PHF13 is a molecular reader and transcriptional co-regulator of H3K4me2/3

PHF13 is a chromatin affiliated protein with a functional role in differentiation, cell division, DNA damage response and higher chromatin order. To gain insight into PHF13's ability to modulate these processes, we elucidate the mechanisms targeting PHF13 to chromatin, its genome wide localization and its molecular chromatin context. Size exclusion chromatography, mass spectrometry, X-ray crystallography and ChIP sequencing demonstrate that PHF13 binds chromatin in a multivalent fashion via direct interactions with H3K4me2/3 and DNA, and indirectly via interactions with PRC2 and RNA PolII. Furthermore, PHF13 depletion disrupted the interactions between PRC2, RNA PolII S5P, H3K4me3 and H3K27me3 and resulted in the up and down regulation of genes functionally enriched in transcriptional regulation, DNA binding, cell cycle, differentiation and chromatin organization. Together our findings argue that PHF13 is an H3K4me2/3 molecular reader and transcriptional co-regulator, affording it the ability to impact different chromatin processes.

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High-throughput Protein Production for X-ray Crystallography and Use of Size Exclusion Chromatography to Validate or Refute Computational Biological Unit Predictions

Journal of Structural and Functional Genomics ◽

10.1007/s10969-005-2898-1 ◽

2005 ◽

Vol 6 (2-3) ◽

pp. 135-141 ◽

Cited By ~ 10

Author(s):

Daniel McMullan ◽

Jaume M. Canaves ◽

Kevin Quijano ◽

Polat Abdubek ◽

Edward Nigoghossian ◽

...

Keyword(s):

Size Exclusion Chromatography ◽

High Throughput ◽

Protein Production ◽

Size Exclusion ◽

Biological Unit ◽

X Ray ◽

X Ray Crystallography ◽

Exclusion Chromatography

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A ribonucleotide reductase from Clostridium botulinum reveals distinct evolutionary pathways to regulation via the overall activity site

Journal of Biological Chemistry ◽

10.1074/jbc.ra120.014895 ◽

2020 ◽

Vol 295 (46) ◽

pp. 15576-15587

Author(s):

Markel Martínez-Carranza ◽

Venkateswara Rao Jonna ◽

Daniel Lundin ◽

Margareta Sahlin ◽

Lars-Anders Carlson ◽

...

Keyword(s):

Ribonucleotide Reductase ◽

Clostridium Botulinum ◽

Building Blocks ◽

Size Exclusion ◽

Class I ◽

Activity Regulation ◽

E Coli ◽

X Ray Crystallography ◽

Exclusion Chromatography ◽

Insight Into

Ribonucleotide reductase (RNR) is a central enzyme for the synthesis of DNA building blocks. Most aerobic organisms, including nearly all eukaryotes, have class I RNRs consisting of R1 and R2 subunits. The catalytic R1 subunit contains an overall activity site that can allosterically turn the enzyme on or off by the binding of ATP or dATP, respectively. The mechanism behind the ability to turn the enzyme off via the R1 subunit involves the formation of different types of R1 oligomers in most studied species and R1–R2 octamers in Escherichia coli. To better understand the distribution of different oligomerization mechanisms, we characterized the enzyme from Clostridium botulinum, which belongs to a subclass of class I RNRs not studied before. The recombinantly expressed enzyme was analyzed by size-exclusion chromatography, gas-phase electrophoretic mobility macromolecular analysis, EM, X-ray crystallography, and enzyme assays. Interestingly, it shares the ability of the E. coli RNR to form inhibited R1–R2 octamers in the presence of dATP but, unlike the E. coli enzyme, cannot be turned off by combinations of ATP and dGTP/dTTP. A phylogenetic analysis of class I RNRs suggests that activity regulation is not ancestral but was gained after the first subclasses diverged and that RNR subclasses with inhibition mechanisms involving R1 oligomerization belong to a clade separated from the two subclasses forming R1–R2 octamers. These results give further insight into activity regulation in class I RNRs as an evolutionarily dynamic process.

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Genome wide profiling of miRNAs relevant to the DNA damage response induced by hexavalent chromium exposure (DDR-related miRNAs in response to Cr (VI) exposure)

Environment International ◽

10.1016/j.envint.2021.106782 ◽

2021 ◽

Vol 157 ◽

pp. 106782

Author(s):

Li Shi ◽

Lingfang Feng ◽

Yan Tong ◽

Junlin Jia ◽

Tao Li ◽

...

Keyword(s):

Dna Damage ◽

Hexavalent Chromium ◽

Dna Damage Response ◽

Genome Wide ◽

Damage Response ◽

Chromium Exposure

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Rational synthesis of an atomically precise carboncone under mild conditions

Science Advances ◽

10.1126/sciadv.aaw0982 ◽

2019 ◽

Vol 5 (8) ◽

pp. eaaw0982 ◽

Cited By ~ 7

Author(s):

Zheng-Zhong Zhu ◽

Zuo-Chang Chen ◽

Yang-Rong Yao ◽

Cun-Hao Cui ◽

Shu-Hui Li ◽

...

