Identification of RNF2-responding loci in long-range chromatin interactions using the novel 4C-ChIP-Cloning technology.

Abstract:

:RNF2 is a core component of Polycomb repressive complex 1 (PRC1), which binds to various chromatic regions to regulate their transcriptional activity. It was recently reported that EZH2, a Polycomb group complex member, helps mediate long-range chromosomal interactions in mammalian cells. The present study investigates whether RNF2-responding loci interact in long-range chromatin. The new 4C-ChIP-Cloning technology was developed based on circular chromosome conformation capture (4C) and ChIP. Use of the 4C-ChIP-Cloning technology successfully identified four loci in long-range cis- or trans-interactions that were mediated by the RNF2 protein. RNAi experiments showed that RNF2 regulated the transcription levels of genes adjacent to the loci. These results suggest that RNF2 protein, as part of PRC1, mediates long-range interactions between RNF2-interation loci and regulates adjacent genes. This 4C-ChIP-Cloning technology may contribute to the study of protein-mediated long-range chromatin interactions with specific regulatory elements.

journal_name

J Biotechnol

journal_title

Journal of biotechnology

authors

Choi D,Goo HG,Yoo J,Kang S

doi

10.1016/j.jbiotec.2011.01.001

subject

Has Abstract

pub_date

2011-02-20 00:00:00

pages

312-8

issue

4

eissn

0168-1656

issn

1873-4863

pii

S0168-1656(11)00029-0

journal_volume

151

pub_type

杂志文章
  • Towards the in vivo production of tocotrienol compounds: engineering of a plasmid-free Escherichia coli strain for the heterologous synthesis of 2-methyl-6-geranylgeranyl-benzoquinol.

    abstract::The vitamin E family consists of 4 tocopherol and 4 tocotrienol compounds. During recent years, tocotrienols have gained increased interest due to their biological activities that are beyond the vitamin E activity. Here we report the engineering of plasmid-free Escherichia coli strains for an efficient synthesis of 2-...

    journal_title:Journal of biotechnology

    pub_type: 杂志文章

    doi:10.1016/j.jbiotec.2012.08.010

    authors: Ghanegaonkar S,Conrad J,Beifuss U,Sprenger GA,Albermann C

    更新日期:2012-12-15 00:00:00

  • Neural network modeling for on-line estimation of nutrient dynamics in a sequentially-operated batch reactor.

    abstract::In monitoring and controlling wastewater treatment processes, on-line information of nutrient dynamics is very important. However, these variables are determined with a significant time delay. Although the final effluent quality can be analyzed after this delay, it is often too late to make proper adjustments. In this...

    journal_title:Journal of biotechnology

    pub_type: 杂志文章

    doi:10.1016/s0168-1656(99)00171-6

    authors: Lee DS,Park JM

    更新日期:1999-10-08 00:00:00

  • Engineering microenvironment for expansion of sensitive anchorage-dependent mammalian cells.

    abstract::Tissue engineering involves ex vivo seeding of anchorage-dependent mammalian cells onto scaffolds, or transplanting cells in vivo. The cell expansion currently requires repeated cell detachment from solid substrata by enzymatic, chemical or mechanical means. The report here presents a high yield three-dimensional cult...

    journal_title:Journal of biotechnology

    pub_type: 杂志文章

    doi:10.1016/j.jbiotec.2005.05.012

    authors: Chia SM,Lin PC,Quek CH,Yin C,Mao HQ,Leong KW,Xu X,Goh CH,Ng ML,Yu H

    更新日期:2005-09-10 00:00:00

  • Screening for improved isoprenoid biosynthesis in microorganisms.

    abstract::The production of isoprenoids in recombinant microbes for flavor & fragrance, pharmaceutical, agricultural or fuel applications is a booming research field. Isoprenoid extraction from natural resources and chemical synthesis is frequently neither ecological nor commercially profitable. However, recombinant microbes al...

    journal_title:Journal of biotechnology

    pub_type: 杂志文章,评审

    doi:10.1016/j.jbiotec.2016.03.051

    authors: Emmerstorfer-Augustin A,Moser S,Pichler H

    更新日期:2016-10-10 00:00:00

  • Engineering biotin prototrophic Corynebacterium glutamicum strains for amino acid, diamine and carotenoid production.

    abstract::The Gram-positive Corynebacterium glutamicum is auxotrophic for biotin. Besides the biotin uptake system BioYMN and the transcriptional regulator BioQ, this bacterium possesses functional enzymes for the last three reactions of biotin synthesis starting from pimeloyl-CoA. Heterologous expression of bioF from the Gram-...

