The Role of Phase Separation in Heterochromatin Formation, Function, and Regulation.

Abstract:

:In eukaryotic cells, structures called heterochromatin play critical roles in nuclear processes ranging from gene repression to chromosome segregation. Biochemical and in vivo studies over the past several decades have implied that the diverse functions of heterochromatin rely on the ability of these structures to spread across large regions of the genome, to compact the underlying DNA, and to recruit different types of activities. Recent observations have suggested that heterochromatin may possess liquid droplet-like properties. Here, we discuss how these observations provide a new perspective on the mechanisms for the assembly, regulation, and functions of heterochromatin.

journal_name

Biochemistry

journal_title

Biochemistry

authors

Larson AG,Narlikar GJ

doi

10.1021/acs.biochem.8b00401

subject

Has Abstract

pub_date

2018-05-01 00:00:00

pages

2540-2548

issue

17

eissn

0006-2960

issn

1520-4995

journal_volume

57

pub_type

杂志文章,评审
  • Effect of salts on the stability and folding of staphylococcal nuclease.

    abstract::The stability and folding kinetics of wild-type and a mutant staphylococcal nuclease (SNase) at neutral pH are significantly perturbed by the presence of moderate to high concentrations of salts. Very substantial increases in stability toward thermal and urea denaturation were observed; for example, 0.4 M sodium sulfa...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi000861k

    authors: Nishimura C,Uversky VN,Fink AL

    更新日期:2001-02-20 00:00:00

  • Characterization of recombinant Saccharomyces cerevisiae manganese-containing superoxide dismutase and its H30A and K170R mutants expressed in Escherichia coli.

    abstract::All known Mn-containing superoxide dismutases (MnSODs) have a highly conserved histidine (His-30 in Escherichia coli FeSOD) in the active-site channel, and nearly all have an active-site arginine (Arg-170) that has been proposed to play a combined structural and functional role [Chan et al., Arch. Biochem. Biophys. 27...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi980167t

    authors: Borders CL Jr,Bjerrum MJ,Schirmer MA,Oliver SG

    更新日期:1998-08-11 00:00:00

  • Mechanistic diversity in a metalloenzyme superfamily.

    abstract::It is now appreciated that the relationships of proteins, particularly enzymes, within a protein superfamily can be understood not only in terms of their sequence similarities and three-dimensional structures but also by chemical threads that relate their functional attributes. The mechanistic ties among superfamily m...

    journal_title:Biochemistry

    pub_type: 杂志文章,评审

    doi:10.1021/bi001814v

    authors: Armstrong RN

    更新日期:2000-11-14 00:00:00

  • Molecular exchange at the lipid-rhodopsin interface: spin-label electron spin resonance studies of rhodopsin-dimyristoylphosphatidylcholine recombinants.

    abstract::The photoreceptor protein rhodopsin has been reconstituted with a single phospholipid species, dimyristoylphosphatidylcholine, at a range of different lipid/protein ratios, and the exchange rate at the lipid-protein interface has been determined from the electron spin resonance spectra of spin-labeled phosphatidylchol...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00385a045

    authors: Ryba NJ,Horváth LI,Watts A,Marsh D

    更新日期:1987-06-02 00:00:00

  • Interaction of profilin with G-actin and poly(L-proline).

    abstract::The interaction of bovine spleen profilin with ATP- and ADP-G-actin and poly(L-proline) has been studied by spectrofluorimetry, analytical ultracentrifugation, and rapid kinetics in low ionic strength buffer. Profilin binding to G-actin is accompanied by a large quenching of tryptophan fluorescence, allowing the measu...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00194a011

    authors: Perelroizen I,Marchand JB,Blanchoin L,Didry D,Carlier MF

    更新日期:1994-07-19 00:00:00

  • Partially folded forms of barley lipid transfer protein are more surface active.

    abstract::Thermal and chemical modification of protein structures is known to affect their interfacial activity. We have looked in detail at the effect of heating on the structure and subsequently the surface properties of LTP1, a nonspecific lipid transfer protein from barley, both in the presence and in the absence of its lip...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi901328f

    authors: Clare Mills EN,Gao C,Wilde PJ,Rigby NM,Wijesinha-Bettoni R,Johnson VE,Smith LJ,Mackie AR

    更新日期:2009-12-29 00:00:00

  • Volumetrically Derived Thermodynamic Profile of Interactions of Urea with a Native Protein.

