Publications by authors named "Jin-Wu Nam"

43 Publications

An Inflammatory Loop Between Spleen-Derived Myeloid Cells and CD4 T Cells Leads to Accumulation of Long-Lived Plasma Cells That Exacerbates Lupus Autoimmunity.

Front Immunol 2021 11;12:631472. Epub 2021 Feb 11.

Laboratory of Autoimmunology, Department of Anatomy and Cell Biology, College of Medicine, Hanyang University, Seoul, South Korea.

Splenic long-lived plasma cells are abnormally numerous and deleterious in systemic autoimmune diseases, yet how they accumulate remains poorly understood. We demonstrate here that a pathological role of spleen-derived CD11bGr-1 myeloid cells (SDMCs) underpins the accumulation of splenic long-lived plasma cells in a lupus-prone model named sanroque. We found that SDMCs were progressively accumulated in sanroque mice from the early clinical phase. Transcriptome profiles revealed that SDMCs have a predominant shift toward an inflammatory phenotype relative to the bone marrow-derived counterparts and are distinct from neutrophils and monocytes. SDMCs were expanded via splenic extramedullary myelopoiesis under the proinflammatory cytokine milieu during lupus progression. SDMCs promoted the development of IFN-γ-secreting Th1 and follicular helper T cells, thereby licensing CD4 T cells to be pathologic activators of SDMCs and plasma cells. SDMCs also directly promoted the survival of plasma cells by providing B-cell activating factor of the TNF family. The frequency of SDMCs correlated with that of splenic long-lived plasma cells. Selective depletion of CD11bGr-1 cells reduced autoantibody production in sanroque mice. Thus, our findings suggest that SDMCs expanded establish a positive feedback loop with CD4 T cells, leading to accumulation of long-lived plasma cells which exacerbates lupus autoimmunity.
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http://dx.doi.org/10.3389/fimmu.2021.631472DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7904883PMC
February 2021

Author Correction: Comprehensive genome and transcriptome analyses reveal genetic relationship, selection signature, and transcriptome landscape of small-sized Korean native Jeju horse.

Sci Rep 2020 Oct 21;10(1):18383. Epub 2020 Oct 21.

Animal Genomics and Bioinformatics Division, National Institute of Animal Science, Rural Development Administration, Wanju, 55365, Republic of Korea.

An amendment to this paper has been published and can be accessed via a link at the top of the paper.
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http://dx.doi.org/10.1038/s41598-020-74979-wDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7577969PMC
October 2020

Single-cell transcriptome maps of myeloid blood cell lineages in Drosophila.

Nat Commun 2020 09 8;11(1):4483. Epub 2020 Sep 8.

Department of Life Sciences, College of Natural Science, Hanyang University, Seoul, 04736, Republic of Korea.

The Drosophila lymph gland, the larval hematopoietic organ comprised of prohemocytes and mature hemocytes, has been a valuable model for understanding mechanisms underlying hematopoiesis and immunity. Three types of mature hemocytes have been characterized in the lymph gland: plasmatocytes, lamellocytes, and crystal cells, which are analogous to vertebrate myeloid cells, yet molecular underpinnings of the lymph gland hemocytes have been less investigated. Here, we use single-cell RNA sequencing to comprehensively analyze heterogeneity of developing hemocytes in the lymph gland, and discover previously undescribed hemocyte types including adipohemocytes, stem-like prohemocytes, and intermediate prohemocytes. Additionally, we identify the developmental trajectory of hemocytes during normal development as well as the emergence of the lamellocyte lineage following active cellular immunity caused by wasp infestation. Finally, we establish similarities and differences between embryonically derived- and larval lymph gland hemocytes. Altogether, our study provides detailed insights into the hemocyte development and cellular immune responses at single-cell resolution.
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http://dx.doi.org/10.1038/s41467-020-18135-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7479620PMC
September 2020

A single-cell survey of blood.

Elife 2020 05 12;9. Epub 2020 May 12.

Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, United States.

blood cells, called hemocytes, are classified into plasmatocytes, crystal cells, and lamellocytes based on the expression of a few marker genes and cell morphologies, which are inadequate to classify the complete hemocyte repertoire. Here, we used single-cell RNA sequencing (scRNA-seq) to map hemocytes across different inflammatory conditions in larvae. We resolved plasmatocytes into different states based on the expression of genes involved in cell cycle, antimicrobial response, and metabolism together with the identification of intermediate states. Further, we discovered rare subsets within crystal cells and lamellocytes that express fibroblast growth factor (FGF) ligand and receptor , respectively. We demonstrate that these FGF components are required for mediating effective immune responses against parasitoid wasp eggs, highlighting a novel role for FGF signaling in inter-hemocyte crosstalk. Our scRNA-seq analysis reveals the diversity of hemocytes and provides a rich resource of gene expression profiles for a systems-level understanding of their functions.
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http://dx.doi.org/10.7554/eLife.54818DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7237219PMC
May 2020

CGD: Comprehensive guide designer for CRISPR-Cas systems.

Comput Struct Biotechnol J 2020 25;18:814-820. Epub 2020 Mar 25.

Department of Life Science, College of Natural Sciences, Hanyang University, Seoul 04763, Republic of Korea.

The Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)-Cas systems, including dead Cas9 (dCas9), Cas9, and Cas12a, have revolutionized genome engineering in mammalian somatic cells. Although computational tools that assess the target sites of CRISPR-Cas systems are inevitably important for designing efficient guide RNAs (gRNAs), they exhibit generalization issues in selecting features and do not provide optimal results in a comprehensive manner. Here, we introduce a Comprehensive Guide Designer (CGD) for four different CRISPR systems, which utilizes the machine learning algorithm, Elastic Net Logistic Regression (ENLOR), to autonomously generalize the models. CGD contains specific models trained with public datasets generated by CRISPRi, CRISPRa, CRISPR-Cas9, and CRISPR-Cas12a (designated as CGDi, CGDa, CGD9, and CGD12a, respectively) in an unbiased manner. The trained CGD models were benchmarked to other regression-based machine learning models, such as ElasticNet Linear Regression (ENLR), Random Forest and Boruta (RFB), and Extreme Gradient Boosting (Xgboost) with inbuilt feature selection. Evaluation with independent test datasets showed that CGD models outperformed the pre-existing methods in predicting the efficacy of gRNAs. All CGD source codes and datasets are available at GitHub (https://github.com/vipinmenon1989/CGD), and the CGD webserver can be accessed at http://big.hanyang.ac.kr:2195/CGD.
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http://dx.doi.org/10.1016/j.csbj.2020.03.020DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7152703PMC
March 2020

Mass Cytometry and Single-Cell RNA-seq Profiling of the Heterogeneity in Human Peripheral Blood Mononuclear Cells Interacting with Silver Nanoparticles.

Small 2020 05 12;16(21):e1907674. Epub 2020 Mar 12.

Center for Next Generation Cytometry, Hanyang University, Seoul, 04763, Republic of Korea.

Understanding the interactions between nanoparticles (NPs) and human immune cells is necessary for justifying their utilization in consumer products and biomedical applications. However, conventional assays may be insufficient in describing the complexity and heterogeneity of cell-NP interactions. Herein, mass cytometry and single-cell RNA-sequencing (scRNA-seq) are complementarily used to investigate the heterogeneous interactions between silver nanoparticles (AgNPs) and primary immune cells. Mass cytometry reveals the heterogeneous biodistribution of the positively charged polyethylenimine-coated AgNPs in various cell types and finds that monocytes and B cells have higher association with the AgNPs than other populations. scRNA-seq data of these two cell types demonstrate that each type has distinct responses to AgNP treatment: NRF2-mediated oxidative stress is confined to B cells, whereas monocytes show Fcγ-mediated phagocytosis. Besides the between-population heterogeneity, analysis of single-cell dose-response relationships further reveals within-population diversity for the B cells and naïve CD4 T cells. Distinct subsets having different levels of cellular responses with respect to their cellular AgNP doses are found. This study demonstrates that the complementary use of mass cytometry and scRNA-seq is helpful for gaining in-depth knowledge on the heterogeneous interactions between immune cells and NPs and can be incorporated into future toxicity assessments of nanomaterials.
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http://dx.doi.org/10.1002/smll.201907674DOI Listing
May 2020

HERES, a lncRNA that regulates canonical and noncanonical Wnt signaling pathways via interaction with EZH2.

Proc Natl Acad Sci U S A 2019 12 15;116(49):24620-24629. Epub 2019 Nov 15.

Department of Life Science, College of Natural Sciences, Hanyang University, 04763 Seoul, Republic of Korea;

Wnt signaling through both canonical and noncanonical pathways plays a core role in development. Dysregulation of these pathways often causes cancer development and progression. Although the pathways independently contribute to the core processes, a regulatory molecule that commonly activates both of them has not yet been reported. Here, we describe a long noncoding RNA (lncRNA), HERES, that epigenetically regulates both canonical and noncanonical Wnt signaling pathways in esophageal squamous cell carcinoma (ESCC). For this study, we performed RNA-seq analysis on Korean ESCC patients and validated these results on a larger ESCC cohort to identify lncRNAs commonly dysregulated in ESCCs. Six of the dysregulated lncRNAs were significantly associated with the clinical outcomes of ESCC patients and defined 4 ESCC subclasses with different prognoses. HERES reduction repressed cell proliferation, migration, invasion, and colony formation in ESCC cell lines and tumor growth in xenograft models. HERES appears to be a transacting factor that regulates , , and simultaneously to activate Wnt signaling pathways through an interaction with EZH2 via its G-quadruple structure-like motif. Our results suggest that HERES holds substantial potential as a therapeutic target for ESCC and probably other cancers caused by defects in Wnt signaling pathways.
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http://dx.doi.org/10.1073/pnas.1912126116DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6900598PMC
December 2019

Comprehensive genome and transcriptome analyses reveal genetic relationship, selection signature, and transcriptome landscape of small-sized Korean native Jeju horse.

Sci Rep 2019 11 13;9(1):16672. Epub 2019 Nov 13.

Animal Genomics and Bioinformatics Division, National Institute of Animal Science, Rural Development Administration, Wanju, 55365, Republic of Korea.

The Jeju horse, indigenous to the Jeju Island in Korea may have originated from Mongolian horses. Adaptations to the local harsh environment have conferred Jeju horse with unique traits such as small-sized body, stocky head, and shorter limbs. These characteristics have not been studied previously at the genomic level. Therefore, we sequenced and compared the genome of 41 horses belonging to 6 breeds. We identified numerous breed-specific non-synonymous SNPs and loss-of-function mutants. Demographic and admixture analyses showed that, though Jeju horse is genetically the closest to the Mongolian breeds, its genetic ancestry is independent of that of the Mongolian breeds. Genome wide selection signature analysis revealed that genes such as LCORL, MSTN, HMGA2, ZFAT, LASP1, PDK4, and ACTN2, were positively selected in the Jeju horse. RNAseq analysis showed that several of these genes were also differentially expressed in Jeju horse compared to Thoroughbred horse. Comparative muscle fiber analysis showed that, the type I muscle fibre content was substantially higher in Jeju horse compared to Thoroughbred horse. Our results provide insights about the selection of complex phenotypic traits in the small-sized Jeju horse and the novel SNPs identified will aid in designing high-density SNP chip for studying other native horse breeds.
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http://dx.doi.org/10.1038/s41598-019-53102-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6853925PMC
November 2019

UPF1/SMG7-dependent microRNA-mediated gene regulation.

