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https://www.readbyqxmd.com/read/28493531/ternary-complex-of-human-ror%C3%AE-ligand-binding-domain-inverse-agonist-and-smrt-peptide-shows-a-unique-mechanism-of-corepressor-recruitment
#1
Masato Noguchi, Akihiro Nomura, Ken Murase, Satoki Doi, Keishi Yamaguchi, Kazuyuki Hirata, Makoto Shiozaki, Shintaro Hirashima, Masayuki Kotoku, Takayuki Yamaguchi, Yoshiaki Katsuda, Ruo Steensma, Xioalin Li, Haiyan Tao, Bruno Tse, Morgan Fenn, Robert Babine, Erin Bradley, Paul Crowe, Scott Thacher, Tsuyoshi Adachi, Masafumi Kamada
Retinoid-related orphan receptor gamma (RORγ) directly controls the differentiation of Th17 cell and the production of interleukin-17, which plays an integral role in autoimmune diseases. To obtain insight into RORγ, we have determined the first crystal structure of a ternary complex containing RORγ ligand-binding domain (LBD) bound with a novel synthetic inhibitor and a repressor peptide, 22-mer peptide from silencing mediator of retinoic acid and thyroid hormone receptor (SMRT). Comparison of a binary complex of nonliganded (apo) RORγ-LBD with a nuclear receptor co-activator (NCoA-1) peptide has shown that our inhibitor displays a unique mechanism different from those caused by natural inhibitor, ursolic acid (UA)...
May 11, 2017: Genes to Cells: Devoted to Molecular & Cellular Mechanisms
https://www.readbyqxmd.com/read/28475868/glucocorticoid-receptor-megatrans-switching-mediates-the-repression-of-an-er%C3%AE-regulated-transcriptional-program
#2
Feng Yang, Qi Ma, Zhijie Liu, Wenbo Li, Yuliang Tan, Chunyu Jin, Wubin Ma, Yiren Hu, Jia Shen, Kenneth A Ohgi, Francesca Telese, Wen Liu, Michael G Rosenfeld
The molecular mechanisms underlying the opposing functions of glucocorticoid receptors (GRs) and estrogen receptor α (ERα) in breast cancer development remain poorly understood. Here we report that, in breast cancer cells, liganded GR represses a large ERα-activated transcriptional program by binding, in trans, to ERα-occupied enhancers. This abolishes effective activation of these enhancers and their cognate target genes, and it leads to the inhibition of ERα-dependent binding of components of the MegaTrans complex...
May 4, 2017: Molecular Cell
https://www.readbyqxmd.com/read/28475176/sly-regulates-genes-involved-in-chromatin-remodeling-and-interacts-with-tbl1xr1-during-sperm-differentiation
#3
Charlotte Moretti, Maria-Elisabetta Serrentino, Côme Ialy-Radio, Marion Delessard, Tatiana A Soboleva, Frederic Tores, Marjorie Leduc, Patrick Nitschké, Joel R Drevet, David J Tremethick, Daniel Vaiman, Ayhan Kocer, Julie Cocquet
Sperm differentiation requires unique transcriptional regulation and chromatin remodeling after meiosis to ensure proper compaction and protection of the paternal genome. Abnormal sperm chromatin remodeling can induce sperm DNA damage, embryo lethality and male infertility, yet, little is known about the factors which regulate this process. Deficiency in Sly, a mouse Y chromosome-encoded gene expressed only in postmeiotic male germ cells, has been shown to result in the deregulation of hundreds of sex chromosome-encoded genes associated with multiple sperm differentiation defects and subsequent male infertility...
May 5, 2017: Cell Death and Differentiation
https://www.readbyqxmd.com/read/28464822/a-high-quality-assembly-of-the-nile-tilapia-oreochromis-niloticus-genome-reveals-the-structure-of-two-sex-determination-regions
#4
Matthew A Conte, William J Gammerdinger, Kerry L Bartie, David J Penman, Thomas D Kocher
BACKGROUND: Tilapias are the second most farmed fishes in the world and a sustainable source of food. Like many other fish, tilapias are sexually dimorphic and sex is a commercially important trait in these fish. In this study, we developed a significantly improved assembly of the tilapia genome using the latest genome sequencing methods and show how it improves the characterization of two sex determination regions in two tilapia species. RESULTS: A homozygous clonal XX female Nile tilapia (Oreochromis niloticus) was sequenced to 44X coverage using Pacific Biosciences (PacBio) SMRT sequencing...
