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Jiamu Du et al.
Biochimica et biophysica acta, 1839(8), 719-727 (2014-04-22)
Epigenetic mechanisms control gene regulation by writing, reading and erasing specific epigenetic marks. Within the context of multi-disciplinary approaches applied to investigate epigenetic regulation in diverse systems, structural biology techniques have provided insights at the molecular level of key interactions
C Derek Ma et al.
Nature, 517(7534), 347-350 (2015-01-17)
The structure of water near non-polar molecular fragments or surfaces mediates the hydrophobic interactions that underlie a broad range of interfacial, colloidal and biophysical phenomena. Substantial progress over the past decade has improved our understanding of hydrophobic interactions in simple
Rakhi Gupta et al.
Developmental biology, 395(1), 38-49 (2014-09-11)
To determine the hierarchy of transcriptional regulation within the in vivo vertebrate embryo, we examined whether developmental enhancers were influenced by Nodal signaling during early embryogenesis in Xenopus tropicalis. We find that developmental enhancers, defined by the active enhancer chromatin
Anna Cascante et al.
Journal of molecular biology, 426(20), 3467-3477 (2014-04-22)
Neural stem cell (NSC) state and fate depend on spatially and temporally synchronized transcriptional and epigenetic regulation of the expression of extrinsic signaling factors and intrinsic cell-specific genes, but the functional roles for chromatin-modifying enzymes in neural differentiation remain poorly
Takashi Toyama et al.
Chemico-biological interactions, 214, 41-48 (2014-03-04)
Covalent modification of cellular proteins by electrophiles affects electrophilic signal transduction and the dysfunction of enzymes that is involved in cytotoxicity. We have recently found a unique reaction which restores glyceraldehyde-3-phosphate dehydrogenase (GAPDH) that has been modified by 1,2-naphthoquinone (1,2-NQ)
Keisuke Miyagawa et al.
Proceedings of the National Academy of Sciences of the United States of America, 111(16), 5950-5955 (2014-04-09)
Telomeres protect DNA ends of linear eukaryotic chromosomes from degradation and fusion, and ensure complete replication of the terminal DNA through recruitment of telomerase. The regulation of telomerase is a critical area of telomere research and includes cis regulation by
Gregory R Wagner et al.
Molecular cell, 54(1), 5-16 (2014-04-15)
Cellular proteins are decorated with a wide range of acetyl and other acyl modifications. Many studies have demonstrated regulation of site-specific acetylation by acetyltransferases and deacetylases. Acylation is emerging as a new type of lysine modification, but less is known
Panagis Filippakopoulos et al.
Nature reviews. Drug discovery, 13(5), 337-356 (2014-04-23)
Lysine acetylation is a key mechanism that regulates chromatin structure; aberrant acetylation levels have been linked to the development of several diseases. Acetyl-lysine modifications create docking sites for bromodomains, which are small interaction modules found on diverse proteins, some of
Li Jiao et al.
The American journal of clinical nutrition, 101(1), 126-134 (2014-12-21)
Advanced glycation end products (AGEs) are a heterogeneous group of compounds present in uncooked foods as well as in foods cooked at high temperatures. AGEs have been associated with insulin resistance, oxidative stress, and chronic inflammation in patients with diabetes.
Audrey Letourneau et al.
Nature, 508(7496), 345-350 (2014-04-18)
Trisomy 21 is the most frequent genetic cause of cognitive impairment. To assess the perturbations of gene expression in trisomy 21, and to eliminate the noise of genomic variability, we studied the transcriptome of fetal fibroblasts from a pair of
Muhammad Zoabi et al.
Nucleic acids research, 42(21), 13026-13038 (2014-11-08)
The JmjC-containing lysine demethylase, KDM4D, demethylates di-and tri-methylation of histone H3 on lysine 9 (H3K9me3). How KDM4D is recruited to chromatin and recognizes its histone substrates remains unknown. Here, we show that KDM4D binds RNA independently of its demethylase activity.
Methylation: a multifaceted modification - looking at transcription and beyond.
Johnathan R Whetstine
Biochimica et biophysica acta, 1839(12), 1351-1352 (2014-09-17)
Jean-Sébastien Jouhanneau et al.
Neuron, 84(5), 1065-1078 (2014-12-03)
Neighboring cortical excitatory neurons show considerable heterogeneity in their responses to sensory stimulation. We hypothesized that a subset of layer 2 excitatory neurons in the juvenile (P18 to 27) mouse whisker somatosensory cortex, distinguished by expression of the activity-dependent fosGFP
Catherine A Musselman et al.
Biochimica et biophysica acta, 1839(8), 686-693 (2014-04-15)
Lysine methylation is the most versatile covalent posttranslational modification (PTM) found in histones and non-histone proteins. Over the past decade a number of methyllysine-specific readers have been discovered and their interactions with histone tails have been structurally and biochemically characterized.
Jennifer C Harr et al.
The Journal of cell biology, 208(1), 33-52 (2015-01-07)
Nuclear organization has been implicated in regulating gene activity. Recently, large developmentally regulated regions of the genome dynamically associated with the nuclear lamina have been identified. However, little is known about how these lamina-associated domains (LADs) are directed to the
Wei Wan et al.
