Human cytomegalovirus microRNA miR-US4-1 inhibits CD8⁺ T cell responses by targeting the aminopeptidase ERAP1

Kim, Sungchul,Lee, Sanghyun,Shin, Jinwook,Kim, Youngkyun,Evnouchidou, Irini,Kim, Donghyun,Kim, Young-Kook,Kim, Young-Eui,Ahn, Jin-Hyun,Riddell, Stanley R,Stratikos, Efstratios,Kim, V Narry,Ahn, Kwangs Nature Publishing Group, a division of Macmillan P 2011 NATURE IMMUNOLOGY Vol.12 No.10

Major histocompatibility complex (MHC) class I molecules present peptides on the cell surface to CD8<SUP>+</SUP> T cells, which is critical for the killing of virus-infected or transformed cells. Precursors of MHC class I??presented peptides are trimmed to mature epitopes by the aminopeptidase ERAP1. The US2??US11 genomic region of human cytomegalovirus (HCMV) is dispensable for viral replication and encodes three microRNAs (miRNAs). We show here that HCMV miR-US4-1 specifically downregulated ERAP1 expression during viral infection. Accordingly, the trimming of HCMV-derived peptides was inhibited, which led to less susceptibility of infected cells to HCMV-specific cytotoxic T lymphocytes (CTLs). Our findings identify a previously unknown viral miRNA??based CTL-evasion mechanism that targets a key step in the MHC class I antigen-processing pathway.

The co-regulation mechanism of transcription factors in the human gene regulatory network

Kim, Junil,Choi, Minsoo,Kim, Jeong-Rae,Jin, Hua,Kim, V. Narry,Cho, Kwang-Hyun Oxford University Press 2012 Nucleic acids research Vol.40 No.18

<P>The co-regulation of transcription factors (TFs) has been widely observed in various species. Why is such a co-regulation mechanism needed for transcriptional regulation? To answer this question, the following experiments and analyses were performed. First, examination of the human gene regulatory network (GRN) indicated that co-regulation was significantly enriched in the human GRN. Second, mathematical simulation of an artificial regulatory network showed that the co-regulation mechanism was related to the biphasic dose–response patterns of TFs. Third, the relationship between the co-regulation mechanism and the biphasic dose–response pattern was confirmed using microarray experiments examining different time points and different doses of the toxicant tetrachlorodibenzodioxin. Finally, two mathematical models were constructed to mimic highly co-regulated networks (HCNs) and little co-regulated networks (LCNs), and we found that HCNs were more robust to parameter perturbation than LCNs, whereas LCNs were faster in adaptation to environmental changes than HCNs.</P>

Re-evaluation of the roles of <i>DROSHA</i>, <i>Exportin 5</i>, and <i>DICER</i> in microRNA biogenesis

Kim, Young-Kook,Kim, Boseon,Kim, V. Narry National Academy of Sciences 2016 PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF Vol.113 No.13

<P>Biogenesis of canonical microRNAs (miRNAs) involves multiple steps: nuclear processing of primary miRNA (pri-miRNA) by DROSHA, nuclear export of precursor miRNA (pre-miRNA) by Exportin 5 (XPO5), and cytoplasmic processing of pre-miRNA by DICER. To gain a deeper understanding of the contribution of each of these maturation steps, we deleted DROSHA, XPO5, and DICER in the same human cell line, and analyzed their effects on miRNA biogenesis. Canonical miRNA production was completely abolished in DROSHA-deleted cells, whereas we detected a few DROSHA-independent miRNAs including three previously unidentified noncanonical miRNAs (miR-7706, miR-3615, and miR-1254). In contrast to DROSHA knockout, many canonical miRNAs were still detected without DICER albeit at markedly reduced levels. In the absence of DICER, pre-miRNAs are loaded directly onto AGO and trimmed at the 3' end, yielding miRNAs from the 5' strand (5p miRNAs). Interestingly, in XPO5 knockout cells, most miRNAs are affected only modestly, suggesting that XPO5 is necessary but not critical for miRNA maturation. Our study demonstrates an essential role of DROSHA and an important contribution of DICER in the canonical miRNA pathway, and reveals that the function of XPO5 can be complemented by alternative mechanisms. Thus, this study allows us to understand differential contributions of key biogenesis factors, and provides with valuable resources for miRNA research.</P>

