• Molecules and Cells
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• 제38권11호
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• pp.925-935
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• 2015

DNA methylation is a well-characterized epigenetic modification that plays central roles in mammalian development, genomic imprinting, X-chromosome inactivation and silencing of retrotransposon elements. Aberrant DNA methylation pattern is a characteristic feature of cancers and associated with abnormal expression of oncogenes, tumor suppressor genes or repair genes. Ten-eleven-translocation (TET) proteins are recently characterized dioxygenases that catalyze progressive oxidation of 5-methylcytosine to produce 5-hydroxymethylcytosine and further oxidized derivatives. These oxidized methylcytosines not only potentiate DNA demethylation but also behave as independent epigenetic modifications per se. The expression or activity of TET proteins and DNA hydroxymethylation are highly dysregulated in a wide range of cancers including hematologic and non-hematologic malignancies, and accumulating evidence points TET proteins as a novel tumor suppressor in cancers. Here we review DNA demethylation-dependent and -independent functions of TET proteins. We also describe diverse TET loss-of-function mutations that are recurrently found in myeloid and lymphoid malignancies and their potential roles in hematopoietic transformation. We discuss consequences of the deficiency of individual Tet genes and potential compensation between different Tet members in mice. Possible mechanisms underlying facilitated oncogenic transformation of TET-deficient hematopoietic cells are also described. Lastly, we address non-mutational mechanisms that lead to suppression or inactivation of TET proteins in cancers. Strategies to restore normal 5mC oxidation status in cancers by targeting TET proteins may provide new avenues to expedite the development of promising anti-cancer agents.

• Asian-Australasian Journal of Animal Sciences
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• 제31권12호
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• pp.1852-1862
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• 2018

Objective: The purpose of this study was to investigate a single step genome-wide association study (ssGWAS) for identifying genomic regions affecting reproductive traits in Landrace and Large White pigs. Methods: The traits included the number of pigs weaned per sow per year (PWSY), the number of litters per sow per year (LSY), pigs weaned per litters (PWL), born alive per litters (BAL), non-productive day (NPD) and wean to conception interval per litters (W2CL). A total of 321 animals (140 Landrace and 181 Large White pigs) were genotyped with the Illumina Porcine SNP 60k BeadChip, containing 61,177 single nucleotide polymorphisms (SNPs), while multiple traits single-step genomic BLUP method was used to calculate variances of 5 SNP windows for 11,048 Landrace and 13,985 Large White data records. Results: The outcome of ssGWAS on the reproductive traits identified twenty-five and twenty-two SNPs associated with reproductive traits in Landrace and Large White, respectively. Three known genes were identified to be candidate genes in Landrace pigs including retinol binding protein 7, and ubiquitination factor E4B genes for PWL, BAL, W2CL, and PWSY and one gene, solute carrier organic anion transporter family member 6A1, for LSY and NPD. Meanwhile, five genes were identified to be candidate genes in Large White, two of which, aldehyde dehydrogenase 1 family member A3 and leucine rich repeat kinase 1, associated with all of six reproduction traits and three genes; retrotransposon Gag like 4, transient receptor potential cation channel subfamily C member 5, and LHFPL tetraspan subfamily member 1 for five traits except W2CL. Conclusion: The genomic regions identified in this study provided a start-up point for marker assisted selection and estimating genomic breeding values for improving reproductive traits in commercial pig populations.

• Molecules and Cells
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• 제42권1호
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• pp.87-95
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• 2019

Long interspersed element-1 (LINE-1 or L1) is an autonomous retrotransposon, which is capable of inserting into a new region of genome. Previous studies have reported that these elements lead to genomic variations and altered functions by affecting gene expression and genetic networks. Mounting evidence strongly indicates that genetic diseases or various cancers can occur as a result of retrotransposition events that involve L1s. Therefore, the development of methodologies to study the structural variations and interpersonal insertion polymorphisms by L1 element-associated changes in an individual genome is invaluable. In this study, we applied a systematic approach to identify human-specific L1s (i.e., L1Hs) through the bioinformatics analysis of high-throughput next-generation sequencing data. We identified 525 candidates that could be inferred to carry non-reference L1Hs in a Korean individual genome (KPGP9). Among them, we randomly selected 40 candidates and validated that approximately 92.5% of non-reference L1Hs were inserted into a KPGP9 genome. In addition, unlike conventional methods, our relatively simple and expedited approach was highly reproducible in confirming the L1 insertions. Taken together, our findings strongly support that the identification of non-reference L1Hs by our novel target enrichment method demonstrates its future application to genomic variation studies on the risk of cancer and genetic disorders.