May 2, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28455781/reduction-in-fecal-microbiota-diversity-and-short-chain-fatty-acid-producers-in-methicillin-resistant-staphylococcus-aureus-infected-individuals-as-revealed-by-pacbio-single-molecule-real-time-sequencing-technology
#5
J Zhao, L Nian, L Y Kwok, T Sun, J Zhao
Methicillin-resistant Staphylococcus aureus (MRSA) may cause potentially lethal infections. Increasing evidence suggests that the gut microbiota is associated with human health. Yet, whether patients with MRSA infections carry specific signatures in their fecal microbiota composition has not been determined. Thus, this study aimed to compare the fecal microbiota profile of MRSA-positive patients (n=15) with individuals without MRSA infection (n=15) by using the PacBio single molecule, real-time (SMRT) DNA sequencing system and real-time quantitative polymerase chain reaction (qPCR)...
April 28, 2017: European Journal of Clinical Microbiology & Infectious Diseases
https://www.readbyqxmd.com/read/28438580/first-complete-genome-sequence-of-bacillus-glycinifermentans-b-27
#6
Kai Bernd Stadermann, Jochen Blom, Claudia Borgmeier, Natalie Sciberras, Sandra Herbold, Maike Kipker, Guido Meurer, Stella Molck, Daniel Petri, Stefan Pelzer, Jessica Schneider
The first complete genome sequence of Bacillus glycinifermentans B-27 was determined by SMRT sequencing generating a genome sequence with a total length of 4,607,442 bases. Based on this sequence 4738 protein-coding sequences were predicted and used to identify gene clusters that are related to the production of secondary metabolites such as Lichenysin, Bacillibactin and Bacitracin. This genomic potential combined with the ability of B. glycinifermentans B-27 to grown in bile containing media might contribute to a future application of this strain as probiotic in productive livestock potentially inhibiting competing and pathogenic organisms...
April 21, 2017: Journal of Biotechnology
https://www.readbyqxmd.com/read/28430818/comparative-genomics-of-burkholderia-multivorans-a-ubiquitous-pathogen-with-a-highly-conserved-genomic-structure
#7
Charlotte Peeters, Vaughn S Cooper, Philip J Hatcher, Bart Verheyde, Aurélien Carlier, Peter Vandamme
The natural environment serves as a reservoir of opportunistic pathogens. A well-established method for studying the epidemiology of such opportunists is multilocus sequence typing, which in many cases has defined strains predisposed to causing infection. Burkholderia multivorans is an important pathogen in people with cystic fibrosis (CF) and its epidemiology suggests that strains are acquired from non-human sources such as the natural environment. This raises the central question of whether the isolation source (CF or environment) or the multilocus sequence type (ST) of B...
2017: PloS One
https://www.readbyqxmd.com/read/28424528/elucidation-of-quantitative-structural-diversity-of-remarkable-rearrangement-regions-shufflons-in-inci2-plasmids
#8
Tsuyoshi Sekizuka, Michiko Kawanishi, Mamoru Ohnishi, Ayaka Shima, Kengo Kato, Akifumi Yamashita, Mari Matsui, Satowa Suzuki, Makoto Kuroda
A multiple DNA inversion system, the shufflon, exists in incompatibility (Inc) I1 and I2 plasmids. The shufflon generates variants of the PilV protein, a minor component of the thin pilus. The shufflon is one of the most difficult regions for de novo genome assembly because of its structural diversity even in an isolated bacterial clone. We determined complete genome sequences, including those of IncI2 plasmids carrying mcr-1, of three Escherichia coli strains using single-molecule, real-time (SMRT) sequencing and Illumina sequencing...
April 19, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28415976/smrt-genome-assembly-corrects-reference-errors-resolving-the-genetic-basis-of-virulence-in-mycobacterium-tuberculosis
#9
Afif Elghraoui, Samuel J Modlin, Faramarz Valafar
BACKGROUND: The genetic basis of virulence in Mycobacterium tuberculosis has been investigated through genome comparisons of virulent (H37Rv) and attenuated (H37Ra) sister strains. Such analysis, however, relies heavily on the accuracy of the sequences. While the H37Rv reference genome has had several corrections to date, that of H37Ra is unmodified since its original publication. RESULTS: Here, we report the assembly and finishing of the H37Ra genome from single-molecule, real-time (SMRT) sequencing...