Nat Commun 2019 09 13;10(1):4181. Epub 2019 Sep 13.

Department of Life Science, College of Natural Sciences, Hanyang University, Seoul, Republic of Korea.

The stability and quality of metazoan mRNAs are under microRNA (miRNA)-mediated and nonsense-mediated control. Although UPF1, a core mediator of nonsense-mediated mRNA decay (NMD), mediates the decay of target mRNA in a 3'UTR-length-dependent manner, the detailed mechanism remains unclear. Here, we suggest that 3'UTR-length-dependent mRNA decay is not mediated by nonsense mRNAs but rather by miRNAs that downregulate target mRNAs via Ago-associated UPF1/SMG7. Global analyses of mRNAs in response to UPF1 RNA interference in miRNA-deficient cells reveal that 3'UTR-length-dependent mRNA decay by UPF1 requires canonical miRNA targeting. The destabilization of miRNA targets is accomplished by the combination of Ago2 and UPF1/SMG7, which may recruit the CCR4-NOT deadenylase complex. Indeed, loss of the SMG7-deadenylase complex interaction increases the levels of transcripts regulated by UPF1-SMG7. This UPF1/SMG7-dependent miRNA-mediated mRNA decay pathway may enable miRNA targeting to become more predictable and expand the miRNA-mRNA regulatory network.
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http://dx.doi.org/10.1038/s41467-019-12123-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6744440PMC
September 2019

Assessment of Inflammation in Pulmonary Artery Hypertension by Ga-Mannosylated Human Serum Albumin.

Am J Respir Crit Care Med 2020 01;201(1):95-106

Cardiovascular Center, Seoul National University Hospital, Seoul, Republic of Korea.

Diagnosis and monitoring of patients with pulmonary artery hypertension (PAH) is currently difficult. We aimed to develop a noninvasive imaging modality for PAH that tracks the infiltration of macrophages into the pulmonary vasculature, using a positron emission tomography (PET) agent, Ga-2-(-isothiocyanatobenzyl)-1,4,7-triazacyclononane-1,4,7-triacetic acid (NOTA) mannosylated human serum albumin (MSA), that targets the mannose receptor (MR). We induced PAH in rats by monocrotaline injection. Tissue analysis, echocardiography, and Ga-NOTA-MSA PET were performed weekly in rats after monocrotaline injection and in those treated with either sildenafil or macitentan. The translational potential of Ga-NOTA-MSA PET was explored in patients with PAH. Gene sets related to macrophages were significantly enriched on whole transcriptome sequencing of the lung tissue in PAH rats. Serial PET images of PAH rats demonstrated increasing uptake of Ga-NOTA-MSA in the lung by time that corresponded with the MR-positive macrophage recruitment observed in immunohistochemistry. In sildenafil- or macitentan-treated PAH rats, the infiltration of MR-positive macrophages by histology and the uptake of Ga-NOTA-MSA on PET was significantly lower than that of the PAH-only group. The pulmonary uptake of Ga-NOTA-MSA was significantly higher in patients with PAH than normal subjects ( = 0.009) or than those with pulmonary hypertension by left heart disease ( = 0.019) ( = 5 per group).Ga-NOTA-MSA PET can help diagnose PAH and monitor the inflammatory status by imaging the degree of macrophage infiltration into the lung. These observations suggest that Ga-NOTA-MSA PET has the potential to be used as a novel noninvasive diagnostic and monitoring tool of PAH.
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http://dx.doi.org/10.1164/rccm.201903-0639OCDOI Listing
January 2020

En bloc and segmental deletions of human XIST reveal X chromosome inactivation-involving RNA elements.

Nucleic Acids Res 2019 05;47(8):3875-3887

Department of Life Science, College of Natural Sciences, Hanyang University, Seoul 04763, Republic of Korea.

The XIST RNA is a non-coding RNA that induces X chromosome inactivation (XCI). Unlike the mouse Xist RNA, how the human XIST RNA controls XCI in female cells is less well characterized, and its functional motifs remain unclear. To systematically decipher the XCI-involving elements of XIST RNA, 11 smaller XIST segments, including repeats A, D and E; human-specific repeat elements; the promoter; and non-repetitive exons, as well as the entire XIST gene, were homozygously deleted in K562 cells using the Cas9 nuclease and paired guide RNAs at high efficiencies, followed by high-throughput RNA sequencing and RNA fluorescence in situ hybridization experiments. Clones containing en bloc and promoter deletions that consistently displayed no XIST RNAs and a global up-regulation of X-linked genes confirmed that the deletion of XIST reactivates the inactive X chromosome. Systematic analyses of segmental deletions delineated that exon 5 harboring the non-repeat element is important for X-inactivation maintenance, whereas exons 2, 3 and 4 as well as the other repeats in exon 1 are less important, a different situation from that of mouse Xist. This Cas9-assisted dissection of XIST allowed us to understand the unique functional domains within the human XIST RNA.
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http://dx.doi.org/10.1093/nar/gkz109DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6486550PMC
May 2019

Transcriptome Analysis Reveals Nonfoamy Rather Than Foamy Plaque Macrophages Are Proinflammatory in Atherosclerotic Murine Models.

Circ Res 2018 10;123(10):1127-1142

From the Department of Life Sciences (K.K., D.S., M.-Y.J., H.S.J., S.H.L., S.-H.Y., J.W.N., J.-H.C.), College of Natural Sciences, Research Institute for Natural Sciences, Hanyang University, Seoul, Republic of Korea.

