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Carbon nanostructures are attracting intense interest because of their many unique and novel properties. The strong and tunable luminescence of carbon materials further enhances their versatile properties; in particular, the quantum effect in carbon is extremely important both fundamentally and technologically. [1][2][3][4] Recently, photoluminescent carbonbased nanoparticles have received much attention. They are usually prepared by laser ablation of graphite, electrochemical oxidation of graphite, electrochemical soaking of carbon nanotubes, thermal oxidation of suitable molecular precursors, vapor deposition of soot, proton-beam irradiation of nanodiamonds, microwave synthesis, and bottom-up methods.[5-13] Although small (ca. 2 nm) graphite nanoparticles show strong blue photoluminescence (PL), [13] definitive experimental evidence for luminescence of carbon structure arising from quantum-confinement effects and size-dependent optical properties of carbon quantum dots (CQDs) remains scarce.Herein, we report the facile one-step alkali-assisted electrochemical fabrication of CQDs with sizes of 1.2-3.8 nm which possess size-dependent photoluminescence (PL) and excellent upconversion luminescence properties. Significantly, we demonstrate the design of photocatalysts (TiO 2 /CQDs and SiO 2 /CQDs complex system) to harness the use of the full spectrum of sunlight (based on the upconversion luminescence properties of CQDs).

Histones comprise the major protein component of chromatin, the scaffold in which the eukaryotic genome is packaged, and are subject to many types of post-translational modifications (PTMs), especially on their flexible tails. These modifications may constitute a 'histone code' and could be used to manage epigenetic information that helps extend the genetic message beyond DNA sequences. This proposed code, read in part by histone PTM-binding 'effector' modules and their associated complexes, is predicted to define unique functional states of chromatin and/or regulate various chromatin-templated processes. A wealth of structural and functional data show how chromatin effector modules target their cognate covalent histone modifications. Here we summarize key features in molecular recognition of histone PTMs by a diverse family of 'reader pockets', highlighting specific readout mechanisms for individual marks, common themes and insights into the downstream functional consequences of the interactions. Changes in these interactions may have far-reaching implications for human biology and disease, notably cancer.The vast majority of DNA in eukaryotic organisms is intimately wrapped around core histone proteins, forming chromatin, the physiological context in which the genomes of these organisms must function. Control of the dynamics of chromatin structure has been implicated widely in regulating both access to and interpretation of the associated DNA template 1 . For example, numerous studies suggest that gene expression patterns can be positively or negatively regulated by complexes of proteins that fine-tune the structural properties of chromatin, often through covalent PTMs of histone proteins or other chromatin-remodeling complexes 2,3 . As chromatin architecture may be transmissible to daughter cells along a particular developmental lineage, histones and their PTMs are likely candidates for epigenetic information carriers that propagate phenotypic determinants not encoded in the DNA sequence. More than 70 different sites for histone PTMs and eight HHS Public Access Author Manuscript Author ManuscriptAuthor ManuscriptAuthor Manuscript types of histone PTMs have been reported, largely from the extensive application of mass spectrometry-and antibody-based detection techniques, as well as from metabolic-labeling studies [1][2][3] . Remarkably, almost two-thirds of potentially modifiable residues on histones have been characterized as PTM sites, and as more sensitive detection methods become available, this number is likely to increase. Despite the large number of histone PTMs, only a subset of amino acid residues in histones are known to be covalently modified, which include lysine (K), arginine (R), serine (S), threonine (T), tyrosine (Y), histidine (H) and glutamic acid (E) 1 . The majority of the PTMs are additions of relatively small yet chemically and structurally distinct moieties, such as acetyl, methyl and phosphate groups (Fig. 1a); these have been identified on sites ranging from the flexible tail...