    abstract::We report the first experimental characterization of the full thermodynamic profile for binding of urea to a native protein. We measured the volumetric parameters of lysozyme at pH 7.0 as a function of urea within a temperature range of 18-45 °C. At neutral pH, lysozyme retains its native conformation between 0 and 8 ...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/acs.biochem.6b00805

    authors: Son I,Chalikian TV

    更新日期:2016-11-29 00:00:00

  • Catalytic function and local proton structure at the type 2 copper of nitrite reductase: the correlation of enzymatic pH dependence, conserved residues, and proton hyperfine structure.

    abstract::Electron nuclear double resonance (ENDOR) of protons at Type 2 and Type 1 cupric active sites correlates with the enzymatic pH dependence, the mutation of nearby conserved, nonligating residues, and electron transfer in heterologously expressed Rhodobacter sphaeroides nitrite reductase. Wild-type enzyme showed a pH 6 ...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi0256274

    authors: Zhao Y,Lukoyanov DA,Toropov YV,Wu K,Shapleigh JP,Scholes CP

    更新日期:2002-06-11 00:00:00

  • Resonance raman analysis of chromophore structure in the lumi-R photoproduct of phytochrome.

    abstract::Resonance Raman vibrational spectra of the Pr, lumi-R, and Pfr forms of phytochrome have been obtained using low-temperature trapping and room temperature flow techniques in conjunction with shifted-excitation Raman difference spectroscopy (SERDS). The Pr to lumi-R photoconversion exhibits a thermal barrier and is com...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi962175k

    authors: Andel F 3rd,Lagarias JC,Mathies RA

    更新日期:1996-12-17 00:00:00

  • Kinetics and thermodynamics of the mechanism of interaction of sodium phytate with alpha-globulin.

    abstract::The precipitation mechanism of alpha-globulin in the presence of myo-inositol hexaphosphate (sodium phytate) was studied in detail. The maximum interaction was found at pH 2.3 where the protein was in a dissociated state having an 8.3S aggregate and a 1.5S monomer. This interaction was predominantly dependent upon the...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00064a035

    authors: Rajendran S,Prakash V

    更新日期:1993-04-06 00:00:00

  • Interparticle interactions and structural changes of nucleosome core particles in low-salt solution.

    abstract::The structural behavior of the nucleosome core particles in the range of solvent Na+ concentration from 10.45 to 0.45 mM has been studied by small-angle neutron and synchroton radiation X-ray scattering, sedimentation, atomic absorption spectroscopy, density measurements, and circular dichroism. With decreasing salt c...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00420a051

    authors: Hirai M,Niimura N,Zama M,Mita K,Ichimura S,Tokunaga F,Ishikawa Y

    更新日期:1988-10-04 00:00:00

  • The stability of chicken nucleoside triphosphate diphosphohydrolase 8 requires both of its transmembrane domains.

    abstract::Chicken nucleoside triphosphate diphosphohydrolase 8 (NTPDase8) is a cell surface ectonucleotidase with a large extracellular domain (ECD) containing the active site and is anchored to the membrane by two transmembrane domains (TMDs) at the N- and C-termini. Unlike other cell surface NTPDases that have been characteri...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi901820c

    authors: Li CS,Lee Y,Knowles AF

    更新日期:2010-01-12 00:00:00

  • The crystal structure of the C-terminal truncated apolipoprotein A-I sheds new light on amyloid formation by the N-terminal fragment.

    abstract::Apolipoprotein A-I (apoA-I) is the main protein of plasma high-density lipoproteins (HDL, or good cholesterol) that remove excess cell cholesterol and protect against atherosclerosis. In hereditary amyloidosis, mutations in apoA-I promote its proteolysis and the deposition of the 9-11 kDa N-terminal fragments as fibri...

    journal_title:Biochemistry

    pub_type: 杂志文章,评审

    doi:10.1021/bi2017014

    authors: Gursky O,Mei X,Atkinson D

    更新日期:2012-01-10 00:00:00

  • Solution structure of a designed spirocyclic helical ligand binding at a two-base bulge site in DNA.

    abstract::The solution structure of the complex formed between an oligodeoxynucleotide containing a two-base bulge (5'-CCATCGTCTACCTTTGGTAGGATGG) and SCA-alpha2, a designed spirocyclic helical molecule, has been elucidated. SCA-alpha2, a close mimic of the metabolite, NCSi-gb, of the DNA bulge-specific enediyne antibiotic neoca...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi602599d

    authors: Zhang N,Lin Y,Xiao Z,Jones GB,Goldberg IH

    更新日期:2007-04-24 00:00:00

  • Interactions between phospholipids and NADH:ubiquinone oxidoreductase (complex I) from bovine mitochondria.