Rationale: Monocyte infiltration into the subintimal space and its intracellular lipid accumulation are the most prominent features of atherosclerosis. To understand the pathophysiology of atherosclerotic disease, we need to understand the characteristics of lipid-laden foamy macrophages in the subintimal space during atherosclerosis.

Objective: We sought to examine the transcriptomic profiles of foamy and nonfoamy macrophages isolated from atherosclerotic intima.

Methods And Results: Single-cell RNA sequencing analysis of CD45 leukocytes from murine atherosclerotic aorta revealed that there are macrophage subpopulations with distinct differentially expressed genes involved in various functional pathways. To specifically characterize the intimal foamy macrophages of plaque, we developed a lipid staining-based flow cytometric method for analyzing the lipid-laden foam cells of atherosclerotic aortas. We used the fluorescent lipid probe BODIPY493/503 and assessed side-scattered light as an indication of cellular granularity. BODIPYSSC foamy macrophages were found residing in intima and expressing CD11c. Foamy macrophage accumulation determined by flow cytometry was positively correlated with the severity of atherosclerosis. Bulk RNA sequencing analysis showed that compared with nonfoamy macrophages, foamy macrophages expressed few inflammatory genes but many lipid-processing genes. Intimal nonfoamy macrophages formed the major population expressing IL (interleukin)-1β and many other inflammatory transcripts in atherosclerotic aorta.

Conclusions: RNA sequencing analysis of intimal macrophages from atherosclerotic aorta revealed that lipid-loaded plaque macrophages are not likely the plaque macrophages that drive lesional inflammation.
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http://dx.doi.org/10.1161/CIRCRESAHA.118.312804DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6945121PMC
October 2018

HuR stabilizes a polyadenylated form of replication-dependent histone mRNAs under stress conditions.

FASEB J 2019 02 10;33(2):2680-2693. Epub 2018 Oct 10.

Creative Research Initiatives Center for Molecular Biology of Translation, Korea University, Seoul, South Korea.

All metazoan mRNAs have a poly(A) tail at the 3' end with the exception of replication-dependent histone (RDH) mRNAs, which end in a highly conserved stem-loop (SL) structure. However, a subset of RDH mRNAs are reported to be polyadenylated under physiologic conditions. The molecular details of the biogenesis of polyadenylated RDH [poly(A) RDH] mRNAs remain unknown. In this study, our genome-wide analyses reveal that puromycin treatment or UVC irradiation stabilizes poly(A) RDH mRNAs, relative to canonical RDH mRNAs, which end in an SL structure. We demonstrate that the stabilization of poly(A) RDH mRNAs occurs in a translation-independent manner and is regulated via human antigen R (HuR) binding to the extended 3' UTR under stress conditions. Our data suggest that HuR regulates the expression of poly(A) RDH mRNAs.-Ryu, I., Park, Y., Seo, J.-W., Park, O. H., Ha, H., Nam, J.-W., Kim, Y. K. HuR stabilizes a polyadenylated form of replication-dependent histone mRNAs under stress conditions.
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http://dx.doi.org/10.1096/fj.201800431RDOI Listing
February 2019

Non-Coding Transcriptome Maps across Twenty Tissues of the Korean Black Chicken, Yeonsan Ogye.

Int J Mol Sci 2018 Aug 10;19(8). Epub 2018 Aug 10.

Department of Life Science, College of Natural Sciences, Hanyang University, Seoul 133791, Korea.

Yeonsan Ogye is a rare Korean domestic chicken breed whose entire body, including feathers and skin, has a unique black coloring. Although some protein-coding genes related to this unique feature have been examined, non-coding elements have not been widely investigated. Thus, we evaluated coding and non-coding transcriptome expression and identified long non-coding RNAs functionally linked to protein-coding genes in Ogye. High-throughput RNA sequencing and DNA methylation sequencing were performed to profile the expression of 14,264 Ogye protein-coding and 6900 long non-coding RNA (lncRNA) genes and detect DNA methylation in 20 different tissues of an individual Ogye. Approximately 75% of Ogye lncRNAs and 45% of protein-coding genes showed tissue-specific expression. For some genes, tissue-specific expression levels were inversely correlated with DNA methylation levels in their promoters. Approximately 39% of tissue-specific lncRNAs displayed functional associations with proximal or distal protein-coding genes. Heat shock transcription factor 2-associated lncRNAs appeared to be functionally linked to protein-coding genes specifically expressed in black skin tissues, more syntenically conserved in mammals, and differentially expressed in black relative to in white tissues. Pending experimental validation, our findings increase the understanding of how the non-coding genome regulates unique phenotypes and can be used for future genomic breeding of chickens.
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http://dx.doi.org/10.3390/ijms19082359DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6121550PMC
August 2018

Whole genome and transcriptome maps of the entirely black native Korean chicken breed Yeonsan Ogye.

Gigascience 2018 07;7(7)

Department of Life Science, Hanyang University, Seoul, 133-791, Republic of Korea.

Background: Yeonsan Ogye (YO), an indigenous Korean chicken breed (Gallus gallus domesticus), has entirely black external features and internal organs. In this study, the draft genome of YO was assembled using a hybrid de novo assembly method that takes advantage of high-depth Illumina short reads (376.6X) and low-depth Pacific Biosciences (PacBio) long reads (9.7X).