Biochimica et biophysica acta, 1844(6), 1059-1070 (2014-03-19)
The genetic incorporation of the 22nd proteinogenic amino acid, pyrrolysine (Pyl) at amber codon is achieved by the action of pyrrolysyl-tRNA synthetase (PylRS) together with its cognate tRNA(Pyl). Unlike most aminoacyl-tRNA synthetases, PylRS displays high substrate side chain promiscuity, low
Nathan R Rose et al.
Biochimica et biophysica acta, 1839(12), 1362-1372 (2014-02-25)
DNA methylation acts as an epigenetic modification in vertebrate DNA. Recently it has become clear that the DNA and histone lysine methylation systems are highly interrelated and rely mechanistically on each other for normal chromatin function in vivo. Here we
Francesca Mattiroli et al.
Nature structural & molecular biology, 21(4), 308-316 (2014-04-05)
Ubiquitin and ubiquitin-like modifications are central to virtually all cellular signaling pathways. They occur primarily on lysine residues of target proteins and stimulate a large number of downstream signals. The diversity of these signals depends on the type, location and
Stefanie Wurm et al.
Genes & development, 29(2), 144-156 (2014-12-31)
Altered epidermal differentiation characterizes numerous skin diseases affecting >25% of the human population. Here we identified Fra-2/AP-1 as a key regulator of terminal epidermal differentiation. Epithelial-restricted, ectopic expression of Fra-2 induced expression of epidermal differentiation genes located within the epidermal
Elizabeth Cox et al.
Biochimica et biophysica acta, 1838(9), 2198-2204 (2014-05-02)
Aminoacylated phosphatidylglycerols are common lipids in bacterial cytoplasmic membranes. Their presence in Staphylococcus aureus has been linked to increased resistance to a number of antibacterial agents, including antimicrobial peptides. Most commonly, the phosphatidylglycerol headgroup is esterified to lysine, which converts
Binuraj R K Menon et al.
The Journal of biological chemistry, 289(49), 34161-34174 (2014-09-13)
Cobalamin-dependent enzymes enhance the rate of C-Co bond cleavage by up to ∼10(12)-fold to generate cob(II)alamin and a transient adenosyl radical. In the case of the pyridoxal 5'-phosphate (PLP) and cobalamin-dependent enzymes lysine 5,6-aminomutase and ornithine 4,5 aminomutase (OAM), it
Mohammad S Eram et al.
The Journal of biological chemistry, 289(17), 12177-12188 (2014-03-19)
PRDM9 (PR domain-containing protein 9) is a meiosis-specific protein that trimethylates H3K4 and controls the activation of recombination hot spots. It is an essential enzyme in the progression of early meiotic prophase. Disruption of the PRDM9 gene results in sterility
Jingjie Yi et al.
The Journal of biological chemistry, 289(49), 33878-33886 (2014-10-11)
The key member of the MOZ (monocyticleukaemia zinc finger protein), Ybf2/Sas3, Sas2, and TIP60 acetyltransferases family, Tat-interactive protein, 60 kD (TIP60), tightly modulates a wide array of cellular processes, including chromatin remodeling, gene transcription, apoptosis, DNA repair, and cell cycle
Cuylar J T Conly et al.
Biochemistry, 53(47), 7396-7406 (2014-11-05)
Dihydrodipicolinate synthase (DHDPS), an enzyme found in most bacteria and plants, controls a critical step in the biosynthesis of l-lysine and meso-diaminopimelate, necessary components for bacterial cell wall biosynthesis. DHDPS catalyzes the condensation of pyruvate and (S)-aspartate-β-semialdehyde, forming an unstable
Julien Fournier et al.
The Journal of neuroscience : the official journal of the Society for Neuroscience, 34(16), 5515-5528 (2014-04-18)
In the primary visual cortex (V1), Simple and Complex receptive fields (RFs) are usually characterized on the basis of the linearity of the cell spiking response to stimuli of opposite contrast. Whether or not this classification reflects a functional dichotomy
Sun-Shin Cha et al.
Biochemical and biophysical research communications, 450(2), 1045-1050 (2014-07-01)
MurF adds d-Ala-d-Ala dipeptide to UDP-N-acetylmuramyl-l-Ala-γ-d-Glu-m-DAP (or l-Lys) in an ATP-dependent manner, which is the last step in the biosynthesis of monomeric precursor of peptidoglycan. Here we report crystal structures of two MurF-ATP complexes: the MurF-ATP complex and the MurF-ATP-UDP
Synthetic biology: Two-for-one designer labels.
E James Petersson et al.
Nature chemistry, 6(5), 379-381 (2014-04-24)
Timothy J Stasevich et al.
Nature, 516(7530), 272-275 (2014-09-26)
In eukaryotic cells, post-translational histone modifications have an important role in gene regulation. Starting with early work on histone acetylation, a variety of residue-specific modifications have now been linked to RNA polymerase II (RNAP2) activity, but it remains unclear if
Hong Wen et al.
Nature, 508(7495), 263-268 (2014-03-05)
Recognition of modified histones by 'reader' proteins plays a critical role in the regulation of chromatin. H3K36 trimethylation (H3K36me3) is deposited onto the nucleosomes in the transcribed regions after RNA polymerase II elongation. In yeast, this mark in turn recruits
Chunaram Choudhary et al.
Nature reviews. Molecular cell biology, 15(8), 536-550 (2014-07-24)
Lysine acetylation is a conserved protein post-translational modification that links acetyl-coenzyme A metabolism and cellular signalling. Recent advances in the identification and quantification of lysine acetylation by mass spectrometry have increased our understanding of lysine acetylation, implicating it in many
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