    abstract::NADH:ubiquinone oxidoreductase (complex I) from bovine heart mitochondria is a highly complicated, energy transducing, membrane-bound enzyme. It contains 46 different subunits and nine redox cofactors: a noncovalently bound flavin mononucleotide and eight iron-sulfur clusters. The mechanism of complex I is not known. ...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi051809x

    authors: Sharpley MS,Shannon RJ,Draghi F,Hirst J

    更新日期:2006-01-10 00:00:00

  • DNA damage by the enediyne C-1027 results in the inhibition of DNA replication by loss of replication protein A function and activation of DNA-dependent protein kinase.

    abstract::Treatment of cells with the enediyne C-1027 is highly efficient at inducing single- and double-strand DNA breaks. This agent is highly cytotoxic when used at picomolar levels over a period of days. For this study, C-1027 has been used at higher levels for a much shorter time period to look at early cellular responses ...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi015680c

    authors: Liu JS,Kuo SR,Yin X,Beerman TA,Melendy T

    更新日期:2001-12-04 00:00:00

  • Protease-sensitive scrapie prion protein in aggregates of heterogeneous sizes.

    abstract::The pathological prion protein PrP(Sc) is the only known component of the infectious prion. In cells infected with prions, PrP(Sc) is formed posttranslationally by the refolding of the benign cell surface glycoprotein PrP(C) into an aberrant conformation. The two PrP isoforms possess very different properties, as PrP(...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi025958g

    authors: Tzaban S,Friedlander G,Schonberger O,Horonchik L,Yedidia Y,Shaked G,Gabizon R,Taraboulos A

    更新日期:2002-10-22 00:00:00

  • Emerging Functional Differences between the Synaptotagmin and Ferlin Calcium Sensor Families.

    abstract::The ferlin family proteins have emerged as multi-C2 domain regulators of calcium-triggered membrane fusion and fission events. While initially determined to share many of the features of members of the synaptotagmin family of calcium sensors, ferlins in more recent studies have been found to interact directly with non...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/acs.biochem.7b00928

    authors: Johnson CP

    更新日期:2017-12-12 00:00:00

  • Comparison of Alicyclobacillus acidocaldarius o-Succinylbenzoate Synthase to Its Promiscuous N-Succinylamino Acid Racemase/ o-Succinylbenzoate Synthase Relatives.

    abstract::Studying the evolution of catalytically promiscuous enzymes like those from the N-succinylamino acid racemase/ o-succinylbenzoate synthase (NSAR/OSBS) subfamily can reveal mechanisms by which new functions evolve. Some enzymes in this subfamily have only OSBS activity, while others catalyze OSBS and NSAR reactions. We...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/acs.biochem.8b00088

    authors: Odokonyero D,McMillan AW,Ramagopal UA,Toro R,Truong DP,Zhu M,Lopez MS,Somiari B,Herman M,Aziz A,Bonanno JB,Hull KG,Burley SK,Romo D,Almo SC,Glasner ME

    更新日期:2018-07-03 00:00:00

  • A fluorescent mutant of the NM domain of the yeast prion Sup35 provides insight into fibril formation and stability.

    abstract::The Sup35 protein of Saccharomyces cerevisiae forms a prion that generates the [PSI(+)] phenotype. Its NM region governs prion status, forming self-seeding amyloid fibers in vivo and in vitro. A tryptophan mutant of Sup35 (NM(F117W)) was used to probe its aggregation. Four indicators of aggregation, Trp 117 maximum em...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi9000276

    authors: Palhano FL,Rocha CB,Bernardino A,Weissmuller G,Masuda CA,Montero-Lomelí M,Gomes AM,Chien P,Fernandes PM,Foguel D

    更新日期:2009-07-28 00:00:00

  • Purification and characterization of an alpha-glucosidase from Saccharomyces carlsbergensis.

    abstract::alpha-Glucosidase (EC 3.2.1.20) was purified to homogeneity from logarithmically growing cells of Saccharomyces carlsbergensis. The purification involved the following steps: (a) ammonium sulfate fractionation; (b) Sephadex G-100 chromatography; (c) DEAE-cellulose chromatography; and (d) hydroxylapatite chromatography...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00615a011

    authors: Needleman RB,Federoff HJ,Eccleshall TR,Buchferer B,Marmur J

    更新日期:1978-10-31 00:00:00

  • Isolation and characterization of a dog serum lipoprotein having apolipoprotein A-I as its predominant protein constituent.

    abstract::The serum high density lipoproteins (HDL) of normolipemic dogs (beagles) were isolated in the density range of p 1.063 to 1.21 g/ml, and characterized in terms of composition and physical properties (flotation and diffusion coefficients, partial specific volume, molecular weight, electrophoretic mobility, ultraviolet ...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00654a022

    authors: Edelstein C,Lewis LL,Shainoff JR,Naito H,Scanu AM

    更新日期:1976-05-04 00:00:00

  • Localization of a trifluoperazine binding site on troponin C.

