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Search Results: 1 - 10 of 9445 matches for " Jung Kyoon Choi "
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Contrasting chromatin organization of CpG islands and exons in the human genome
Jung Kyoon Choi
Genome Biology , 2010, DOI: 10.1186/gb-2010-11-7-r70
Abstract: Here I show that CpG islands were associated not only with methylation-free promoters but also with nucleosome-free promoters. Nucleosome-free regions were observed only in promoters containing a CpG island. However, the DNA sequences of CpG islands predicted the opposite pattern, implying a limitation of sequence programs for the determination of nucleosome occupancy. In contrast to the methylation-and nucleosome-free states of CpG-island promoters, exons were densely methylated at CpGs and packaged into nucleosomes. Exon-enrichment of DNA methylation was specifically found in spliced exons and in exons with weak splice sites. The enrichment patterns were less pronounced in initial exons and in non-coding exons, potentially reflecting a lower need for their splicing. I also found that nucleosomes, DNA methylation, and H3K36me3 marked the exons of transcripts with low, medium, and high gene expression levels, respectively.Human promoters containing a CpG island tend to remain nucleosome-free as well as methylation-free. In contrast, exons demonstrate a high degree of methylation and nucleosome occupancy. Exonic DNA methylation seems to function together with exonic nucleosomes and H3K36me3 for the proper splicing of transcripts with different expression levels.A CpG island (CGI) is a stretch of DNA in which the frequency of CpGs is higher than that present in other regions [1]. This unique genomic element is found only in vertebrate genomes and is usually present in the promoters of housekeeping genes. CGIs remain typically unmethylated even with many potential target sites for DNA methylation and their aberrant methylation often leads to gene silencing, for example in cancer cells [2].Gene silencing by DNA methylation is accompanied by local changes in the chromatin structure. A more direct mechanism to regulate chromatin structure is the assembly and disassembly of histone-DNA complexes, or nucleosomes. A hallmark of recent whole-genome profiles of nucleosome posi
New Records of Two Stichotrichid Ciliates, Afroamphisiella multinucleata and Pseudokahliella marina (Ciliophora: Spirotrichea: Stichotrichida) from Korea
Jung Min Choi,Mann Kyoon Shin
Animal Systematics, Evolution and Diversity , 2012, DOI: http://dx.doi.org/10.5635/ased.2012.28.3.168
Abstract: Two stichotrichid ciliates, collected from marine waters in Jeju Island, were identified as Afroamphisiella multinucleata Foissner et al., 2002 and Pseudokahliella marina (Foissner et al., 1982) Berger et al., 1985. They are recorded for the first time in Korea. The descriptions are based on examinations of living as well as protargol- impregnated specimens. These species are characterized as follows. Afroamphisiella multinucleata has a body size in vivo of 70-95×20-35 μm; elongate rectangular in shape; contractile vacuole located slightly above mid-body. The adoral zone is bipartited into 3 distal and 13-17 proximal membranelles and occupies 28-35% of the body length. The frontal row comprises 1-4 cirri and one buccal cirrus. The amphisiellid median cirral row is composed of 14-21 cirri, 10-19 left marginal cirri, and 21-30 right marginal cirri. Cortical granules are yellowish. 11-20 globular/ellipsoidal macronuclear nodules arrange proximally along the cell margins. Pseudokahliella marina has a body size in vivo of 110-195×40-110 μm and broadly elliptical in shape. The adoral zone of the membranelles occupies 50-60% of the body length, and is composed of 41-70 membranelles. A prominent frontal scutum is present. The contractile vacuole is located below the mid-body. There are 11- 13 frontoventral rows, including marginal rows. Caudal cirri and transverse cirri are absent. Three invariable non-fragmented bipolar dorsal kineties are present. The left and right marginal rows are composed of 22-35 and 28-40 cirri, respectively. Colourless cortical granules are present. 8-11 spherical/ellipsoidal macronuclear nodules are connected with each other by thread-like tructures, forming an inverted C-shape.