TUT7 controls the fate of precursor microRNAs by using three different uridylation mechanisms

Kim, Boseon,Ha, Minju,Loeff, Luuk,Chang, Hyeshik,Simanshu, Dhirendra K,Li, Sisi,Fareh, Mohamed,Patel, Dinshaw J,Joo, Chirlmin,Kim, V Narry John WileySons, Ltd 2015 The EMBO journal Vol.34 No.13

<P>Terminal uridylyl transferases (TUTs) function as integral regulators of microRNA (miRNA) biogenesis. Using biochemistry, single-molecule, and deep sequencing techniques, we here investigate the mechanism by which human TUT7 (also known as ZCCHC6) recognizes and uridylates precursor miRNAs (pre-miRNAs) in the absence of Lin28. We find that the overhang of a pre-miRNA is the key structural element that is recognized by TUT7 and its paralogues, TUT4 (ZCCHC11) and TUT2 (GLD2/PAPD4). For group II pre-miRNAs, which have a 1-nt 3′ overhang, TUT7 restores the canonical end structure (2-nt 3′ overhang) through mono-uridylation, thereby promoting miRNA biogenesis. For pre-miRNAs where the 3′ end is further recessed into the stem (as in 3′ trimmed pre-miRNAs), TUT7 generates an oligo-U tail that leads to degradation. In contrast to Lin28-stimulated oligo-uridylation, which is processive, a distributive mode is employed by TUT7 for both mono- and oligo-uridylation in the absence of Lin28. The overhang length dictates the frequency (but not duration) of the TUT7-RNA interaction, thus explaining how TUT7 differentiates pre-miRNA species with different overhangs. Our study reveals dual roles and mechanisms of uridylation in repair and removal of defective pre-miRNAs.</P>

microRNA Biogenesis

Kim, V. Narry The Korean Society for Integrative Biology 2004 Korean journal of biological sciences Vol.8 No.S

Bias-minimized quantification of microRNA reveals widespread alternative processing and 3′ end modification

Kim, Haedong,Kim, Jimi,Kim, Kijun,Chang, Hyeshik,You, Kwontae,Kim, V ,Narry Oxford University Press 2019 Nucleic acids research Vol.47 No.5

<P><B>Abstract</B></P><P>MicroRNAs (miRNAs) modulate diverse biological and pathological processes via post-transcriptional gene silencing. High-throughput small RNA sequencing (sRNA-seq) has been widely adopted to investigate the functions and regulatory mechanisms of miRNAs. However, accurate quantification of miRNAs has been limited owing to the severe ligation bias in conventional sRNA-seq methods. Here, we quantify miRNAs and their variants (known as isomiRs) by an improved sRNA-seq protocol, termed AQ-seq (accurate quantification by sequencing), that utilizes adapters with terminal degenerate sequences and a high concentration of polyethylene glycol (PEG), which minimize the ligation bias during library preparation. Measurement using AQ-seq allows us to correct the previously misannotated 5′ end usage and strand preference in public databases. Importantly, the analysis of 5′ terminal heterogeneity reveals widespread alternative processing events which have been underestimated. We also identify highly uridylated miRNAs originating from the 3p strands, indicating regulations mediated by terminal uridylyl transferases at the pre-miRNA stage. Taken together, our study reveals the complexity of the miRNA isoform landscape, allowing us to refine miRNA annotation and to advance our understanding of miRNA regulation. Furthermore, AQ-seq can be adopted to improve other ligation-based sequencing methods including crosslinking-immunoprecipitation-sequencing (CLIP-seq) and ribosome profiling (Ribo-seq).</P>

Biogenesis of small RNAs in animals

Kim, V. Narry,Han, Jinju,Siomi, Mikiko C. Nature Publishing Group 2009 NATURE REVIEWS MOLECULAR CELL BIOLOGY Vol.10 No.2

Small RNAs of 20–30 nucleotides can target both chromatin and transcripts, and thereby keep both the genome and the transcriptome under extensive surveillance. Recent progress in high-throughput sequencing has uncovered an astounding landscape of small RNAs in eukaryotic cells. Various small RNAs of distinctive characteristics have been found and can be classified into three classes based on their biogenesis mechanism and the type of Argonaute protein that they are associated with: microRNAs (miRNAs), endogenous small interfering RNAs (endo-siRNAs or esiRNAs) and Piwi-interacting RNAs (piRNAs). This Review summarizes our current knowledge of how these intriguing molecules are generated in animal cells.