    journal_title:Journal of biotechnology

    pub_type: 杂志文章

    doi:10.1016/j.jbiotec.2014.01.023

    authors: Peters-Wendisch P,Götker S,Heider SA,Komati Reddy G,Nguyen AQ,Stansen KC,Wendisch VF

    更新日期:2014-12-20 00:00:00

  • Complete genome sequence of the methanogenic neotype strain Methanobacterium formicicum MF(T.).

    abstract::The neotype strain Methanobacterium formicicum MF(T) (DSM1535), a hydrogenotrophic methanogenic Archaeon, was isolated from a domestic sewage sludge digestor in Urbana (IL, USA). Here, the complete genome sequence of the methanogen is reported. The genome is 2,478,074bp in size, featuring a GC content of 41.23%. M. fo...

    journal_title:Journal of biotechnology

    pub_type: 杂志文章

    doi:10.1016/j.jbiotec.2014.09.018

    authors: Maus I,Stantscheff R,Wibberg D,Stolze Y,Winkler A,Pühler A,König H,Schlüter A

    更新日期:2014-12-20 00:00:00

  • High performance flow injection analysis of recombinant protein G.

    abstract::Chromatographic discs were investigated for their potential to substitute for the hitherto used cartridges in heterogeneous flow injection analysis. Originally designed for fast high performance liquid chromatography (HPLC) of biopolymers, the discs combine reliability with speed and resolution. This together with the...

    journal_title:Journal of biotechnology

    pub_type: 杂志文章

    doi:10.1016/s0168-1656(98)00181-3

    authors: Hagedorn J,Kasper C,Freitag R,Tennikova T

    更新日期:1999-03-26 00:00:00

  • Enhancement of wound healing by chitosan/hyaluronan polyelectrolyte membrane loaded with glutathione: in vitro and in vivo evaluations.

    abstract::The inflammation of chronic wounds generally causes delaying their healing process. The present work aims to formulate a wound dressing polyelectrolyte membrane based on chitosan (Ch) and sodium hyaluronate (HA) loaded with glutathione (GSH). The membrane types (Ch/HA and Ch/HA/GSH) were examined by Fourier transform ...

    journal_title:Journal of biotechnology

    pub_type: 杂志文章

    doi:10.1016/j.jbiotec.2020.02.002

    authors: Tamer TM,Hassan MA,Valachová K,Omer AM,El-Shafeey MEA,Mohy Eldin MS,Šoltés L

    更新日期:2020-02-20 00:00:00

  • Modeling enzyme reactivity in organic solvents and water through computer simulations.

    abstract::In this article, we review how molecular modeling techniques can be used to shed light on how water and organic solvents influence the reactivity of enzymes. The application of thermodynamics-based models allowed the first qualitative predictions on the selectivity of many reaction types. However, it was with the appl...

    journal_title:Journal of biotechnology

    pub_type: 杂志文章,评审

    doi:10.1016/s0168-1656(02)00034-2

    authors: Colombo G,Carrea G

    更新日期:2002-06-13 00:00:00

  • Effect of the temperature in a mixed culture pilot scale aerobic process for food waste and sewage sludge conversion into polyhydroxyalkanoates.

    abstract::The utilisation of urban organic waste as feedstock for polyhydroxyalkanoates (PHA) production is growing since it allows to solve the main concerns about their disposal and simultaneously to recover added-value products. A pilot scale platform has been designed for this purpose. The VFA-rich fermentation liquid comin...

    journal_title:Journal of biotechnology

    pub_type: 杂志文章

    doi:10.1016/j.jbiotec.2020.07.022

    authors: Valentino F,Lorini L,Gottardo M,Pavan P,Majone M

    更新日期:2020-11-10 00:00:00

  • Enhancement of pyruvate productivity in Torulopsis glabrata: Increase of NAD+ availability.

    abstract::This study aimed at increasing the pyruvate productivity from a multi-vitamin auxotrophic yeast Torulopsis glabrata, by increasing the availability of NAD+. We examined two strategies for increasing availability of NAD+. To supplement nicotinic acid (NA), the precursor of NAD+; and to increase the activity of alcohol ...