Keyword(s):

Apex Angle ◽

Facile Synthesis ◽

Reaction Conditions ◽

X Ray ◽

Carbon Allotropes ◽

X Ray Crystallography ◽

Mild Conditions ◽

Research Opportunity ◽

Insight Into ◽

Structural Strain

Carboncones, a special family of all-carbon allotropes, are predicted to have unique properties that distinguish them from fullerenes, carbon nanotubes, and graphenes. Owing to the absence of methods to synthesize atomically well-defined carboncones, however, experimental insight into the nature of pure carboncones has been inaccessible. Herein, we describe a facile synthesis of an atomically well-defined carboncone[1,2] (C70H20) and its soluble penta-mesityl derivative. Identified by x-ray crystallography, the carbon skeleton is a carboncone with the largest possible apex angle. Much of the structural strain is overcome in the final step of converting the bowl-shaped precursor into the rigid carboncone under mild reaction conditions. This work provides a research opportunity for investigations of atomically precise single-layered carboncones having even higher cone walls and/or smaller apex angles.

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Cloning, expression, purification, crystallization and preliminary X-ray diffraction of a lysine-specific permease fromPseudomonas aeruginosa

Acta Crystallographica Section F Structural Biology Communications ◽

10.1107/s2053230x14017865 ◽

2014 ◽

Vol 70 (10) ◽

pp. 1362-1367 ◽

Cited By ~ 3

Author(s):

Emmanuel Nji ◽

Dianfan Li ◽

Declan A. Doyle ◽

Martin Caffrey

Keyword(s):

Metal Ion ◽

Cell Volume Regulation ◽

Ion Concentration ◽

Size Exclusion ◽

Substrate Selectivity ◽

X Ray Diffraction ◽

Unit Cell Parameters ◽

X Ray ◽

Cell Parameters ◽

Exclusion Chromatography

The prokaryotic lysine-specific permease (LysP) belongs to the amino acid–polyamine–organocation (APC) transporter superfamily. In the cell, members of this family are responsible for the uptake and recycling of nutrients, for the maintenance of a constant internal ion concentration and for cell volume regulation. The detailed mechanism of substrate selectivity and transport of L-lysine by LysP is not understood. A high-resolution crystal structure would enormously facilitate such an understanding. To this end, LysP fromPseudomonas aeruginosawas recombinantly expressed inEscherichia coliand purified to near homogeneity by immobilized metal ion-affinity chromatography (IMAC) and size-exclusion chromatography (SEC). Hexagonal- and rod-shaped crystals were obtained in the presence of L-lysine and the L-lysine analogue L-4-thialysine by vapour diffusion and diffracted to 7.5 Å resolution. The diffraction data were indexed in space groupP21, with unit-cell parametersa= 169.53,b= 169.53,c= 290.13 Å, γ = 120°.

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How big is big? Separation by conventional methods, X-ray and electronic structures of positional isomers of bis-tert-butylisocyano adduct of 2(3),9(10),16(17),23(24)-tetrachloro-3(2),10(9),17(16),24(23)-tetra(2,6-di-iso-propylphenoxy)-phthalocyaninato iron(II) complex

Journal of Porphyrins and Phthalocyanines ◽

10.1142/s1088424616500164 ◽

2016 ◽

Vol 20 (01n04) ◽

pp. 337-351 ◽

Cited By ~ 4

Author(s):

Derrick R. Anderson ◽

Pavlo V. Solntsev ◽

Hannah M. Rhoda ◽

Victor N. Nemykin

Keyword(s):

Electronic Structures ◽

Density Functional ◽

Positional Isomers ◽

Excitation Energies ◽

Functional Theory ◽

X Ray ◽

Vertical Excitation ◽

X Ray Crystallography ◽

Tddft Calculations ◽

Insight Into

A presence of bulky 2,6-di-iso-propylphenoxy groups in bis-tert-butylisocyano adduct of 2(3),9(10),16(17),23(24)-tetrachloro-3(2),10(9),17(16),24(23)-tetra(2,6-di-iso-propylphenoxy)-phthalocyaninato iron(II) complex allows separation of two individual positional isomers and a mixture of the remaining two isomers using conventional chromatography. X-ray structures of “[Formula: see text]” and “[Formula: see text]” isomers were confimed by X-ray crystallography. Density functional theory (DFT) and time-dependent DFT (TDDFT) calculations of each individual positional isomer allowed insight into their electronic structures and vertical excitation energies, which were correlated with the experimental UV-vis and MCD spectra.

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