Stochastic and Regulatory Role of Chromatin Silencing in Genomic Response to Environmental Changes
Jung Kyoon Choi, Sohyun Hwang, Young-Joon Kim
PLOS ONE , 2008, DOI: 10.1371/journal.pone.0003002
Abstract: Phenotypic diversity and fidelity can be balanced by controlling stochastic molecular mechanisms. Epigenetic silencing is one that has a critical role in stress response. Here we show that in yeast, incomplete silencing increases stochastic noise in gene expression, probably owing to unstable chromatin structure. Telomere position effect is suggested as one mechanism. Expression diversity in a population achieved in this way may render a subset of cells to readily respond to various acute stresses. By contrast, strong silencing tends to suppress noisy expression of genes, in particular those involved in life cycle control. In this regime, chromatin may act as a noise filter for precisely regulated responses to environmental signals that induce huge phenotypic changes such as a cell fate transition. These results propose modulation of chromatin stability as an important determinant of environmental adaptation and cellular differentiation.
Genetic and Metabolic Characterization of Insomnia
Hyo-Jeong Ban,Sang Cheol Kim,Jungmin Seo,Ho-Bum Kang,Jung Kyoon Choi
PLOS ONE , 2012, DOI: 10.1371/journal.pone.0018455
Abstract: Insomnia is reported to chronically affect 10~15% of the adult population. However, very little is known about the genetics and metabolism of insomnia. Here we surveyed 10,038 Korean subjects whose genotypes have been previously profiled on a genome-wide scale. About 16.5% reported insomnia and displayed distinct metabolic changes reflecting an increase in insulin secretion, a higher risk of diabetes, and disrupted calcium signaling. Insomnia-associated genotypic differences were highly concentrated within genes involved in neural function. The most significant SNPs resided in ROR1 and PLCB1, genes known to be involved in bipolar disorder and schizophrenia, respectively. Putative enhancers, as indicated by the histone mark H3K4me1, were discovered within both genes near the significant SNPs. In neuronal cells, the enhancers were bound by PAX6, a neural transcription factor that is essential for central nervous system development. Open chromatin signatures were found on the enhancers in human pancreas, a tissue where PAX6 is known to play a role in insulin secretion. In PLCB1, CTCF was found to bind downstream of the enhancer and interact with PAX6, suggesting that it can probably inhibit gene activation by PAX6. PLCB4, a circadian gene that is closely located downstream of PLCB1, was identified as a candidate target gene. Hence, dysregulation of ROR1, PLCB1, or PLCB4 by PAX6 and CTCF may be one mechanism that links neural and pancreatic dysfunction not only in insomnia but also in the relevant psychiatric disorders that are accompanied with circadian rhythm disruption and metabolic syndrome.
Regulation of the Boundaries of Accessible Chromatin
Xiaoran Chai equal contributor,Sanjanaa Nagarajan equal contributor,Kwoneel Kim,Kibaick Lee,Jung Kyoon Choi
PLOS Genetics , 2013, DOI: 10.1371/journal.pgen.1003778
Abstract: Regulatory regions maintain nucleosome-depleted, open chromatin status but simultaneously require the presence of nucleosomes for specific histone modifications. It remains unclear how these can be achieved for proper regulatory function. Here we demonstrate that nucleosomes positioned within accessible chromatin regions near the boundaries provide platforms for histone modifications while preventing the occlusion of regulatory elements. These boundary nucleosomes were particularly enriched for active or poised regulatory marks in human, such as histone acetylations, H3K4 methylations, H3K9me3, H3K79me2, and H4K20me1. Additionally, we found that based on a genome-wide profiling of ~100 recombinant yeast strains, the location of open chromatin borders tends to vary mostly within 150 bp upon genetic perturbation whereas this positional variation increases in proportion to the sequence preferences of the underlying DNA for nucleosome formation. More than 40% of the local boundary shifts were associated with genetic variation in cis- or trans-acting factors. A sizeable fraction of the identified genetic factors was also associated with nearby gene expression, which was correlated with the distance between the transcription start site (tss) and the boundary that faces the tss. Taken together, the variation in the width of accessible chromatin regions may arise in conjunction with the modulation of the boundary nucleosomes by post-translational modifications or by chromatin regulators and in association with the activity of nearby gene transcription.
