Genome-scale analysis of <i>Acetobacterium bakii</i> reveals the cold adaptation of psychrotolerant acetogens by post-transcriptional regulation

Shin, Jongoh,Song, Yoseb,Jin, Sangrak,Lee, Jung-Kul,Kim, Dong Rip,Kim, Sun Chang,Cho, Suhyung,Cho, Byung-Kwan Cold Spring Harbor Laboratory Press 2018 RNA Vol.24 No.12

<P>Acetogens synthesize acetyl-CoA via CO<SUB>2</SUB> or CO fixation, producing organic compounds. Despite their ecological and industrial importance, their transcriptional and post-transcriptional regulation has not been systematically studied. With completion of the genome sequence of <I>Acetobacterium bakii</I> (4.28-Mb), we measured changes in the transcriptome of this psychrotolerant acetogen in response to temperature variations under autotrophic and heterotrophic growth conditions. Unexpectedly, acetogenesis genes were highly up-regulated at low temperatures under heterotrophic, as well as autotrophic, growth conditions. To mechanistically understand the transcriptional regulation of acetogenesis genes via changes in RNA secondary structures of 5′-untranslated regions (5′-UTR), the primary transcriptome was experimentally determined, and 1379 transcription start sites (TSS) and 1100 5′-UTR were found. Interestingly, acetogenesis genes contained longer 5′-UTR with lower RNA-folding free energy than other genes, revealing that the 5′-UTRs control the RNA abundance of the acetogenesis genes under low temperature conditions. Our findings suggest that post-transcriptional regulation via RNA conformational changes of 5′-UTRs is necessary for cold-adaptive acetogenesis.</P>

Learning strategy selection in the water maze and hippocampal CREB phosphorylation differ in two inbred strains of mice.

Sung, Jin-Young,Goo, June-Seo,Lee, Dong-Eun,Jin, Da-Qing,Bizon, Jennifer L,Gallagher, Michela,Han, Jung-Soo Cold Spring Harbor Laboratory Press 2008 Learning & Memory Vol.15 No.4

<P>Learning strategy selection was assessed in two different inbred strains of mice, C57BL/6 and DBA/2, which are used for developing genetically modified mouse models. Male mice received a training protocol in a water maze using alternating blocks of visible and hidden platform trials, during which mice escaped to a single location. After training, mice were required to choose between the spatial location where the platform had been during training (a place strategy) and a visible platform presented in a new location (a cued/response strategy). Both strains of mice had similar escape performance on the visible and hidden platform trials during training. However, in the strategy preference test, C57BL/6 mice selected a place strategy significantly more often than DBA/2 mice. Because much evidence implicates the hippocampus and striatum as important neural substrates for spatial/place and cued/response learning, respectively, the engagement of the hippocampus was then assessed after either place or cue training by determining levels of cAMP response element-binding protein (CREB) and phosphorylated CREB (pCREB) in these two mouse strains. Results revealed that hippocampal CREB levels in both strains of mice were significantly increased after place in comparison to cued training. However, the relation of hippocampal pCREB levels to training was strain dependent; pCREB was significantly higher in C57BL/6 mice than in DBA/2 mice after place training, while hippocampal pCREB levels did not differ between strains after cued training. These findings indicate that pCREB, specifically associated with place/spatial training, is closely tied to differences in spatial/place strategy preference between C57BL/6 and DBA/2 mice.</P>

New class of microRNA targets containing simultaneous 5'-UTR and 3'-UTR interaction sites.

Lee, Inhan,Ajay, Subramanian S,Yook, Jong In,Kim, Hyun Sil,Hong, Su Hyung,Kim, Nam Hee,Dhanasekaran, Saravana M,Chinnaiyan, Arul M,Athey, Brian D Cold Spring Harbor Laboratory Press 2009 Genome research Vol.19 No.7

<P>MicroRNAs (miRNAs) are known to post-transcriptionally regulate target mRNAs through the 3'-UTR, which interacts mainly with the 5'-end of miRNA in animals. Here we identify many endogenous motifs within human 5'-UTRs specific to the 3'-ends of miRNAs. The 3'-end of conserved miRNAs in particular has significant interaction sites in the human-enriched, less conserved 5'-UTR miRNA motifs, while human-specific miRNAs have significant interaction sites only in the conserved 5'-UTR motifs, implying both miRNA and 5'-UTR are actively evolving in response to each other. Additionally, many miRNAs with their 3'-end interaction sites in the 5'-UTRs turn out to simultaneously contain 5'-end interaction sites in the 3'-UTRs. Based on these findings we demonstrate combinatory interactions between a single miRNA and both end regions of an mRNA using model systems. We further show that genes exhibiting large-scale protein changes due to miRNA overexpression or deletion contain both UTR interaction sites predicted. We provide the predicted targets of this new miRNA target class, miBridge, as an efficient way to screen potential targets, especially for nonconserved miRNAs, since the target search space is reduced by an order of magnitude compared with the 3'-UTR alone. Efficacy is confirmed by showing SEC24D regulation with hsa-miR-605, a miRNA identified only in primate, opening the door to the study of nonconserved miRNAs. Finally, miRNAs (and associated proteins) involved in this new targeting class may prevent 40S ribosome scanning through the 5'-UTR and keep it from reaching the start-codon, preventing 60S association.</P>