Modifications of Small RNAs and Their Associated Proteins

Kim, Young-Kook,Heo, Inha,Kim, V. Narry Elsevier 2010 Cell Vol.143 No.5

<P>Small regulatory RNAs and their associated proteins are subject to diverse modifications that can impinge on their abundance and function. Some of the modifications are under the influence of cellular signaling, thus contributing to the dynamic regulation of RNA silencing.</P>

Functional links between clustered microRNAs: suppression of cell-cycle inhibitors by microRNA clusters in gastric cancer

Kim, Young-Kook,Yu, Jieun,Han, Tae Su,Park, Seong-Yeon,Namkoong, Bumjin,Kim, Dong Hyuk,Hur, Keun,Yoo, Moon-Won,Lee, Hyuk-Joon,Yang, Han-Kwang,Kim, V. Narry Oxford University Press 2009 Nucleic acids research Vol.37 No.5

<P>microRNAs (miRNAs) play integral roles in diverse processes including tumorigenesis. miRNA gene loci are often found in close conjunction, and such clustered miRNA genes are transcribed from a common promoter to generate polycistronic primary transcript. The primary transcript (pri-miRNA) is then processed by two RNase III proteins to release the mature miRNAs. Although it has been speculated that the miRNAs in the same cluster may play related biological functions, this has not been experimentally addressed. Here we report that the miRNAs in two clusters (miR-106b∼93 ∼ 25 and miR-222 ∼ 221) suppress the Cip/Kip family members of Cdk inhibitors (p57<SUP>Kip2</SUP>, p21<SUP>Cip1</SUP> and p27<SUP>Kip1</SUP>). We show that miR-25 targets p57 through the 3′-UTR. Furthermore, miR-106b and miR-93 control p21 while miR-222 and miR-221 regulate both p27 and p57. Ectopic expression of these miRNAs results in activation of Cdk2 and facilitation of G1/S phase transition. Consistent with these results, both clusters are abnormally upregulated in gastric cancer tissues compared to the corresponding normal tissues. Ectopic expression of miR-222 cluster enhanced tumor growth in the mouse xenograft model. Our study demonstrates the functional associations between clustered miRNAs and further implicates that effective cancer treatment may require a combinatorial approach to target multiple oncogenic miRNA clusters.</P>

microRNA-directed cleavage of ATHB15 mRNA regulates vascular development in Arabidopsis inflorescence stems : microRNA-directed repression of ATHB15

Kim, Joonki,Jung, Jae-Hoon,Reyes, Jose L.,Kim, Youn-Sung,Kim, Sun-Young,Chung, Kyung-Sook,Kim, Jin A.,Lee, Minsun,Lee, Yoontae,Narry Kim, V.,Chua, Nam-Hai,Park, Chung-Mo Wiley (Blackwell Publishing) 2005 The Plant journal Vol.42 No.1

<P>Class III homeodomain-leucine zipper proteins regulate critical aspects of plant development, including lateral organ polarity, apical and lateral meristem formation, and vascular development. ATHB15, a member of this transcription factor family, is exclusively expressed in vascular tissues. Recently, a microRNA (miRNA) binding sequence has been identified in ATHB15 mRNA, suggesting that a molecular mechanism governed by miRNA binding may direct vascular development through ATHB15. Here, we show that miR166-mediated ATHB15 mRNA cleavage is a principal mechanism for the regulation of vascular development. In a gain-of-function MIR166a mutant, the decreased transcript level of ATHB15 was accompanied by an altered vascular system with expanded xylem tissue and interfascicular region, indicative of accelerated vascular cell differentiation from cambial/procambial cells. A similar phenotype was observed in Arabidopsis plants with reduced ATHB15 expression but reversed in transgenic plants overexpressing an miR166-resistant ATHB15. ATHB15 mRNA cleavage occurred in standard wheat germ extracts and in Arabidopsis and was mediated by miR166 in Nicotiana benthamiana cells. miR166-assisted ATHB15 repression is likely to be a conserved mechanism that regulates vascular development in all vascular plants.</P>