Regional Brain Atrophy and Functional Disconnection in Broca’s Area in Individuals at Ultra-High Risk for Psychosis and Schizophrenia
Wi Hoon Jung, Joon Hwan Jang, Na Young Shin, Sung Nyun Kim, Chi-Hoon Choi, Suk Kyoon An, Jun Soo Kwon
PLOS ONE , 2012, DOI: 10.1371/journal.pone.0051975
Abstract: Background Abnormalities in cognitive abilities such as verbal fluency and in cognitive-related brain regions, particularly Broca’s area, have been reported in patients with schizophrenia. Additionally, previous studies have demonstrated that structural and functional abnormalities in Broca’s area were associated with clinical symptoms and cognitive deficits in patients with schizophrenia, suggesting that deficits in this area may reflect the core pathology of schizophrenia. Thus, it is important to understand how the structural volume and functional connectivity in this area changes at rest according to the course of the illness. Methods/Principal Findings We used magnetic resonance imaging (MRI) to measure the structural volume of Broca’s area as a region of interest in 16 schizophrenia, 16 ultra-high risk (UHR), and 23 healthy matched controls. We also assessed verbal fluency and analyzed differences across groups in the functional connectivity patterns using resting-state functional MRI. The UHR group showed significantly reduced structural volume in Broca’s area and significantly reduced functional connectivity between Broca’s area and the lateral and medial frontal cortex as well as decreased cognitive performance. Altered functional connectivity in patients was correlated with their positive symptoms. Conclusions/Significance Our results suggest the existence of functional disconnections in Broca’s area, even during resting-states, among those with schizophrenia as well as those at UHR for this disorder. These alterations may contribute to their clinical symptoms, suggesting that this is one of the key regions involved in the pathophysiology of schizophrenia.
Morphometric Changes in Lateral Ventricles of Patients with Recent-Onset Type 2 Diabetes Mellitus
Junghyun H. Lee, Sujung Yoon, Perry F. Renshaw, Tae-Suk Kim, Jiyoung J. Jung, Yera Choi, Binna N. Kim, Alan M. Jacobson, In Kyoon Lyoo
PLOS ONE , 2013, DOI: 10.1371/journal.pone.0060515
Abstract: It is becoming increasingly evident that type 2 diabetes mellitus can have effects on global and regional brain morphology. Ventricular enlargement reflecting cerebral atrophy has been reported particularly in elderly type 2 diabetes patients. However, little is known about its timing through the disease course and morphological variability. Using the combined volumetric and advanced three-dimensional morphological approach, we identified differences in size and shape of the lateral ventricles between recent-onset type 2 diabetes patients and healthy individuals. High-resolution T1-weighted images were obtained from 23 type 2 diabetes patients whose illness duration was less than 1 year and 23 carefully matched healthy individuals. By volume measurement, we found enlarged lateral and third ventricles in type 2 diabetes patients, relative to healthy individuals (F1,41 = 7.96, P = 0.007; F1,41 = 11.16, P = 0.002, respectively). Morphological analysis revealed that the expansion of lateral ventricles in the diabetic brain was prominent in the bilateral frontal horns. The current findings suggest that atrophic changes particularly of the anterior frontal lobe can occur as early as the first year after the clinical diagnosis of type 2 diabetes mellitus.
Identification of DNA methylation changes associated with human gastric cancer
Jung-Hoon Park, Jinah Park, Jung Kyoon Choi, Jaemyun Lyu, Min-Gyun Bae, Young-Gun Lee, Jae-Bum Bae, Dong Yoon Park, Han-Kwang Yang, Tae-You Kim, Young-Joon Kim
BMC Medical Genomics , 2011, DOI: 10.1186/1755-8794-4-82
Abstract: We profiled the methylome of human gastric cancer tissue at 50-bp resolution using a methylated DNA enrichment technique (methylated CpG island recovery assay) in combination with a genome analyzer and a new normalization algorithm.We were able to gain a comprehensive view of promoters with various CpG densities, including CpG Islands (CGIs), transcript bodies, and various repeat classes. We found that gastric cancer was associated with hypermethylation of 5' CGIs and the 5'-end of coding exons as well as hypomethylation of repeat elements, such as short interspersed nuclear elements and the composite element SVA. Hypermethylation of 5' CGIs was significantly correlated with downregulation of associated genes, such as those in the HOX and histone gene families. We also discovered long-range epigenetic silencing (LRES) regions in gastric cancer tissue and identified several hypermethylated genes (MDM2, DYRK2, and LYZ) within these regions. The methylation status of CGIs and gene annotation elements in metastatic lymph nodes was intermediate between normal and cancerous tissue, indicating that methylation of specific genes is