April 17, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28400415/recombination-dependent-replication-and-gene-conversion-homogenize-repeat-sequences-and-diversify-plastid-genome-structure
#10
Tracey A Ruhlman, Jin Zhang, John C Blazier, Jamal S M Sabir, Robert K Jansen
PREMISE OF THE STUDY: There is a misinterpretation in the literature regarding the variable orientation of the small single copy region of plastid genomes (plastomes). The common phenomenon of small and large single copy inversion, hypothesized to occur through intramolecular recombination between inverted repeats (IR) in a circular, single unit-genome, in fact, more likely occurs through recombination-dependent replication (RDR) of linear plastome templates. If RDR can be primed through both intra- and intermolecular recombination, then this mechanism could not only create inversion isomers of so-called single copy regions, but also an array of alternative sequence arrangements...
April 11, 2017: American Journal of Botany
https://www.readbyqxmd.com/read/28396297/the-co-regulators-src-1-and-smrt-are-involved-in-interleukin-6-induced-androgen-receptor-activation
#11
Qi Wang, Hui Wang, Qiang Ju, Zhen Ding, Xing Ge, Qiao-Mei Shi, Ji-Long Zhou, Xiao-Long Zhou, Jin-Peng Zhang, Mei-Rong Zhang, Hong-Min Yu, Li-Chun Xu
BACKGROUND: The androgen receptor (AR) can be stimulated by interleukin-6 (IL-6) in the absence of androgens to induce prostate cancer progression. The purpose of this study was to investigate whether the co-activator steroid receptor coactivator-1 (SRC-1) and co-repressor silencing mediator for retinoid and thyroid hormone receptors (SMRT) are involved in IL-6-induced AR activation. METHODS: The effects of IL-6 on LNCaP cell proliferation were monitored using real-time cell analysis (RTCA) iCELLigence system...
November 1, 2016: European Cytokine Network
https://www.readbyqxmd.com/read/28388540/transcriptional-regulation-of-mixed-lineage-kinase-3-by-estrogen-and-its-implication-in-er-positive-breast-cancer-pathogenesis
#12
Navin Viswakarma, Rakesh Sathish Nair, Gautam Sondarva, Subhasis Das, Lucas Ibrahimi, Zhiyong Chen, Subhash Sinha, Basabi Rana, Ajay Rana
Mixed Lineage Kinase 3 (MLK3), also called as MAP3K11 is a tightly regulated MAP3K member but its cellular function is still not fully understood. Earlier we reported post-translational regulation of MLK3 by estrogen (E2) that inhibited the kinase activity and favored survival of ER+ breast cancer cells. Here we report that MLK3 is also transcriptionally downregulated by E2 in ER+ breast cancer cells. Publicly available data and in situ hybridization of human breast tumors showed significant down regulation of MLK3 transcripts in ER+ tumors...
May 16, 2017: Oncotarget
https://www.readbyqxmd.com/read/28381259/halc-high-throughput-algorithm-for-long-read-error-correction
#13
Ergude Bao, Lingxiao Lan
BACKGROUND: The third generation PacBio SMRT long reads can effectively address the read length issue of the second generation sequencing technology, but contain approximately 15% sequencing errors. Several error correction algorithms have been designed to efficiently reduce the error rate to 1%, but they discard large amounts of uncorrected bases and thus lead to low throughput. This loss of bases could limit the completeness of downstream assemblies and the accuracy of analysis. RESULTS: Here, we introduce HALC, a high throughput algorithm for long read error correction...
April 5, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28369806/identification-of-microbial-profile-of-koji-using-single-molecule-real-time-sequencing-technology
#14
Wenyan Hui, Qiangchuan Hou, Chenxia Cao, Haiyan Xu, Yi Zhen, Lai-Yu Kwok, Tiansong Sun, Heping Zhang, Wenyi Zhang
Koji is a kind of Japanese traditional fermented starter that has been used for centuries. Many fermented foods are made from koji, such as sake, miso, and soy sauce. This study used the single molecule real-time sequencing technology (SMRT) to investigate the bacterial and fungal microbiota of 3 Japanese koji samples. After SMRT analysis, a total of 39121 high-quality sequences were generated, including 14354 bacterial and 24767 fungal sequence reads. The high-quality gene sequences were assigned to 5 bacterial and 2 fungal plyla, dominated by Proteobacteria and Ascomycota, respectively...
