The MTUS1 gene consists of 17 known exons. Alternative exon utilization leads to the generation of 5 known transcript variants (designated as variant 1 to 5), and consequentially 5 different protein isoforms (designated as isoform 1 to 5). It has been suggested that the transcription of variant 1, 2, and 3 are driven by a common gene promoter, while variant 4 and 5 are driven by 2 additional promoters. This hypothesis is supported by the observation of differential tissue distribution of different MTUS1 variants, which further suggests the differential regulation of MTUS1 gene transcription through these different promoters.

The production of transcript variant 1, 2 and 3, which are driven by a common promoter, are produced by alternative splicing of exon 3 and exon 4. The splice junctions contain the conserved nucleotides (GT-AG) for the donor and acceptor splice sites. An in-frame stop codon in exon 3 indicates that the MTUS1 protein isoform 3 (the only isoform to utilize exon 3) may be interrupted at this position. This sequence feature also makes the transcript variant 3 a candidate for nonsense-mediated mRNA decay (NMD). Indeed, it is absent (or weakly expressed) in all normal tissues examined. While both transcript variant 1 and 2 show similar tissue distribution patterns, variant 1 is more expressed than variant 2 in most tissues. However, in the salivar gland, variant 2 accounts for more than 90% of all the MTUS1 transcript members. Apparently, the exon 4 is the only alternatively spliced exon out of 17 exons of the MTUS1 gene, which leads to the production of MTUS1 transcript variant 1 and 2. Alternatively, variant 2 may be a transcript from the MTUS1 gene with a recently identified polymorphic copy number variant at DNA level (Var del Ex4 that lacking the coding exon 4). Interestingly, an association of this MTUS1 gene Var del Ex4 polymorphism and familial breast cancer has been observed in a Germany patient cohort.

- MTUS1 isoform 1 and 2 are the major MTUS1 transcripts in all tissues except brain
- MTUS1 isoform 3 is absent (or weakly expressed) in all normal tissues examined
- MTUS1 isoform 4 is exclusively expressed in the brain, and is particularly abundant in the cerebellum and in the fetal brain.

MTUS1 isoform 5 is the only isoform localized in mitochondria.

The MTUS1 isoform 5 was the first one among the 5 different isoforms to be characterized independently in 2 laboratories, as a gene that is transiently upregulated during initiation of differentiation and quiescence in a 3-dimensional human umbilical vein endothelial cell culture, and as a early component of growth inhibitory signaling cascade that interacts with angiotensin II AT2 receptor. The exon 8, which is exclusively utilized by MTUS1 isoform 5, contains a mitochondrial targeting signal. This protein isoform has indeed been shown to co-localize with mitochondria, which eventually lead to its current name mitochondrial tumor suppressor 1. These early evidences on MTUS1 isoform 5 suggest the tumor suppressor function of this gene. As a consequence, the majority of the functional analyses have been focused on this specific isoform. As demonstrated in a pancreatic tumor cell line (MIA PaCa-2), recombinant expression of MTUS1 isoform 5 led to a 30% reduction in cell growth as measured by BrdU uptake. Using a CHO cell line stably transfected with both angiotensin II AT2 receptor and MTUS1 isoform 5, Nouet et al. demonstrated that the growth factors (insulin, bFGF, EGF) induced extracellular regulated kinase ( ERK2 ) activation was inhibited. This MTUS1 isoform 5 mediated inhibitory effect was also observed at cell proliferation level as measured by DNA synthesis. The results from Nouet et al., 2006 study also suggested that MTUS1 isoform 5 functions through cooperating with the angiotensin II AT2 receptor to trans-inactivate growth factor receptor tyrosine kinases. The localization of the MTUS1 isoform 5 to mitochondria also lead to speculation that this protein achieves its tumor suppressor function by regulating different mitochondrial functions, such as the maintenance of energy supply, the production of reactive oxygen intermediates and their interactions with other cell cycle regulators.
While ample evidence suggested the tumor suppressor function of isoform 5, it is important to notice that isoform 1 and 2 are the major MTUS1 transcripts in all tissues except brain, and account for an average of 72% of total MTUS1 mRNA. Evidence supporting the tumor suppressor function of MTUS1 isoform 1 and 2 come from the study on Xenopus Icis gene, a homolog of MTUS1 isoform 1/2. Using inactivating antibodies, Ohi et al. found that absence of Icis caused excessive microtubule growth and inhibited spindle formation, a function consistent with tumor suppressor activity. Prior to anaphase, Icis localized to inner centromeres in a Mitotic Centromere Associated Kinesin ( Mcak )-dependent manner. From Xenopus extracts, Icis coimmunoprecipitated Mcak and the inner centromere proteins Incenp and AuroraB, which are thought to promote chromosome biorientation. Immunoelectron microscopy detected Icis on the surface of inner centromeres, in an ideal location to depolymerize microtubules associated laterally with inner centromeres. Ohi et al. hypothesized that Mcak-Icis may destabilize these microtubules and provide a mechanism that prevents kinetochore-microtubule attachment errors.
The MTUS1 isoform 1 and isoform 2 differ in their use of exon 4; exon 4 is contained in isoform 1 but not in isoform 2 (Figure 2). This difference may be a result of alternative splicing. Alternatively, this isoform 2 may be a protein product from the MTUS1 gene with a recently identified polymorphic copy number variant at DNA level (Var del Ex4 that lacking the exon 4).
The existence of MTUS1 isoform 3 is not entirely certain. The expression of MTUS1 isoform 3 appears to be under the control of the same gene promoter that drives the expression of the isoform 1 and 2. However, as a result of alternative splicing, exon 3, which contains an in-frame stop codon, is incorporated into the transcript. This sequence feature makes the transcript variant 3 a candidate for nonsense-mediated mRNA decay (NMD). Indeed, it is absent (or weakly expressed) in all normal tissues examined. Hence, the sequence for this variant in the GenBank (NM_001001927) was permanently suppressed. Nevertheless, it is possible that this alternative splice to include exon 3 in the transcript may provide a mechanism to switch-off the expression of isoform 1 and 2 at posttranscriptional level.
The MTUS1 isoform 4 is exclusively expressed in the brain, and is particularly abundant in the cerebellum and in the fetal brain. It appears that the expression of isoform 4 is driven by a gene promoter specific to central nervous system. These findings suggest multiple cellular/physiological functions of MTUS1 gene, including tumor suppression as well as brain function and/or development.

Xenopus Icis gene is a homolog of MTUS1 isoform 1 and 2.

Sequence analyses of this gene in liver cancer and head and neck cancer revealed that MTUS1 gene is prone to various point mutations and small deletions. Many of these mutations lead to substitutions of conserved amino acid residues or interfere with the physiological splice sites that may functionally silence the MTUS1 gene. In particular, a point mutation in exon 7 (Var3 G17615042T), identified in an 8p21.3-p22 LOH-positive liver cancer cell line, abolished a physiological splicing acceptor site of exon 7. Additional experiment confirmed that this point mutation indeed leads to a transcript that lacking exon 7. Thus, this point mutation results in the deletion of the entire exon 7, which codes for several important motifs, including a nuclear localization signal.