    journal_title:Journal of biotechnology

    pub_type: 杂志文章

    doi:10.1016/j.jbiotec.2006.04.014

    authors: Liu L,Li Y,Shi Z,Du G,Chen J

    更新日期:2006-11-01 00:00:00

  • Rapid degradation of ferulic acid via 4-vinylguaiacol and vanillin by a newly isolated strain of bacillus coagulans.

    abstract::A new strain Bacillus coagulans BK07 was isolated from decomposed wood-bark, based on its ability to grow on ferulic acid as a sole carbon source. This strain rapidly decarboxylated ferulic acid to 4-vinylguaiacol, which was immediately converted to vanillin and then oxidized to vanillic acid. Vanillic acid was furthe...

    journal_title:Journal of biotechnology

    pub_type: 杂志文章

    doi:10.1016/s0168-1656(00)00248-0

    authors: Karmakar B,Vohra RM,Nandanwar H,Sharma P,Gupta KG,Sobti RC

    更新日期:2000-07-14 00:00:00

  • Refolding of hexameric porcine leucine aminopeptidase using a cationic detergent and dextrin-10 as artificial chaperones.

    abstract::The application of artificial chaperones in biotechnology has been inspired by the mechanism of molecular chaperones like GroEL/GroES. It involves addition of a capturing detergent during dilution of the chaotropic reagent, that prevents protein aggregation, and finally, addition of a oligosaccharide that removes the ...

    journal_title:Journal of biotechnology

    pub_type: 杂志文章

    doi:10.1016/j.jbiotec.2009.01.023

    authors: Laslo AC,Ganea E,Obinger C

    更新日期:2009-03-25 00:00:00

  • Magnetic combined cross-linked enzyme aggregates (Combi-CLEAs) for cofactor regeneration in the synthesis of chiral alcohol.

    abstract::Magnetic Fe3O4 nanoparticles were prepared and embedded into the Combi-CLEAs to produce the magnetic Combi-CLEAs in this work. The process for magnetic Combi-CLEAs preparation was optimized, and its properties were investigated. The optimum temperature, thermal stability and optimum pH of magnetic Combi-CLEAs were sim...

    journal_title:Journal of biotechnology

    pub_type: 杂志文章

    doi:10.1016/j.jbiotec.2018.02.007

    authors: Su E,Meng Y,Ning C,Ma X,Deng S

    更新日期:2018-04-10 00:00:00

  • 'Structural constraints in cyanobacteria-mediated whole-cell biotransformation of methoxylated and methylated derivatives of 2'-hydroxychalcone.

    abstract::Halophilic and freshwater strains of cyanobacteria representing the Oscillatoriales, Nostocales, Chroococcales, and Synechococcales orders of Cyanophyta were examined to determine (i) the resistance of their cultures when suppressed by the presence of exogenous methoxylated and methylated derivatives of 2'-hydroxychal...

    journal_title:Journal of biotechnology

    pub_type: 杂志文章

    doi:10.1016/j.jbiotec.2019.01.005

    authors: Żyszka-Haberecht B,Poliwoda A,Lipok J

    更新日期:2019-03-10 00:00:00

  • Biosynthesis of glycolate-based polyesters containing medium-chain-length 3-hydroxyalkanoates in recombinant Escherichia coli expressing engineered polyhydroxyalkanoate synthase.

    abstract::Glycolate(GL)-based polyesters were for the first time produced in the recombinant Escherichia coli fatty acid β-oxidation pathway reinforcing mutant LS5218, using extracellularly added GL as a monomer precursor. Cells expressing a Ser325Thr/Gln481Lys mutant of polyhydroxyalkanoate synthase (PhaC1STQK) from Pseudomona...

    journal_title:Journal of biotechnology

    pub_type: 杂志文章

    doi:10.1016/j.jbiotec.2011.07.040

    authors: Matsumoto K,Ishiyama A,Sakai K,Shiba T,Taguchi S

    更新日期:2011-12-10 00:00:00

  • D-xylose detection in Escherichia coli by a xylose binding protein-dependent response.

    abstract::A gene circuit for the controlled expression of a marker gene and for the assay of xylose concentration in Escherichia coli has been designed and tested. The xylF coding sequence for the xylose binding protein (XBP) was cloned in pT7T318U downstream from the promoter for xylanase A from B. subtilis (Pbsu), together wi...

    journal_title:Journal of biotechnology

    pub_type: 杂志文章

    doi:10.1016/j.jbiotec.2013.10.019

    authors: Ribeiro LF,Bressan F,Furtado GP,Meireles F,Ward RJ

    更新日期:2013-12-01 00:00:00

  • Microbiome response to controlled shifts in ammonium and LCFA levels in co-digestion systems.