Various chemical modifications on histones and regions of associated DNA play crucial roles in genome management by binding specific factors that, in turn, serve to alter the structural properties of chromatin. These so-called effector proteins have typically been studied with the biochemist's paring knife -the capacity to recognize specific chromatin modifications has been mapped to an increasing number of domains that frequently appear in the nuclear subset of the proteome, often present in large, multisubunit complexes that bristle with modification-dependent binding potential. We propose that multivalent interactions on a single histone tail and beyond may have a significant, if not dominant, role in chromatin transactions.The eukaryotic genome is assembled into chromatin, and the nucleosome serves as its fundamental organizational unit. This unit is composed of an octamer of core histone proteins (two copies of H2A, H2B, H3 and H4) encircled by ∼146 bp of DNA. Histones project unstructured N-terminal 'tails' from the α-helical protein core of the nucleosome through the superhelical turns of DNA that enshroud the radial surface of the histone octamer. The majority of known histone post-translational modifications (PTMs) localize to residues in the unstructured tails, particularly at the N termini, yet a burgeoning number of modifications also appear to reside within the helical secondary structure and loops of folded histones 1 . Further diversifying the nucleosome core particle is a set of histone isoforms known as histone variants, some of which appear to have essential roles in various stages of DNA management [2][3][4][5] .The lowest order of chromatin structure is the nucleosomal unit iterated in extended conformation to resemble 'beads on a string', which can be consolidated into higher-order structures through the intermediacy of attendant proteins, RNA and cations. Physiological chromatin structure is a vital arbiter of DNA function, in that structural variation appears to regulate the accessibility of underlying DNA, ranging from condensed heterochromatin to more 'open' euchromatin 6,7 . Rather than mere static packaging of the genome, the spatial arrangement of chromatin serves as an information carrier that may help to preserve cell Correspondence to C.D.A., D.J.P and A.J.R. alliscd@rockefeller.edu, pateld@mskcc.org, aruthenbur@rockefeller.edu. HHS Public Access Author Manuscript Author ManuscriptAuthor ManuscriptAuthor Manuscript identity through mitotic division 8 , and yet the local structure is sufficiently dynamic that it may be rapidly modulated by signalling cascades in response to external stimuli 9-11 .Phenotypic traits that are not encoded in the Watson-Crick base pairing of the genome are collectively referred to as epigenetic phenomena and appear to manifest physically as the faithful heritability of chromatin states by daughter cells [12][13][14] . The precise mechanisms of epigenetic phenomena are poorly understood, but causal connections between chemical modifications to DN...

The slicer activity of the RNA-induced silencing complex resides within its Argonaute (Ago) component, whose PIWI domain provides the catalytic residues governing guide-strand mediated site-specific cleavage of target RNA. We report on structures of ternary complexes of T. thermophilus Ago catalytic mutants with 5′-phosphorylated 21-nt guide DNA and complementary target RNAs of length 12-, 15- and 19-nt, which define the molecular basis for Mg2+-facilitated site-specific cleavage of the target. We observe pivot-like domain movements within the Ago scaffold on proceeding from nucleation to propagation steps of guide-target duplex formation, with duplex zippering beyond one turn of helix requiring release of the 3′-end of the guide from the PAZ pocket. Cleavage assays on targets of various lengths supported this model, and sugar-phosphate backbone modified target strands revealed the importance of structural and catalytic divalent metal ions observed in the crystal structures.

Mono-, di- and trimethylated states of particular histone lysine residues are selectively found in different regions of chromatin, thereby implying specialized biological functions for these marks ranging from heterochromatin formation to X-chromosome inactivation and transcriptional regulation. A major challenge in chromatin biology has centred on efforts to define the connection between specific methylation states and distinct biological read-outs impacting on function. For example, histone H3 trimethylated at lysine 4 (H3K4me3) is associated with transcription start sites of active genes, but the molecular 'effectors' involved in specific recognition of H3K4me3 tails remain poorly understood. Here we demonstrate the molecular basis for specific recognition of H3(1-15)K4me3 (residues 1-15 of histone H3 trimethylated at K4) by a plant homeodomain (PHD) finger of human BPTF (bromodomain and PHD domain transcription factor), the largest subunit of the ATP-dependent chromatin-remodelling complex, NURF (nucleosome remodelling factor). We report on crystallographic and NMR structures of the bromodomain-proximal PHD finger of BPTF in free and H3(1-15)K4me3-bound states. H3(1-15)K4me3 interacts through anti-parallel beta-sheet formation on the surface of the PHD finger, with the long side chains of arginine 2 (R2) and K4me3 fitting snugly in adjacent pre-formed surface pockets, and bracketing an invariant tryptophan. The observed stapling role by non-adjacent R2 and K4me3 provides a molecular explanation for H3K4me3 site specificity. Binding studies establish that the BPTF PHD finger exhibits a modest preference for K4me3- over K4me2-containing H3 peptides, and discriminates against monomethylated and unmodified counterparts. Furthermore, we identified key specificity-determining residues from binding studies of H3(1-15)K4me3 with PHD finger point mutants. Our findings call attention to the PHD finger as a previously uncharacterized chromatin-binding module found in a large number of chromatin-associated proteins.