Findings: The contig and scaffold NG50s of the hybrid de novo assembly were 362.3 Kbp and 16.8 Mbp, respectively. The completeness (97.6%) of the draft genome (Ogye_1.1) was evaluated with single-copy orthologous genes using Benchmarking Universal Single-Copy Orthologs and found to be comparable to the current chicken reference genome (galGal5; 97.4%; contigs were assembled with high-depth PacBio long reads (50X) and scaffolded with short reads) and superior to other avian genomes (92%-93%; assembled with short read-only or hybrid methods). Compared to galGal4 and galGal5, the draft genome included 551 structural variations including the fibromelanosis (FM) locus duplication, related to hyperpigmentation. To comprehensively reconstruct transcriptome maps, RNA sequencing and reduced representation bisulfite sequencing data were analyzed from 20 tissues, including 4 black tissues (skin, shank, comb, and fascia). The maps included 15,766 protein-coding and 6,900 long noncoding RNA genes, many of which were tissue-specifically expressed and displayed tissue-specific DNA methylation patterns in the promoter regions.

Conclusions: We expect that the resulting genome sequence and transcriptome maps will be valuable resources for studying domestic chicken breeds, including black-skinned chickens, as well as for understanding genomic differences between breeds and the evolution of hyperpigmented chickens and functional elements related to hyperpigmentation.
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http://dx.doi.org/10.1093/gigascience/giy086DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6065499PMC
July 2018

The small peptide world in long noncoding RNAs.

Brief Bioinform 2019 09;20(5):1853-1864

Department of Life Science, College of Natural Sciences, Hanyang University, Seoul 04763, Republic of Korea.

Long noncoding RNAs (lncRNAs) are a group of transcripts that are longer than 200 nucleotides (nt) without coding potential. Over the past decade, tens of thousands of novel lncRNAs have been annotated in animal and plant genomes because of advanced high-throughput RNA sequencing technologies and with the aid of coding transcript classifiers. Further, a considerable number of reports have revealed the existence of stable, functional small peptides (also known as micropeptides), translated from lncRNAs. In this review, we discuss the methods of lncRNA classification, the investigations regarding their coding potential and the functional significance of the peptides they encode.
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http://dx.doi.org/10.1093/bib/bby055DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6917221PMC
September 2019

TERIUS: accurate prediction of lncRNA via high-throughput sequencing data representing RNA-binding protein association.

BMC Bioinformatics 2018 02 19;19(Suppl 1):41. Epub 2018 Feb 19.

Department of Life Science, College of Natural Sciences, Hanyang University, Seoul, 04763, Republic of Korea.

Background: LncRNAs are long regulatory non-coding RNAs, some of which are arguably predicted to have coding potential. Despite coding potential classifiers that utilize ribosome profiling data successfully detected actively translated regions, they are less sensitive to lncRNAs. Furthermore, lncRNA annotation can be susceptible to false positives obtained from 3' untranslated region (UTR) fragments of mRNAs.

Results: To lower these limitations in lncRNA annotation, we present a novel tool TERIUS that provides a two-step filtration process to distinguish between bona fide and false lncRNAs. The first step successfully separates lncRNAs from protein-coding genes showing enhanced sensitivity compared to other methods. To eliminate 3'UTR fragments, the second step takes advantage of the 3'UTR-specific association with regulator of nonsense transcripts 1 (UPF1), leading to refined lncRNA annotation. Importantly, TERIUS enabled the detection of misclassified transcripts in published lncRNA annotations.

Conclusions: TERIUS is a robust method for lncRNA annotation, which provides an additional filtration step for 3'UTR fragments. TERIUS was able to successfully re-classify GENCODE and miTranscriptome lncRNA annotations. We believe that TERIUS can benefit construction of extensive and accurate non-coding transcriptome maps in many genomes.
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http://dx.doi.org/10.1186/s12859-018-2013-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5836835PMC
February 2018

The long noncoding RNA LUCAT1 promotes tumorigenesis by controlling ubiquitination and stability of DNA methyltransferase 1 in esophageal squamous cell carcinoma.

Cancer Lett 2018 03 14;417:47-57. Epub 2017 Dec 14.

Brain Korea 21 PLUS Project for Medical Science, Yonsei University, Republic of Korea; Division of Gastroenterology, Institute of Gastroenterology, Department of Internal Medicine, Yonsei University College of Medicine, Severance Hospital, Seoul, Republic of Korea. Electronic address:

Available targeted therapies for esophageal squamous cell carcinoma (ESCC) are limited; thus, further genetic and epigenetic studies are needed. Recently, many long noncoding RNAs (lncRNAs) have been reported to be involved in various cancers. Here, we investigated whether the lncRNA LUCAT1 was related to the carcinogenesis of ESCC based on previous studies in lung cancer. LUCAT1 was significantly upregulated in ESCC cell lines and cancer tissue compared with normal cells and adjacent normal tissues. LUCAT1 knockdown reduced cell proliferation, induced apoptosis, and upregulated tumor-suppressor genes by reducing DNA methylation in KYSE-30 cells. Moreover, LUCAT1 siRNA reduced DNA methyltransferase 1 (DNMT1) protein levels without affecting transcription. Patients with high LUCAT1 expression had significantly lower survival rates than patients with low LUCAT1 expression. Our results thus suggest that LUCAT1 regulates the stability of DNMT1 and inhibits the expression of tumor suppressors through DNA methylation, leading to the formation and metastasis of ESCC. We identified LUCAT1 as a potential target for drug development and as a biomarker for ESCC.
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http://dx.doi.org/10.1016/j.canlet.2017.12.016DOI Listing
March 2018

Targeted exome sequencing of Korean triple-negative breast cancer reveals homozygous deletions associated with poor prognosis of adjuvant chemotherapy-treated patients.

Oncotarget 2017 Sep 27;8(37):61538-61550. Epub 2017 Jun 27.