May 2017: Journal of Food Science
https://www.readbyqxmd.com/read/28364362/advantages-of-genome-sequencing-by-long-read-sequencer-using-smrt-technology-in-medical-area
#15
REVIEW
Kazuma Nakano, Akino Shiroma, Makiko Shimoji, Hinako Tamotsu, Noriko Ashimine, Shun Ohki, Misuzu Shinzato, Maiko Minami, Tetsuhiro Nakanishi, Kuniko Teruya, Kazuhito Satou, Takashi Hirano
PacBio RS II is the first commercialized third-generation DNA sequencer able to sequence a single molecule DNA in real-time without amplification. PacBio RS II's sequencing technology is novel and unique, enabling the direct observation of DNA synthesis by DNA polymerase. PacBio RS II confers four major advantages compared to other sequencing technologies: long read lengths, high consensus accuracy, a low degree of bias, and simultaneous capability of epigenetic characterization. These advantages surmount the obstacle of sequencing genomic regions such as high/low G+C, tandem repeat, and interspersed repeat regions...
March 31, 2017: Human Cell
https://www.readbyqxmd.com/read/28361880/genomic-structure-of-the-horse-major-histocompatibility-complex-class-ii-region-resolved-using-pacbio-long-read-sequencing-technology
#16
Agnese Viļuma, Sofia Mikko, Daniela Hahn, Loren Skow, Göran Andersson, Tomas F Bergström
The mammalian Major Histocompatibility Complex (MHC) region contains several gene families characterized by highly polymorphic loci with extensive nucleotide diversity, copy number variation of paralogous genes, and long repetitive sequences. This structural complexity has made it difficult to construct a reliable reference sequence of the horse MHC region. In this study, we used long-read single molecule, real-time (SMRT) sequencing technology from Pacific Biosciences (PacBio) to sequence eight Bacterial Artificial Chromosome (BAC) clones spanning the horse MHC class II region...
March 31, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28348836/evolution-of-a-zoonotic-pathogen-investigating-prophage-diversity-in-enterohaemorrhagic-escherichia-coli-o157-by-long-read-sequencing
#17
Sharif Shaaban, Lauren A Cowley, Sean P McAteer, Claire Jenkins, Timothy J Dallman, James L Bono, David L Gally
Enterohaemorrhagic Escherichia coli (EHEC) O157 is a zoonotic pathogen for which colonization of cattle and virulence in humans is associated with multiple horizontally acquired genes, the majority present in active or cryptic prophages. Our understanding of the evolution and phylogeny of EHEC O157 continues to develop primarily based on core genome analyses; however, such short-read sequences have limited value for the analysis of prophage content and its chromosomal location. In this study, we applied Single Molecule Real Time (SMRT) sequencing, using the Pacific Biosciences long-read sequencing platform, to isolates selected from the main sub-clusters of this clonal group...
December 2016: Microbial Genomics
https://www.readbyqxmd.com/read/28348241/structure-of-the-mecp2-tblr1-complex-reveals-a-molecular-basis-for-rett-syndrome-and-related-disorders
#18
Valdeko Kruusvee, Matthew J Lyst, Ceitidh Taylor, Žygimantė Tarnauskaitė, Adrian P Bird, Atlanta G Cook
Rett syndrome (RTT) is an X-linked neurological disorder caused by mutations in the methyl-CpG-binding protein 2 (MeCP2) gene. The majority of RTT missense mutations disrupt the interaction of the MeCP2 with DNA or the nuclear receptor corepressor (NCoR)/silencing mediator of retinoic acid and thyroid receptors (SMRT) corepressor complex. Here, we show that the "NCoR/SMRT interaction domain" (NID) of MeCP2 directly contacts transducin beta-like 1 (TBL1) and TBL1 related (TBLR1), two paralogs that are core components of NCoR/SMRT...
April 18, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28344213/over-expression-of-tbl1xr1-indicates-poor-prognosis-of-serous-epithelial-ovarian-cancer
#19
Ming Ma, Nina Yu
Transducin (β)-like 1 X-linked receptor 1 (TBL1XR1) is a core component of the NCoR/SMRT transcription co-repressor complex, and its role in regulating cancer progression has been reported. Serous epithelial ovarian cancer (EOC) is the most common histological type of EOC. Here we explored the significance of TBL1XR1 expression in predicting outcomes of patients with serous EOC. Real-time quantitative PCR analysis showed that the expression level of TBL1XR1 mRNA was significantly higher in EOC tissues compared with adjacent non-tumorous tissues...
March 2017: Tohoku Journal of Experimental Medicine
https://www.readbyqxmd.com/read/28336599/complete-genome-sequence-and-methylome-analysis-of-acinetobacter-calcoaceticus-65
#20
Alexey Fomenkov, Tamas Vincze, Sergey K Degtyarev, Richard J Roberts
Acinetobacter calcoaceticus 65 is the original source strain for the restriction enzyme Acc65I. Its complete sequence and full methylome were determined using single-molecule real-time (SMRT) sequencing.
March 23, 2017: Genome Announcements
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