Cilia and flagella are microtubule-based structures nucleated by modified centrioles termed basal bodies. These biochemically complex organelles have more than 250 and 150 polypeptides, respectively. To identify the proteins involved in ciliary and basal body biogenesis and function, we undertook a comparative genomics approach that subtracted the nonflagellated proteome of Arabidopsis from the shared proteome of the ciliated/flagellated organisms Chlamydomonas and human. We identified 688 genes that are present exclusively in organisms with flagella and basal bodies and validated these data through a series of in silico, in vitro, and in vivo studies. We then applied this resource to the study of human ciliation disorders and have identified BBS5, a novel gene for Bardet-Biedl syndrome. We show that this novel protein localizes to basal bodies in mouse and C. elegans, is under the regulatory control of daf-19, and is necessary for the generation of both cilia and flagella.

Here we report on a 3.0 Å crystal structure of a ternary complex of wild-type Thermus thermophilus argonaute bound to a 5′-phosphorylated 21-nucleotide guide DNA and a 20-nucleotide target RNA containing cleavage-preventing mismatches at the 10-11 step. The seed segment (positions 2 to 8) adopts an A-helical-like Watson-Crick paired duplex, with both ends of the guide strand anchored in the complex. An arginine, inserted between guide-strand bases 10 and 11 in the binary complex, locking it in an inactive conformation, is released on ternary complex formation. The nucleic-acid-binding channel between the PAZ-and PIWI-containing lobes of argonaute widens on formation of a more open ternary complex. The relationship of structure to function was established by determining cleavage activity of ternary complexes containing position-dependent base mismatch, bulge and 2′-O-methyl modifications. Consistent with the geometry of the ternary complex, bulges residing in the seed segments of the target, but not the guide strand, were better accommodated and their complexes were catalytically active.RNA-induced silencing complex (RISC)-associated argonaute (Ago) proteins composed of PAZ-and PIWI-containing modules have a central role in mediating distinct assembly and cleavage steps of the RNA interference (RNAi) catalytic cycle [1][2][3][4] . The Ago protein, as the sole component of RISC exhibiting RNA 'slicer' activity [5][6][7] , is a critical player in the RNAi pathway 8 , effecting transcriptional and post-transcriptional gene regulation in plants and animals [1][2][3][4] . In this capacity, Agos have essential roles ranging from maintaining genomic integrity to heterochromatin formation. Some Ago proteins with active endonuclease domains contribute to the maturation of bound short interfering RNAs (siRNAs) by degradative cleavage of the passenger strand and subsequent guide-strand-mediated sequence-specific ©2008 Macmillan Publishers Limited. All rights reservedCorrespondence and requests for materials should be addressed to D.J.P. (pateld@mskcc.org) or T.T. (ttuschl@mail.rockefeller.edu). Author Contributions Y.W. and G.S. expressed and purified T. thermophilus Ago, and grew crystals of the ternary complex. H.L. and Y.W. collected X-ray diffraction data on the micro-focus beam line, and Y.W. solved the structure of the ternary complex. The structural studies were undertaken with the supervision of D.J.P. S.J. was responsible for the cleavage assays on Ago with modified guide strands under the supervision of T.T. D.J.P. and T.T. were primarily responsible for writing the paper and all authors read and approved the submitted manuscript. Author InformationThe structural coordinates of the ternary complex of T. thermophilus Ago bound to 5′-phosphorylated 21-nucleotide guide DNA and 20-nucleotide target RNA have been submitted to the Protein Data Bank under accession number 3F73. Reprints and permissions information is available at www.nature.com/reprints.Supplementary Information is linked to the online version of...