Department of Pharmacy, College of Pharmacy, Seoul National University, Seoul, South Korea.

Triple-negative breast cancer is characterized by the absence of estrogen and progesterone receptors and human epidermal growth factor receptor 2, and is associated with a poorer outcome than other subtypes of breast cancer. Moreover, there are no accurate prognostic genes or effective therapeutic targets, thereby necessitating continued intensive investigation. This study analyzed the genetic mutation landscape in 70 patients with triple-negative breast cancer by targeted exome sequencing of tumor and matched normal samples. Sequencing showed that more than 50% of these patients had deleterious mutations and homozygous deletions of DNA repair genes, such as , , , , and . These findings suggested that a large number of patients with triple-negative breast cancer have impaired DNA repair function and that therefore a poly ADP-ribose polymerase inhibitor may be an effective drug in the treatment of this disease. Notably, homozygous deletion of three genes, , , and 3, was significantly associated with an increased risk of recurrence or distant metastasis in adjuvant chemotherapy-treated patients.
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http://dx.doi.org/10.18632/oncotarget.18618DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5617443PMC
September 2017

DROSHA targets its own transcript to modulate alternative splicing.

RNA 2017 07 11;23(7):1035-1047. Epub 2017 Apr 11.

Department of Agricultural Biotechnology, Seoul National University, Seoul 08826, Republic of Korea.

The nuclear RNase III enzyme DROSHA interacts with its cofactor DGCR8 to form the Microprocessor complex, which initiates microRNA (miRNA) maturation by cleaving hairpin structures embedded in primary transcripts. Apart from its central role in the biogenesis of miRNAs, DROSHA is also known to recognize and cleave miRNA-like hairpins in a subset of transcripts without apparent small RNA production. Here, we report that the human transcript is one such noncanonical target of DROSHA. Mammalian genes have evolved a conserved hairpin structure spanning a specific exon-intron junction, which serves as a substrate for the Microprocessor in human cells but not in murine cells. We show that it is this hairpin element that decides whether the overlapping exon is alternatively or constitutively spliced. We further demonstrate that DROSHA promotes skipping of the overlapping exon in human cells independently of its cleavage function. Our findings add to the expanding list of noncanonical DROSHA functions.
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http://dx.doi.org/10.1261/rna.059808.116DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5473138PMC
July 2017

High-confidence coding and noncoding transcriptome maps.

Genome Res 2017 06 10;27(6):1050-1062. Epub 2017 Apr 10.

Department of Life Science, College of Natural Sciences, Hanyang University, Seoul 133791, Republic of Korea.

The advent of high-throughput RNA sequencing (RNA-seq) has led to the discovery of unprecedentedly immense transcriptomes encoded by eukaryotic genomes. However, the transcriptome maps are still incomplete partly because they were mostly reconstructed based on RNA-seq reads that lack their orientations (known as unstranded reads) and certain boundary information. Methods to expand the usability of unstranded RNA-seq data by predetermining the orientation of the reads and precisely determining the boundaries of assembled transcripts could significantly benefit the quality of the resulting transcriptome maps. Here, we present a high-performing transcriptome assembly pipeline, called CAFE, that significantly improves the original assemblies, respectively assembled with stranded and/or unstranded RNA-seq data, by orienting unstranded reads using the maximum likelihood estimation and by integrating information about transcription start sites and cleavage and polyadenylation sites. Applying large-scale transcriptomic data comprising 230 billion RNA-seq reads from the ENCODE, Human BodyMap 2.0, The Cancer Genome Atlas, and GTEx projects, CAFE enabled us to predict the directions of about 220 billion unstranded reads, which led to the construction of more accurate transcriptome maps, comparable to the manually curated map, and a comprehensive lncRNA catalog that includes thousands of novel lncRNAs. Our pipeline should not only help to build comprehensive, precise transcriptome maps from complex genomes but also to expand the universe of noncoding genomes.
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http://dx.doi.org/10.1101/gr.214288.116DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5453319PMC
June 2017

Post-transcriptional and translational regulation of mRNA-like long non-coding RNAs by microRNAs in early developmental stages of zebrafish embryos.

BMB Rep 2017 Apr;50(4):226-231

Department of Life Science, College of Natural Sciences, Hanyang University; Research Institute for Natural Sciences, Hanyang University; Research Institute for Convergence of Basic Sciences, Hanyang University, Seoul 133791, Korea.

At the post-transcriptional and translational levels, microRNA (miRNA) represses protein-coding genes via seed pairing to the 3' untranslated regions (UTRs) of mRNA. Although working models of miRNA-mediated gene silencing are successfully established using miRNA transfections and knockouts, the regulatory interaction between miRNA and long non-coding RNA (lncRNA) remain unknown. In particular, how the mRNA-resembling lncRNAs with 5' cap, 3' poly(A)-tail, or coding features, are regulated by miRNA is yet to be examined. We therefore investigated the functional interaction between miRNAs and lncRNAs with/without those features, in miRNAtransfected early zebrafish embryos. We observed that the greatest determinants of the miRNA-mediated silencing of lncRNAs were the 5' cap and 3' poly(A)-tails in lncRNAs, at both the post-transcriptional and translational levels. The lncRNAs confirmed to contain 5' cap, 3' poly(A)-tail, and the canonical miRNA target sites, were observed to be repressed in the level of both RNA and ribosome-protected fragment, while those with the miRNA target sites and without 5' cap and 3' poly(A)-tail, were not robustly repressed by miRNA introduction, thus suggesting a role as a miRNA-decoy. [BMB Reports 2017; 50(4): 226-231].
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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5437968PMC
http://dx.doi.org/10.5483/bmbrep.2017.50.4.025DOI Listing
April 2017

In vivo high-throughput profiling of CRISPR-Cpf1 activity.