Global analysis of protein homomerization in <i>Saccharomyces cerevisiae</i>

Kim, Yeonsoo,Jung, Jong Pil,Pack, Chan-Gi,Huh, Won-Ki Cold Spring Harbor Laboratory Press 2019 Genome research Vol.29 No.1

<P>In vivo analyses of the occurrence, subcellular localization, and dynamics of protein–protein interactions (PPIs) are important issues in functional proteomic studies. The bimolecular fluorescence complementation (BiFC) assay has many advantages in that it provides a reliable way to detect PPIs in living cells with minimal perturbation of the structure and function of the target proteins. Previously, to facilitate the application of the BiFC assay to genome-wide analysis of PPIs, we generated a collection of yeast strains expressing full-length proteins tagged with the N-terminal fragment of Venus (VN), a yellow fluorescent protein variant, from their own native promoters. In the present study, we constructed a VC (the C-terminal fragment of Venus) fusion library consisting of 5671 <I>MAT</I>α strains expressing C-terminally VC-tagged proteins (representing ∼91% of the yeast proteome). For genome-wide analysis of protein homomer formation, we mated each strain in the VC fusion library with its cognate strain in the VN fusion library and performed the BiFC assay. From this analysis, we identified 186 homomer candidates. We further investigated the functional relevance of the homomerization of Pln1, a yeast perilipin. Our data set provides a useful resource for understanding the physiological roles of protein homomerization. Furthermore, the VC fusion library together with the VN fusion library will provide a valuable platform to systematically analyze PPIs in the natural cellular context.</P>

Targeted genome editing in human cells with zinc finger nucleases constructed via modular assembly.

Kim, Hye Joo,Lee, Hyung Joo,Kim, Hyojin,Cho, Seung Woo,Kim, Jin-Soo Cold Spring Harbor Laboratory Press 2009 Genome research Vol.19 No.7

<P>Broad applications of zinc finger nuclease (ZFN) technology-which allows targeted genome editing-in research, medicine, and biotechnology are hampered by the lack of a convenient, rapid, and publicly available method for the synthesis of functional ZFNs. Here we describe an efficient and easy-to-practice modular-assembly method using publicly available zinc fingers to make ZFNs that can modify the DNA sequences of predetermined genomic sites in human cells. We synthesized and tested hundreds of ZFNs to target dozens of different sites in the human CCR5 gene-a co-receptor required for HIV infection-and found that many of these nucleases induced site-specific mutations in the CCR5 sequence. Because human cells that harbor CCR5 null mutations are functional and normal, these ZFNs might be used for (1) knocking out CCR5 to produce T-cells that are resistant to HIV infection in AIDS patients or (2) inserting therapeutic genes at 'safe sites' in gene therapy applications.</P>

Food-derived sensory cues modulate longevity via distinct neuroendocrine insulin-like peptides

Artan, Murat,Jeong, Dae-Eun,Lee, Dongyeop,Kim, Young-Il,Son, Heehwa G.,Husain, Zahabiya,Kim, Jinmahn,Altintas, Ozlem,Kim, Kyuhyung,Alcedo, Joy,Lee, Seung-Jae V. Cold Spring Harbor Laboratory Press 2016 Genes & development Vol.30 No.9

<P>Environmental fluctuations influence organismal aging by affecting various regulatory systems. One such system involves sensory neurons, which affect life span in many species. However, how sensory neurons coordinate organismal aging in response to changes in environmental signals remains elusive. Here, we found that a subset of sensory neurons shortens Caenorhabditis elegans' life span by differentially regulating the expression of a specific insulin-like peptide (ILP), INS-6. Notably, treatment with food-derived cues or optogenetic activation of sensory neurons significantly increases ins-6 expression and decreases life span. INS-6 in turn relays the longevity signals to nonneuronal tissues by decreasing the activity of the transcription factor DAF-16/FOXO. Together, our study delineates a mechanism through which environmental sensory cues regulate aging rates by modulating the activities of specific sensory neurons and ILPs.</P>

Comprehensive genome- and transcriptome-wide analyses of mutations associated with microsatellite instability in Korean gastric cancers