    abstract::Trifluoperazine (TFP) was shown to interact with the cyanogen bromide fragment 9 (CB9) (residues 84-135) of rabbit skeletal troponin C and with a synthetic peptide representing the N-terminal region of CB9. The phenothiazine did not affect the calcium binding property of CB9 as observed by proton magnetic resonance an...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00276a010

    authors: Gariépy J,Hodges RS

    更新日期:1983-03-29 00:00:00

  • Isolation and characterization of a human colon carcinoma-secreted enzyme with pancreatic ribonuclease-like activity.

    abstract::A ribonuclease was isolated from serum-free supernatants of the human colon adenocarcinoma cell line HT-29. It was purified by cation-exchange and C18 reversed-phase high-performance liquid chromatography. The protein is basic, has a molecular weight of approximately 16,000, and has an amino acid composition that is s...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00371a002

    authors: Shapiro R,Fett JW,Strydom DJ,Vallee BL

    更新日期:1986-11-18 00:00:00

  • Patterns of proteolytic cleavage and carbodiimide derivatization in sarcoplasmic reticulum adenosinetriphosphatase.

    abstract::Two series of experiments were carried out to characterize (a) peptide fragments of sarcoplasmic reticulum (SR) ATPase, based on proteolysis with different enzymes and distribution of known labels, and (b) specific labeling and functional inactivation patterns, following ATPase derivatization with dicyclohexylcarbodii...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00405a061

    authors: de Ancos JG,Inesi G

    更新日期:1988-03-08 00:00:00

  • Trehalose-containing lipooligosaccharides of Mycobacterium gordonae: presence of a mono-O-methyltetra-O-acyltrehalose "core" and branching in the oligosaccharide backbone.

    abstract::Past evidence has indicated that Mycobacterium gordonae, as isolated from soil and as an occasional opportunistic pathogen, exists as a serocomplex. We now demonstrate that the basis of seroreactivity and diversity is a novel series of alkali-labile, trehalose-containing lipooligosaccharides (LOS). The structures from...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00210a020

    authors: Besra GS,McNeil MR,Khoo KH,Dell A,Morris HR,Brennan PJ

    更新日期:1993-11-30 00:00:00

  • Presence of divalent cation is not mandatory for the formation of intramolecular purine-motif triplex containing human c-jun protooncogene target.

    abstract::Modulation of endogenous gene function, through sequence-specific recognition of double helical DNA via oligonucleotide-directed triplex formation, is a promising approach. Compared to the formation of pyrimidine motif triplexes, which require relatively low pH, purine motif appears to be the most gifted for their sta...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi1012589

    authors: Kaushik S,Kaushik M,Svinarchuk F,Malvy C,Fermandjian S,Kukreti S

    更新日期:2011-05-17 00:00:00

  • Effects of polyamines, polyamine analogs, and inhibitors of protein synthesis on spermidine-spermine N1-acetyltransferase gene expression.

    abstract::The key polyamine catabolizing enzyme spermidine-spermine N1-acetyltransferase (SSAT) is among the few genes known to be inducible by the natural polyamines. Certain polyamine analogs markedly exaggerate this response and thus provide useful tools for studying the underlying regulatory mechanisms. As shown here, the a...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi9612273

    authors: Fogel-Petrovic M,Vujcic S,Brown PJ,Haddox MK,Porter CW

    更新日期:1996-11-12 00:00:00

  • Inhibition of in vitro transcription by a triplex-forming oligonucleotide targeted to human c-myc P2 promoter.

    abstract::Triplex-forming oligonucleotides (TFOs) have been shown to bind in a sequence-specific manner to polypurine/polypyrimidine sequences in several human gene promoters, including the c-myc P1 promoter. TFOs have been shown to inhibit transcription in vitro and the expression of target genes in cell culture. The human c-m...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00025a023

    authors: Kim HG,Miller DM

    更新日期:1995-06-27 00:00:00

  • Binding of ncd to microtubules induces a conformational change near the junction of the motor domain with the neck.

    abstract::We have covalently attached an electron paramagnetic resonance (EPR) spin probe to Cys-670 of the motor domain of ncd (nonclaret disjunctional protein) in order to investigate conformational changes associated with the chemomechanical cycle. Spin-labeling is highly specific and does not affect ncd function as monitore...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi9706881

    authors: Naber N,Cooke R,Pate E

    更新日期:1997-08-12 00:00:00