Nat Methods 2017 02 19;14(2):153-159. Epub 2016 Dec 19.

Department of Pharmacology, Yonsei University College of Medicine, Seoul, South Korea.

CRISPR from Prevotella and Francisella 1 (Cpf1) is an effector endonuclease of the class 2 CRISPR-Cas (clustered regularly interspaced short palindromic repeats-CRISPR-associated proteins) gene editing system. We developed a method for evaluating Cpf1 activity, based on target sequence composition in mammalian cells, in a high-throughput manner. A library of >11,000 target sequence and guide RNA pairs was delivered into human cells using lentiviral vectors. Subsequent delivery of Cpf1 into this cell library induced insertions and deletions (indels) at the integrated synthetic target sequences, which allowed en masse evaluation of Cpf1 activity by using deep sequencing. With this approach, we determined protospacer-adjacent motif sequences of two Cpf1 nucleases, one from Acidaminococcus sp. BV3L6 (hereafter referred to as AsCpf1) and the other from Lachnospiraceae bacterium ND2006 (hereafter referred to as LbCpf1). We also defined target-sequence-dependent activity profiles of AsCpf1, which enabled the development of a web tool that predicts the indel frequencies for given target sequences (http://big.hanyang.ac.kr/cindel). Both the Cpf1 characterization profile and the in vivo high-throughput evaluation method will greatly facilitate Cpf1-based genome editing.
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http://dx.doi.org/10.1038/nmeth.4104DOI Listing
February 2017

Measuring intratumor heterogeneity by network entropy using RNA-seq data.

Sci Rep 2016 11 24;6:37767. Epub 2016 Nov 24.

Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul, 151-742, Korea.

Intratumor heterogeneity (ITH) is observed at different stages of tumor progression, metastasis and reouccurence, which can be important for clinical applications. We used RNA-sequencing data from tumor samples, and measured the level of ITH in terms of biological network states. To model complex relationships among genes, we used a protein interaction network to consider gene-gene dependency. ITH was measured by using an entropy-based distance metric between two networks, nJSD, with Jensen-Shannon Divergence (JSD). With nJSD, we defined transcriptome-based ITH (tITH). The effectiveness of tITH was extensively tested for the issues related with ITH using real biological data sets. Human cancer cell line data and single-cell sequencing data were investigated to verify our approach. Then, we analyzed TCGA pan-cancer 6,320 patients. Our result was in agreement with widely used genome-based ITH inference methods, while showed better performance at survival analysis. Analysis of mouse clonal evolution data further confirmed that our transcriptome-based ITH was consistent with genetic heterogeneity at different clonal evolution stages. Additionally, we found that cell cycle related pathways have significant contribution to increasing heterogeneity on the network during clonal evolution. We believe that the proposed transcriptome-based ITH is useful to characterize heterogeneity of a tumor sample at RNA level.
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http://dx.doi.org/10.1038/srep37767DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5121893PMC
November 2016

The present and future of de novo whole-genome assembly.

Brief Bioinform 2018 01;19(1):23-40

As the advent of next-generation sequencing (NGS) technology, various de novo assembly algorithms based on the de Bruijn graph have been developed to construct chromosome-level sequences. However, numerous technical or computational challenges in de novo assembly still remain, although many bright ideas and heuristics have been suggested to tackle the challenges in both experimental and computational settings. In this review, we categorize de novo assemblers on the basis of the type of de Bruijn graphs (Hamiltonian and Eulerian) and discuss the challenges of de novo assembly for short NGS reads regarding computational complexity and assembly ambiguity. Then, we discuss how the limitations of the short reads can be overcome by using a single-molecule sequencing platform that generates long reads of up to several kilobases. In fact, the long read assembly has caused a paradigm shift in whole-genome assembly in terms of algorithms and supporting steps. We also summarize (i) hybrid assemblies using both short and long reads and (ii) overlap-based assemblies for long reads and discuss their challenges and future prospects. This review provides guidelines to determine the optimal approach for a given input data type, computational budget or genome.
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http://dx.doi.org/10.1093/bib/bbw096DOI Listing
January 2018

LIN28A enhances the therapeutic potential of cultured neural stem cells in a Parkinson's disease model.

Brain 2016 Oct 18;139(Pt 10):2722-2739. Epub 2016 Aug 18.

1 Department of Biochemistry and Molecular Biology, College of Medicine, Hanyang University, 222 Wangsimni-ro, Seongdong-gu, Seoul, 04763, Korea 2 Hanyang Biomedical Research Institute, Hanyang University, 222 Wangsimni-ro, Seongdong-gu, Seoul, 04763, Korea 3 Graduate School of Biomedical Science and Engineering, Hanyang University, 222 Wangsimni-ro, Seongdong-gu, Seoul, 04763, Korea

The original properties of tissue-specific stem cells, regardless of their tissue origins, are inevitably altered during in vitro culturing, lessening the clinical and research utility of stem cell cultures. Specifically, neural stem cells derived from the ventral midbrain lose their dopamine neurogenic potential, ventral midbrain-specific phenotypes, and repair capacity during in vitro cell expansion, all of which are critical concerns in using the cultured neural stem cells in therapeutic approaches for Parkinson's disease. In this study, we observed that the culture-dependent changes of neural stem cells derived from the ventral midbrain coincided with loss of RNA-binding protein LIN28A expression. When LIN28A expression was forced and sustained during neural stem cell expansion using an inducible expression-vector system, loss of dopamine neurogenic potential and midbrain phenotypes after long-term culturing was blocked. Furthermore, dopamine neurons that differentiated from neural stem cells exhibited remarkable survival and resistance against toxic insults. The observed effects were not due to a direct action of LIN28A on the differentiated dopamine neurons, but rather its action on precursor neural stem cells as exogene expression was switched off in the differentiating/differentiated cultures. Remarkable and reproducible behavioural recovery was shown in all Parkinson's disease rats grafted with neural stem cells expanded with LIN28A expression, along with extensive engraftment of dopamine neurons expressing mature neuronal and midbrain-specific markers. These findings suggest that LIN28A expression during stem cell expansion could be used to prepare therapeutically competent donor cells.
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http://dx.doi.org/10.1093/brain/aww203DOI Listing
October 2016

Incredible RNA: Dual Functions of Coding and Noncoding.