• 한국해양바이오학회지
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• 제1권3호
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• pp.186-192
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• 2006

짧은 집단 반복 요소 (Short Interspersed Repetitive Elements, SINE) 는 수백개 정도의 염기로 구성된 반복염기서열로서 LINE (Long Interspersed Nucleotide Elements)와 함께 바이러스와는 구별되는 레트로트랜스포존 (Retrotransposon)의 하나로 알려져 있다. 이들의 생체 내 역할은 정확하게 밝혀진 것은 없지만 게놈 내에서 반복염기서열의 재배열을 통해 완전히 새로운 유전자를 창조하거나 기존의 유전자를 변형시킴으로써 유전물질의 운반수단 및 진화적 변화에 있어서 중요한 역할을 할 것이라 예상되며, 질병의 원인이 된다고도 밝혀져 있다. 본 연구에서는 미꾸라지로부터 SINE의 새로운 두 그룹을 분리하였다. 두 SINE 그룹, mlSINE-L과 mlSINE-S는 각각 약 410bp와 270bp의 염기로 구성되어 있다. 두 SINE 그룹의 5'과 3'말단의 서열은 RSg-1와 SmaI SINE 의 그것과 높은 유사도를 보였다. 계통발생분석결과, mlSINE들은 미꾸라지에서 유일하였으며, dot blot hybridization의 결과는 mlSINE-L이 미꾸라지 게놈 $2{\times}10^9bp$ (2.8 pg)당 $1{\times}10^3$ copy를 가지는 것으로 추정되며, loop DNA보다 핵기질부착부위 (nuclear matrix attachment regions, MARs)에서 그 분포도가 높았다. 이런 결과는 미꾸라지의 새로운 SINE 들이 핵기질 부착부위 내에서나 혹은 가까운 주변에 우선적으로 삽입될 수 있음을 나타낸다.

• Molecules and Cells
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• 제40권5호
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• pp.346-354
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• 2017

Long interspersed nuclear element-1 (LINE-1) is a retrotransposon that contains a CpG island in its 5'-untranslated region. The CpG island of LINE-1 is often heavily methylated in normal somatic cells, which is associated with poor prognosis in various cancers. DNA methylation can differ between formalin-fixed paraffin-embedded (FFPE) and frozen tissues. Therefore, this study aimed to compare the LINE-1 methylation status between the two tissue-storage conditions in gastric cancer (GC) clinical samples and to evaluate whether LINE-1 can be used as an independent prognostic marker for each tissue-storage type. We analyzed four CpG sites of LINE-1 and examined the methylation levels at these sites in 25 FFPE and 41 frozen GC tissues by quantitative bisulfite pyrosequencing. The LINE-1 methylation status was significantly different between the FFPE and frozen GC tissues (p < 0.001). We further analyzed the clinicopathological features in the two groups separately. In the frozen GC tissues, LINE-1 was significantly hypomethylated in GC tissues compared to their corresponding normal gastric mucosa tissues (p < 0.001), and its methylation status was associated with gender, differentiation state, and lymphatic and venous invasion of GC. In the FFPE GC tissues, the methylation levels of LINE-1 differed according to tumor location and venous invasion of GC. In conclusion, LINE-1 can be used as a useful methylation marker for venous invasion in both FFPE and frozen tumor tissues of GC.

• 생명과학회지
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• 제14권4호
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• pp.650-656
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• 2004

야생벼의 일종인 Oryza grandiglumis (CCDD, 2n=48)는 도열병, 잎집무늬마름병, 흰빛잎마름병, 그리고 벼멸구와 같은 병충해에 저항성을 가지는 것으로 알려져 있다. 이와 같은 곰팡이와 해충에 반응하여 차별 발현하는 유전자를 클로닝 하기 위하여 상처처리와 yeast extract를 Oryza grandiglumis에 0시간과 24시간 각각 처리하였다. 유전자의 클로닝을 위하여 희귀 발현유전자의 클로닝에 효율적인 것으로 알려진 Suppression Subtractive Hybridization (SSH) 방법이 처리 후 24시간 된 식물을 재료로 사용되었다. 그 결과, 776개의 cDNA clones이 확보되었으며, 유전자 발현의 진위여부를 빠르게 스크린하기 위하여 colony array가 수행되었다. 115개의 colony가 positive로 판명되었고, 이들의 평균 insert size는 400 bp에서 700 bp에 이르렀고, 이들에 대한 염기서열 분석이 수행되었다. 염기서열 분석 결과, 68개 clone들이 알려진 기능의 유전자와 homology를 나타냈으며, 이중에서 16개 clone이 일차대사에 관련된 것과 유사성을, 5개가 plant retrotransposon과 유사성을, 5개가 식물 방어기작 관련 metallothionein-like gene과 염기서열 유사성을 보였다. 이외에 다양한 유전자들이 아미노산 합성관련, membrane transport, signal transduction등에 관여하는 유전자들과 상동성을 나타내었다. 이들 유전자중에서 4 개의 클론(ogwfi-161, ogwfi-646, ogwfi-663, ogwfi-695)들이 선발되었고 이들에 대한 Northern 분석이 수행되었다. Northern 분석 결과 ogwfi-161, ogwfi-646, ogwfi-663, ogwfi-695는 wounding과 yeast extract처리 에 의한 차별 발현이 확인되었다. 이상의 결과를 종합하여 볼 때, SSH방법은 병충해등과 같은 조건에 의해 차별 발현되는 유전자들을 빠른 시간 내에 다량으로 발굴할 수 있는 매우 효율적인 방법이라고 생각된다.