Transcriptome analysis of human gastric cancer

Oh, Jung‐Hwa; Yang, Jin Ok; Hahn, Yoonsoo; Kim, Mirang; Byun, Sang-Soon; Jeon, Yeo-Jin; Kim, Jeongmin; Song, Kyu‐Sang; Noh, Seung Man; Kim, Sang Soo; Yoo, Hyang–Sook; Kim, Yong‐Sung; Kim, Nam-Soon

doi:10.1007/s00335-005-0075-2

Cited by 27 publications

(20 citation statements)

References 46 publications

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“…To better understand the relationship between G clusters and GTP-binding activity, we characterized the sequence requirements of one of these aptamers, clone 4–56, in greater detail. This aptamer was chosen for initial characterization efforts because ( i ) it is known to be expressed (as part of a 486-nucleotide transcript of unknown function) (Oh et al, 2005); ( ii ) pilot experiments revealed that its GTP-binding activity is conserved in primates (Figure S1), consistent with a possible biological role; and ( iii ) it is small (40 nts), which we anticipated would simplify its minimization.…”

Section: Resultsmentioning

confidence: 99%

Discovery of Widespread GTP-Binding Motifs in Genomic DNA and RNA

Curtis

Liu

2013

Chemistry & Biology

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SUMMARY Biological RNAs that bind small-molecules have been implicated in a variety of regulatory and catalytic processes. Inspired by these examples, we used in vitro selection to search a pool of genomeencoded RNA fragments for naturally occurring GTP aptamers. Several classes of aptamers were identified, including one ("the G motif") with a G-quadruplex structure. Further analysis revealed that most RNA and DNA G-quadruplexes bind GTP. The G motif is abundant in eukaryotes, and the human genome contains ∼75,000 examples with dissociation constants comparable to the GTP concentration of a eukaryotic cell (∼300 µM). G-quadruplexes play roles in diverse cellular processes, and our findings raise the possibility that GTP may play a role in the function of these elements. Consistent with this possibility, the sequence requirements of several classes of regulatory G-quadruplexes parallel those of GTP binding.

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Section: Resultsmentioning

confidence: 99%

Discovery of Widespread GTP-Binding Motifs in Genomic DNA and RNA

Curtis

Liu

2013

Chemistry & Biology

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“…KsgA orthologs from non-bacterial sources are represented by Dim1 from Saccharomyces cerevisiae (Sc-Dim1) (Lafontaine et al, 1995; Lafontaine et al, 1998) and from human (Hs-Dim1) (Law et al, 1998; Oh et al, 2005), Pfc1 from Arabidopsis thaliana (Tokuhisa et al, 1998) and mitochondria mtTFB from human (Hs-mtTFB) (Cotney and Shadel, 2006; McCulloch et al, 2002; Seidel-Rogol et al, 2003). The mtTFB from yeast (Sc-mtTFB), however, has lost its MTase activity (Klootwijk et al, 1975).…”

Section: Introductionmentioning

confidence: 99%

Structural Basis for Binding of RNA and Cofactor by a KsgA Methyltransferase

Tropea

Austin

et al. 2009

Structure

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Summary Among methyltransferases, KsgA and the reaction it catalyzes are conserved throughout evolution. However, the specifics of substrate recognition by the enzyme remain unknown. Here, we report structures of Aquifex aeolicus KsgA, in its ligand-free form, in complex with RNA and in complex with both RNA and S-adenosylhomocysteine (SAH, reaction product of cofactor S-adenosylmethionine), providing the first pieces of structural information on KsgA-RNA and KsgA-SAH interactions. Moreover, the structures show how conformational changes that occur upon RNA binding create the cofactor-binding site. There are nine conserved functional motifs (motifs I-VIII and X) in KsgA. Prior to RNA binding, motifs I and VIII are flexible, each exhibiting two distinct conformations. Upon RNA binding, the two motifs become stabilized in one of these conformations, which is compatible with the binding of SAH. Motif X, which is also stabilized upon RNA binding, is directly involved in the binding of SAH.

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“…TOPBP1 (topoisomerase DNA II-binding protein 1) represents a very interesting candidate for CRC genetic susceptibility as it contains multiple BRCT domains, the C-terminal portion of the BRCA-1 gene, and it has a critical role in the control of DNA damage and replication checkpoint (Gong et al , 2010). On the other hand, CDV3 (carnitine deficiency-associated gene expressed in ventricle 3), also known as H41 , seems to be involved in cell proliferation and altered in gastric cancer (Oh et al , 2005). It is noteworthy that the TOPBP1 and CDV3 genes lie next to each other in 3q22 and rs1444601 and rs13088006 are only 34 kb apart.…”

Section: Discussionmentioning

confidence: 99%

A two-phase case–control study for colorectal cancer genetic susceptibility: candidate genes from chromosomal regions 9q22 and 3q22

et al. 2011

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Background:Colorectal cancer (CRC) is the second cause of cancer-related death in the Western world. Much of the CRC genetic risk remains unidentified and may be attributable to a large number of common, low-penetrance genetic variants. Genetic linkage studies in CRC families have reported additional association with regions 9q22–31, 3q21–24, 7q31, 11q, 14q and 22q. There are several plausible candidate genes for CRC susceptibility within the aforementioned linkage regions including PTCH1, XPA and TGFBR1 in 9q22–31, and EPHB1 and MRAS in 3q21–q24.Methods:CRC cases and matched controls were from EPICOLON, a prospective, multicentre, nationwide Spanish initiative, composed of two independent phases. Phase 1 corresponded to 515 CRC cases and 515 controls, whereas phase 2 consisted of 901 CRC cases and 909 controls. Genotyping was performed for 172 single-nucleotide polymorphisms (SNPs) in 84 genes located within regions 9q22–31 and 3q21–q24.Results:None of the 172 SNPs analysed in our study could be formally associated with CRC risk. However, rs1444601 (TOPBP1) and rs13088006 (CDV3) in region 3q22 showed interesting results and may have an effect on CRC risk.Conclusions:TOPBP1 and CDV3 genetic variants on region 3q22 may modulate CRC risk. Further validation and meta-analysis should be undertaken in larger CRC cohorts.

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Transcriptome analysis of human gastric cancer

Cited by 27 publications

References 46 publications

Discovery of Widespread GTP-Binding Motifs in Genomic DNA and RNA

Discovery of Widespread GTP-Binding Motifs in Genomic DNA and RNA

Structural Basis for Binding of RNA and Cofactor by a KsgA Methyltransferase

A two-phase case–control study for colorectal cancer genetic susceptibility: candidate genes from chromosomal regions 9q22 and 3q22

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