Mol Cells 2016 May 3;39(5):367-74. Epub 2016 May 3.

Department of Life Science, College of Natural Sciences, Hanyang University, Seoul 04763, Korea.

Since the RNA world hypothesis was proposed, a large number of regulatory noncoding RNAs (ncRNAs) have been identified in many species, ranging from microorganisms to mammals. During the characterization of these newly discovered RNAs, RNAs having both coding and noncoding functions were discovered, and these were considered bifunctional RNAs. The recent use of computational and high-throughput experimental approaches has revealed increasing evidence of various sources of bifunctional RNAs, such as protein-coding mRNAs with a noncoding isoform and long ncRNAs bearing a small open reading frame. Therefore, the genomic diversity of Janus-faced RNA molecules that have dual characteristics of coding and noncoding indicates that the functional roles of RNAs have to be revisited in cells on a genome-wide scale. Such studies would allow us to further understand the complex gene-regulatory network in cells. In this review, we discuss three major genomic sources of bifunctional RNAs and present a handful of examples of bifunctional RNA along with their functional roles.
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http://dx.doi.org/10.14348/molcells.2016.0039DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4870183PMC
May 2016

Pseudo-Reference-Based Assembly of Vertebrate Transcriptomes.

Genes (Basel) 2016 Feb 24;7(3). Epub 2016 Feb 24.

Department of Life Science, College of Natural Sciences, Hanyang University, Seoul 04763, Korea.

High-throughput RNA sequencing (RNA-seq) provides a comprehensive picture of the transcriptome, including the identity, structure, quantity, and variability of expressed transcripts in cells, through the assembly of sequenced short RNA-seq reads. Although the reference-based approach guarantees the high quality of the resulting transcriptome, this approach is only applicable when the relevant reference genome is present. Here, we developed a pseudo-reference-based assembly (PRA) that reconstructs a transcriptome based on a linear regression function of the optimized mapping parameters and genetic distances of the closest species. Using the linear model, we reconstructed transcriptomes of four different aves, the white leg horn, turkey, duck, and zebra finch, with the Gallus gallus genome as a pseudo-reference, and of three primates, the chimpanzee, gorilla, and macaque, with the human genome as a pseudo-reference. The resulting transcriptomes show that the PRAs outperformed the de novo approach for species with within about 10% mutation rate among orthologous transcriptomes, enough to cover distantly related species as far as chicken and duck. Taken together, we suggest that the PRA method can be used as a tool for reconstructing transcriptome maps of vertebrates whose genomes have not yet been sequenced.
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http://dx.doi.org/10.3390/genes7030010DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4808791PMC
February 2016

The expression and functional roles of microRNAs in stem cell differentiation.

BMB Rep 2016 Jan;49(1):3-10

Department of Life Science, College of Natural Sciences and Research Institute of Natural Sciences, Hanyang University, Seoul 04763, Korea.

microRNAs (miRNAs) are key regulators of cell state transition and retention during stem cell proliferation and differentiation by post-transcriptionally downregulating hundreds of conserved target genes via seed-pairing in their 3' untranslated region. In embryonic and adult stem cells, dozens of miRNAs that elaborately control stem cell processes by modulating the transcriptomic context therein have been identified. Some miRNAs accelerate the change of cell state into progenitor cell lineages-such as myoblast, myeloid or lymphoid progenitors, and neuro precursor stem cells-and other miRNAs decelerate the change but induce proliferative activity, resulting in cell state retention. This cell state choice can be controlled by endogenously or exogenously changing miRNA levels or by including or excluding target sites. This control of miRNA-mediated gene regulation could improve our understanding of stem cell biology and facilitate their development as therapeutic tools.
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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4914210PMC
http://dx.doi.org/10.5483/BMBRep.2016.49.1.217DOI Listing
January 2016

Predicting effective microRNA target sites in mammalian mRNAs.

Elife 2015 Aug 12;4. Epub 2015 Aug 12.

Howard Hughes Medical Institute, Whitehead Institute for Biomedical Research, Cambridge, United States.

MicroRNA targets are often recognized through pairing between the miRNA seed region and complementary sites within target mRNAs, but not all of these canonical sites are equally effective, and both computational and in vivo UV-crosslinking approaches suggest that many mRNAs are targeted through non-canonical interactions. Here, we show that recently reported non-canonical sites do not mediate repression despite binding the miRNA, which indicates that the vast majority of functional sites are canonical. Accordingly, we developed an improved quantitative model of canonical targeting, using a compendium of experimental datasets that we pre-processed to minimize confounding biases. This model, which considers site type and another 14 features to predict the most effectively targeted mRNAs, performed significantly better than existing models and was as informative as the best high-throughput in vivo crosslinking approaches. It drives the latest version of TargetScan (v7.0; targetscan.org), thereby providing a valuable resource for placing miRNAs into gene-regulatory networks.
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http://dx.doi.org/10.7554/eLife.05005DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4532895PMC
August 2015