    abstract::Anaerobic co-digestion using protein-rich and lipid-rich co-substrates is limited by the accumulation of ammonia and long chain fatty acids (LCFAs), which are important inhibitors of the anaerobic microorganisms. This work aimed to study the microbial community dynamics during gradual and abrupt increase in ammonium a...

    journal_title:Journal of biotechnology

    pub_type: 杂志文章

    doi:10.1016/j.jbiotec.2016.01.006

    authors: Regueiro L,Carballa M,Lema JM

    更新日期:2016-02-20 00:00:00

  • Protein response of insect cells to bioreactor environmental stresses.

    abstract::Protein expression of Spodoptera frugiperda (Sf9) insect cells was characterized upon exposure to environmental stresses typically present in bioreactors including heat shock, oxygen deprivation, shear stress, change of pH, and salinity or ethanol shock. This study fills the void in knowledge as to how bioreactor hydr...

    journal_title:Journal of biotechnology

    pub_type: 杂志文章

    doi:10.1016/j.jbiotec.2005.05.009

    authors: Huhtala A,Linko P,Mutharasan R

    更新日期:2005-08-22 00:00:00

  • Transcriptome analysis of salt stress responsiveness in the seedlings of wild and cultivated Ricinus communis L.

    abstract::Soil salinity is one of the major environmental factors, influencing agricultural productivity of crops. As a non-edible and ideal oilseed crop, castor (Ricinus communis L.) has great industrial value in biofuel, but molecular mechanisms of salt stress regulation are still unknown. In this study, the differentially ex...

    journal_title:Journal of biotechnology

    pub_type: 杂志文章

    doi:10.1016/j.jbiotec.2020.12.020

    authors: Lei P,Liu Z,Hu Y,Kim H,Liu S,Liu J,Xu L,Li J,Zhao Y,Yu Z,Qu Y,Huang F,Meng F

    更新日期:2021-01-06 00:00:00

  • Characterization of cytochrome P450 CYP109E1 from Bacillus megaterium as a novel vitamin D3 hydroxylase.

    abstract::In this study the ability of CYP109E1 from Bacillus megaterium to metabolize vitamin D3 (VD3) was investigated. In an in vitro system using bovine adrenodoxin reductase (AdR) and adrenodoxin (Adx4-108), VD3 was converted by CYP109E1 into several products. Furthermore, a whole-cell system in B. megaterium MS941 was est...

    journal_title:Journal of biotechnology

    pub_type: 杂志文章

    doi:10.1016/j.jbiotec.2016.12.023

    authors: Abdulmughni A,Jóźwik IK,Putkaradze N,Brill E,Zapp J,Thunnissen AW,Hannemann F,Bernhardt R

    更新日期:2017-02-10 00:00:00

  • A novel direct screening method for alkyl glucoside production by glucosidases expressed in E. coli in 96-well plates.

    abstract::The present work describes the development of a novel direct screening method, assayed in 96-well format, for evaluation of enzymatic alkyl glycoside production in a hexanol-water two-phase system. Alkyl glycosides are surfactants with a range of applications and with good biodegradability and low toxicity. Enzymatic ...

    journal_title:Journal of biotechnology

    pub_type: 杂志文章

    doi:10.1016/j.jbiotec.2009.11.005

    authors: Gräber M,Andersson M,Rundbäck F,Pozzo T,Karlsson EN,Adlercreutz P

    更新日期:2010-01-15 00:00:00

  • Differential induction of autophagy in caspase-3/7 down-regulating and Bcl-2 overexpressing recombinant CHO cells subjected to sodium butyrate treatment.

    abstract::Previous research showed that co-down-regulation of caspase-3/7 in rCHO cells, unlike Bcl-2 overexpression, did not effectively block apoptotic cell death induced by 3mM sodium butyrate (NaBu). Here, it is found that the control of autophagy is also related to this different response to NaBu treatment. With NaBu treat...

    journal_title:Journal of biotechnology

    pub_type: 杂志文章

    doi:10.1016/j.jbiotec.2012.05.011

    authors: Lee JS,Kim YJ,Kim CL,Lee GM

    更新日期:2012-09-15 00:00:00

  • Significantly improved thermostability of a reductase CgKR1 from Candida glabrata with a key mutation at Asp 138 for enhancing bioreduction of aromatic α-keto esters.

