouse Ilf3 gene generating two long and short isoforms of Ilf3 and NF90

Abstract

The mammalian IlF3 and NF90 proteins, involved in several cellular functions, have common N-terminal and central sequences and specific C-terminal regions. These proteins exhibit a large heterogeneity generated by posttranscriptional and posttranslational modifications. Part of their polymorphism is due to the alternative splicing of exon 3 located just downstream of the translation initiation codon. This 39-nucleotide-long exon, not described so far, codes for an N-terminal sequence of 13 residues (ALYHHHFITRRRR) also present in rat and human IlF3 or NF90. Four mRNAs are expressed in mouse brain, two for Ilf3 and two for NF90, differing in their 3' sequence to generate the specific Ilf3 and NF90 C-terminal domains and in the presence or the absence of exon 3 to generate long and short isoforms of both proteins. By RT-PCR, no other variants were found. Combining our results and GenBank sequences, we determined the exon-intron organization of the entire mouse Ilf3 gene divided into 22 exons.

Tissue Type-Specific Expression of the dsRNA-Binding Protein 76 and Genome-Wide Elucidation of Its Target mRNAs

“…Under the specific electrophoresis conditions employed we distinguished at least two major DRBP76 isoforms of ∼75 to 80 kDa in normal brain, while a single form of ∼90 kDa predominates in HEK293 and HTB-14 glioma cells. A similar DRBP76 doublet in immunoblots of mouse brain lysates has been observed previously [25], but that study did not show comparison with cell lines.…”

“…Extensive heterogeneity of NFAR proteins in mammalian brain has been observed before [25] and may be due to splice variation [25] and post-translational modifications, e.g., arginine methylation [26], lysine acetylation [27] or phosphorylation [8]. To better resolve anti-DRBP76 immunoreactive material in the 75–90 kDa size range and to begin assessing subcellular localization of NFAR proteins in the normal CNS, we tested fractionated (cytoplasmic vs. nuclear) tissue lysates by immunoblotting after gel electrophoresis in 7% Tris-acetate gels (Fig.…”

“…Intron-exon organization of the ILF3 gene [25], [33]. Exons are indicated by black boxes (top); alternative splicing yields diverse transcripts encoding DRBP76/ILF3 proteins with distinct C-termini (bottom; coding sequences are indicated by solid boxes).…”

“…Exons are indicated by black boxes (top); alternative splicing yields diverse transcripts encoding DRBP76/ILF3 proteins with distinct C-termini (bottom; coding sequences are indicated by solid boxes). Hatched lines indicate proposed alternative splicing of exon 3 [25]. B .…”

Nuclear Factor 45 (NF45) Is a Regulatory Subunit of Complexes with NF90/110 Involved in Mitotic Control

“…For example, MPP4 (M-phase phosphoprotein 4) is similar, if not identical, to NF90 and is phosphorylated during M phase (23), and closely related proteins 4F.1 and 4F.2 were characterized in Xenopus as doublestranded RNA (dsRNA)-binding proteins (3). NF90 is also known as DRBP76, NFAR1, and TCP80 (34, 43, 55), and NF110 is also known as ILF3, NFAR2, TCP110, and CBTF 122 (4,43,53,55). Underlining the importance of these proteins, knockout of the mouse ILF3 gene led to muscle degeneration, respiratory failure, and death soon after birth (44).…”