Yoon, Kwiyeom,Lee, Sunghoon,Han, Tae-Su,Moon, So Yeon,Yun, Sun Mi,Kong, Seong-Ho,Jho, Sungwoong,Choe, Jinny,Yu, Jieun,Lee, Hyuk-Joon,Park, Ji Hyun,Kim, Hak-Min,Lee, So Yeun,Park, Jongsun,Kim, Woo-Ho,B Cold Spring Harbor Laboratory Press 2013 Genome research Vol.23 No.7

<P>Microsatellite instability (MSI) is a critical mechanism that drives genetic aberrations in cancer. To identify the entire MS mutation, we performed the first comprehensive genome- and transcriptome-wide analyses of mutations associated with MSI in Korean gastric cancer cell lines and primary tissues. We identified 18,377 MS mutations of five or more repeat nucleotides in coding sequences and untranslated regions of genes, and discovered 139 individual genes whose expression was down-regulated in association with UTR MS mutation. In addition, we found that 90.5% of MS mutations with deletions in gene regions occurred in UTRs. This analysis emphasizes the genetic diversity of MSI-H gastric tumors and provides clues to the mechanistic basis of instability in microsatellite unstable gastric cancers.</P>

A KAP1 phosphorylation switch controls MyoD function during skeletal muscle differentiation

Singh, Kulwant,Cassano, Marco,Planet, Evarist,Sebastian, Soji,Jang, Suk Min,Sohi, Gurjeev,Faralli, Hervé,Choi, Jinmi,Youn, Hong-Duk,Dilworth, F. Jeffrey,Trono, Didier Cold Spring Harbor Laboratory Press 2015 Genes & development Vol.29 No.5

<P>The transcriptional activator MyoD serves as a master controller of myogenesis. Singh et al. identify KAP1/TRIM28 as a key regulator of MyoD function. In myoblasts, KAP1 is present with MyoD and Mef2 at many muscle genes, where it acts as a scaffold to recruit not only coactivators such as p300 and LSD1 but also corepressors such as G9a and HDAC1, with promoter silencing as the net outcome. Upon differentiation, MSK1-mediated phosphorylation of KAP1 releases the corepressors from the scaffold, unleashing transcriptional activation by MyoD/Mef2 and their positive cofactors.</P><P>The transcriptional activator MyoD serves as a master controller of myogenesis. Often in partnership with Mef2 (myocyte enhancer factor 2), MyoD binds to the promoters of hundreds of muscle genes in proliferating myoblasts yet activates these targets only upon receiving cues that launch differentiation. What regulates this off/on switch of MyoD function has been incompletely understood, although it is known to reflect the action of chromatin modifiers. Here, we identify KAP1 (KRAB [Kréééüppel-like associated box]-associated protein 1)/TRIM28 (tripartite motif protein 28) as a key regulator of MyoD function. In myoblasts, KAP1 is present with MyoD and Mef2 at many muscle genes, where it acts as a scaffold to recruit not only coactivators such as p300 and LSD1 but also corepressors such as G9a and HDAC1 (histone deacetylase 1), with promoter silencing as the net outcome. Upon differentiation, MSK1-mediated phosphorylation of KAP1 releases the corepressors from the scaffold, unleashing transcriptional activation by MyoD/Mef2 and their positive cofactors. Thus, our results reveal KAP1 as a previously unappreciated interpreter of cell signaling, which modulates the ability of MyoD to drive myogenesis.</P>

Crystal structure of Streptococcus pneumoniae Sp1610, a putative tRNA methyltransferase, in complex with S-adenosyl-L-methionine

Ta, H. M.,Kim, K. K. Cold Spring Harbor Laboratory Press 2010 Protein science Vol.19 No.3

Role of dentate gyrus in aligning internal spatial map to external landmark.

Lee, Jong Won,Kim, Woon Ryoung,Sun, Woong,Jung, Min Whan Cold Spring Harbor Laboratory Press 2009 Learning & Memory Vol.16 No.9

<P>Humans and animals form internal representations of external space based on their own body movement (dead reckoning) as well as external landmarks. It is poorly understood, however, how different types of information are integrated to form a unified representation of external space. To examine the role of dentate gyrus (DG) in this process, we conducted physiological and behavioral experiments using Bax knockout (Bax-KO) mice in which newly generated granule cells continue to accumulate disrupting neural circuitry specifically in the DG. Unlike in wild-type (WT) littermates, spatial firing of hippocampal neurons was completely dissociated from a distinct visual cue and instead, tended to stay constant relative to the recording room in Bax-KO mice. Behaviorally, whereas spatial learning was intact in conventional spatial reference memory tasks, Bax-KO mice were impaired in finding a target location based on visual landmarks when target locations predicted by dead reckoning and visual landmarks were made incongruent. These results provide converging evidence for the role of DG in binding animal's internal spatial map with the sensory information on external landmarks in building a distinct spatial representation for each environment.</P>