gradually increased in cancerous tissue.Our findings will provide valuable data for future analysis of CpG methylation patterns, useful markers for the diagnosis of stomach cancer, as well as a new analysis method for clinical epigenomics investigations.Gastric cancer is the second leading cause of cancer deaths worldwide after lung cancer, resulting in more than 800,000 deaths worldwide every year [1]. The current 5-year survival rate of individuals diagnosed with gastric cancer is only 20-30%, with this low rate being attributable to the fact that most cases are already in an advanced stage when diagnosed. As in all cancers, early detection remains the most promising approach for improving the survival rate. Hence, understanding the cause of tumorigenesis in human gastric tissue is essential.Infection with H. pylori is a well-established and co
Genetic Landscape of Open Chromatin in Yeast
Kibaick Lee equal contributor,Sang Cheol Kim equal contributor,Inkyung Jung equal contributor,Kwoneel Kim,Jungmin Seo,Heun-Sik Lee,Gireesh K. Bogu,Dongsup Kim,Sanghyuk Lee,Byungwook Lee ,Jung Kyoon Choi
PLOS Genetics , 2013, DOI: 10.1371/journal.pgen.1003229
Abstract: Chromatin regulation underlies a variety of DNA metabolism processes, including transcription, recombination, repair, and replication. To perform a quantitative genetic analysis of chromatin accessibility, we obtained open chromatin profiles across 96 genetically different yeast strains by FAIRE (formaldehyde-assisted isolation of regulatory elements) assay followed by sequencing. While 5~10% of open chromatin region (OCRs) were significantly affected by variations in their underlying DNA sequences, subtelomeric areas as well as gene-rich and gene-poor regions displayed high levels of sequence-independent variation. We performed quantitative trait loci (QTL) mapping using the FAIRE signal for each OCR as a quantitative trait. While individual OCRs were associated with a handful of specific genetic markers, gene expression levels were associated with many regulatory loci. We found multi-target trans-loci responsible for a very large number of OCRs, which seemed to reflect the widespread influence of certain chromatin regulators. Such regulatory hotspots were enriched for known regulatory functions, such as recombinational DNA repair, telomere replication, and general transcription control. The OCRs associated with these multi-target trans-loci coincided with recombination hotspots, telomeres, and gene-rich regions according to the function of the associated regulators. Our findings provide a global quantitative picture of the genetic architecture of chromatin regulation.
Zollinger-Ellison syndrome associated with neurofibromatosis type 1: a case report
Wan-Sik Lee, Yang-Seok Koh, Jung-Chul Kim, Chang-Hwan Park, Young-Eun Joo, Hyun-Soo Kim, Chol-Kyoon Cho, Sung-Kyu Choi, Jong-Sun Rew, Sei-Jong Kim
BMC Cancer , 2005, DOI: 10.1186/1471-2407-5-85
Abstract: A 41-year-old female affected by neurofibromatosis type 1 presented with a history of recurrent epigastric soreness, diarrhea, and relapsing chronic duodenal ulcer. Her serum fasting gastrin level was over 1000 pg/mL. An abdominal CT scan revealed a 3 × 2-cm, well-enhanced mass adjacent to the duodenal loop. She was not associated with multiple endocrine neoplasia type 1. Operative resection was performed and gastrinoma was diagnosed by immunohistochemical staining. The serum gastrin level decreased to 99.1 pg/mL after surgery, and symptoms and endoscopic findings completely resolved without recurrences.Gastrinoma is difficult to detect even in the general population, and hence symptoms such as recurrent idiopathic peptic ulcer and diarrhea in neurofibromatosis type 1 patients should be accounted for as possibly contributing to Zollinger-Ellison syndrome.Neurofibromatosis type 1 (NF1) is an autosomal dominant neurocutaneous disorder with an estimated prevalence of 2 to 3 cases per 10,000 population [1]. NF1 is characterized by neurocutaneous signs such as café-au-lait spots, axillary freckling, and cutaneous neurofibromas. Cognitive deficits and academic learning difficulties are the most common neurological complications of NF1 in childhood. Moreover, patients with NF1 are at an increased risk of developing nervous system neoplasms. Malignancy other than of nervous system origin can develop, with the prevalence of such malignant tumors reportedly being four times higher in NF1 patients than in the general population [2]. Gastrointestinal malignancy was reported to be associated with NF1 patients, with neuroendocrine tumors being the most prevalent [3]. However, there have been only one report about gastrinoma associated with NF1.Zollinger-Ellison syndrome (ZES) is characterized by hypersecretion of gastrin from a gastrinoma that leads to gastric acid hypersecretion and, most notably, clinical symptoms of refractory peptic ulcer disease. Zollinger and Ellison were t
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