    abstract::The keto ester reductase from Candida glabrata, designated as CgKR1, is a highly versatile biocatalyst with a broad substrate spectrum. Its substrate preference was altered by rational design of the active pocket for bioreduction of aromatic α-keto esters in our previous work. However, its practical application is sti...

    journal_title:Journal of biotechnology

    pub_type: 杂志文章

    doi:10.1016/j.jbiotec.2015.02.035

    authors: Huang L,Xu JH,Yu HL

    更新日期:2015-06-10 00:00:00

  • Horizontal gene transfer as a biosafety issue: a natural phenomenon of public concern.

    abstract::The transfer of genetic information between distantly or even unrelated organisms during evolution had been inferred from nucleotide sequence comparisons. These studies provided circumstantial evidence that in rare cases genes had been laterally transmitted amongst organisms of the domains bacteria, archaea and eukary...

    journal_title:Journal of biotechnology

    pub_type: 杂志文章,评审

    doi:10.1016/s0168-1656(98)00105-9

    authors: Dröge M,Pühler A,Selbitschka W

    更新日期:1998-09-17 00:00:00

  • Cell growth and enzyme synthesis of a mutant of Arthrobacter sp. (DSM 3747) used for the production of L-amino acids from D,L-5-monosubstituted hydantoins.

    abstract::A microorganism with the ability to form L-tryptophan from D,L-5-(3-indolyl-methyl)hydantoin (D,L-5-IMH) was isolated and identified as Arthrobacter sp. (DSM 3747). After isolation of a mutant with high tryptophan production activity but low tryptophan degradation, cultural conditions were optimized to achieve high am...

    journal_title:Journal of biotechnology

    pub_type: 杂志文章

    doi:10.1016/0168-1656(90)90118-u

    authors: Syldatk C,Mackowiak V,Höke H,Gross C,Dombach G,Wagner F

    更新日期:1990-06-01 00:00:00

  • Glucose oxidase immobilization on a novel cellulose acetate-polymethylmethacrylate membrane.

    abstract::Glucose oxidase (GOD) was immobilized on cellulose acetate-polymethylmethacrylate (CA-PMMA) membrane. The immobilized GOD showed better performance as compared to the free enzyme in terms of thermal stability retaining 46% of the original activity at 70 degrees C where the original activity corresponded to that obtain...

    journal_title:Journal of biotechnology

    pub_type: 杂志文章

    doi:10.1016/j.jbiotec.2005.08.019

    authors: Rauf S,Ihsan A,Akhtar K,Ghauri MA,Rahman M,Anwar MA,Khalid AM

    更新日期:2006-02-10 00:00:00

  • Metabolic flux analysis gives an insight on verapamil induced changes in central metabolism of HL-1 cells.

    abstract::Verapamil has been shown to inhibit glucose transport in several cell types. However, the consequences of this inhibition on central metabolism are not well known. In this study we focused on verapamil induced changes in metabolic fluxes in a murine atrial cell line (HL-1 cells). These cells were adapted to serum free...

    journal_title:Journal of biotechnology

    pub_type: 杂志文章

    doi:10.1016/j.jbiotec.2011.07.028

    authors: Strigun A,Noor F,Pironti A,Niklas J,Yang TH,Heinzle E

    更新日期:2011-09-20 00:00:00

  • Complete genome sequence of Lysinibacillus sphaericus LMG 22257, a strain with ureolytic activity inducing calcium carbonate precipitation.

    abstract::Microbiologically induced calcium carbonate precipitation shows the potential for use in bioremediation and construction consolidation, but the efficiency of this process must be improved. Lysinibacillus sphaericus LMG 22257 is a gram-positive ureolytic strain that has recently been applied for consolidating construct...

    journal_title:Journal of biotechnology

    pub_type: 杂志文章

    doi:10.1016/j.jbiotec.2017.02.016

    authors: Yan W,Xiao X,Zhang Y

    更新日期:2017-03-20 00:00:00

  • Engineered riboswitches as novel tools in molecular biology.

    abstract::During the last years the great importance of RNA for regulating gene expression in all organisms has become obvious. Consequently, several recent approaches aim to utilize the outstanding chemical properties of RNA to develop artificial RNA regulators for conditional gene expression systems. A combination of rational...

    journal_title:Journal of biotechnology

    pub_type: 杂志文章,评审

    doi:10.1016/j.jbiotec.2005.12.006

    authors: Bauer G,Suess B

    更新日期:2006-06-25 00:00:00