Genomic characterization of human SEC14L1 splice variants within a 17q25 candidate tumor suppressor gene region and identification of an unrelated embedded expressed sequence tag

Abstract

Human SEC14L1 shows partial sequence homology to the budding yeast SEC14 protein and the Japanese flying squid retinal-binding protein and was previously generally localized to 17q25. We more precisely mapped SEC14L1 within a discrete region of 17q25 that likely harbors at least one putative breast and ovarian tumor suppressor gene. We determined that this gene consists of 18 exons ranging in size from 70 bp (exon 11) to 3088 bp (exon 17) and spanning at least 58 kb of DNA. Exon 17 contained a highly polymorphic variable number of tandem repeats (VNTR) and was present only in the larger ubiquitously expressed 5.5-kb transcript. The 3.0-kb ubiquitously expressed transcript included sequences at the beginning of exon 17 (designated exon 17a) and the end of exon 17 (designated exon 18), but lacked the internal 2439 bp of exon 17, including the VNTR. This alternative splicing resulted in a predicted protein of 719 residues from the smaller transcript with four more terminal amino acids than the 715 residue protein predicted from the larger transcript. EST H49244 spanned exon 11 of SEC14L1 and was specifically expressed in human peripheral blood leukocytes. One intragenic single nucleotide polymorphism (SNP) was confirmed. SEC14L1 contained the CRAL/TRIO domain also found in alpha-tocopherol transfer protein (TTPA) and cellular retinaldehyde-binding protein (CRALBP). As retinoids have been shown to inhibit the growth of breast cancer cells, loss of the proposed SEC14L1 retinal-binding function may contribute to breast tumorigenesis. As TTPA and CRALBP have been implicated in retinitis pigmentosa (RP), altered SEC14L1 expression may contribute to RP in previously unlinked families. Coding exon-specific PCR primers were designed to aid in future expression and mutational analyses.

Non-coding cancer driver candidates identified with a sample- and position-specific model of the somatic mutation rate

“…This is approximately four times the amount of expected mutations (q = 8.9 × 10 −5 , ncdDetect), and the majority (58%) of these are found in breast- and colorectal cancer. Although little is known about SEC14L1 in cancer, one study hypothesized that altered expression of the gene could contribute to breast tumorigenesis (Kalikin et al, 2001). Another study found SEC14L1 to be overexpressed in prostate cancer (Burdelski et al, 2015).…”

Regulation of the α‐tocopherol transfer protein in mice: Lack of response to dietary vitamin E or oxidative stress

“…Based on sequence analysis, TTP is classified as a member of the SEC14-like protein family, with a characteristic CRAL_TRIO lipid-binding domain (7,8). In the closed TTP crystal structure, a mobile helical surface segment seals the hydrophobic binding pocket (9,10) and is responsible for the TTP selectivity for α-tocopherol (11).…”

Negative Regulation of RIG-I-Mediated Innate Antiviral Signaling by SEC14L1

“…We screened 3 ϫ 10 6 independent clones, and 1 of 19 positive clones encoded the C-terminal region of SEC14L1 (amino acids [aa] 287 to 715). SEC14L1 is a poorly characterized member of the SEC14 family in mammals with the potential to control the local phospholipid content in membranes (25)(26)(27). Because SEC14L1 interacted with RIG-I in the yeast two-hybrid system, we determined whether this interaction also occurs in mammalian cells.…”