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Dynamic gene expression is crucial for coordinating diverse cellular activities, but challenging to modulate with high spatiotemporal precision. Now, a photoswitchable DNA structure-specific, small-molecule ligand enables reversible, light-controlled regulation of gene expression and cell proliferation in live cells.

A small-molecule-affinity tag has been designed to mediate the selective isolation of G-quadruplex nucleic acids in a structure-dependant manner. This concept has been applied to the pull-down of G-quadruplex-containing fragments from human cells, and the methodology holds promise for the elucidation of their putative biological functions.

Synthetic nanomotors convert chemical energy into motion. Here, they have been implemented in a motion-based assay that allows specific DNA and ribosomal RNA detection. The technique is fast, simple and sensitive, and the concentration-dependant distance signals of the magnetically aligned nanomotors are detected by optical microscopy.

The presence of RNA G-quadruplex structures in human cells using a structure-specific antibody is demonstrated. Using small molecules, the selective stabilization of cytoplasmic RNA G-quadruplexes versus nuclear DNA G-quadruplexes is demonstrated. These findings validate the existence of RNA G-quadruplexes and their specific targeting by small molecules within a cellular context.

DNA G-quadruplexes (G4s) are guanine-rich sequences that fold into four-stranded structures. Recent progress in the detection and mapping of genomic G4 structures has provided new insights into their functions in regulating transcription and genome stability, and has revealed their potential relevance for cancer therapy.

5-Formylcytosine (5fC) is implicated in active DNA demethylation and has been proposed to act as an epigenetic signal. Balasubramanian and colleagues now report that this base modification imparts a unique, previously undescribed conformation to DNA.

Cytosine base modifications 5-methylcytosine (5mC), 5-hydroxymethylcytosine (5hmC) and 5-formylcytosine (5fC) are present in mammalian DNA. Reduced bisulfite sequencing is now developed for quantitatively sequencing 5fC at single-base resolution. This method is then applied with oxidative bisulfite sequencing to gain a map of 5mC, 5hmC and 5fC in mouse embryonic stem cells.

Reduction of 5-hydroxymethylcytosine (hmC) levels in DNA often occurs in cancers. Using isotope tracing experiments, this epigenetic DNA modification, which was thought to be an intermediate of demethylation, is now shown to be stable. A delay in the generation of hmC on newly synthesized DNA is responsible for the reduction of hmC levels in cancers.

A structure-specific antibody generated and employed to visualize DNA G-quadruplex structures in human cells shows that these structures are modulated during the cell cycle and can be stabilized by a small-molecule ligand. This provides substantive evidence for endogenous DNA G-quadruplex formation in mammalian cells.

Shankar Balasubramanian and colleagues examine endogenous DNA G-quadruplex (G4) structures in the context of chromatin by using G4 antibody-based ChIP–seq. They find that G4 structures are enriched in nucleosome-depleted regions and the promoters and 5′ UTRs of highly transcribed genes, suggesting a relationship between chromatin state, transcriptional output and G4 status.

To mark the occasion of Nature Chemistry turning 10 years old, we asked scientists working in different areas of chemistry to tell us what they thought the most exciting, interesting or challenging aspects related to the development of their main field of research will be — here is what they said.

Identifying DNA sequences that adopt alternative structures within the context of genomic DNA presents a major challenge. Pyridostatin, a G-quadruplex–specific chemical probe, was shown to induce DNA damage at specific genomic sites, including the proto-oncogene SRC, leading to cell cycle arrest in human cancer cells.

ATR inhibitors are being developed for treating cancers, but mechanisms that determine their efficacy are unclear. Here, the authors show that transcription factor KLF5 loss sensitizes cells to ATR inhibition through regulating BRD4 chromatin recruitment. This work also identifies KLF5 as a potential target for treating ARID1A-deficient cancers.

Whether G-quadruplexes (G4s) regulate stem cell self-renewal and fate determination during embryonic development is not well understood. Here, the authors reveal that the embryonic stem cell state is defined by very high G4 abundance. G4s are progressively lost during differentiation as cells transit to lower lineage potential while artificial G4 stabilisation leads to delayed differentiation.

Biophysical analysis reveals that conserved G-rich sequences within the mRNAs of gammaherpesvirus genome maintenance proteins (GMPs) form G-quadruplexes (G4). Stabilization of mRNA G4 motifs represses GMP translation, whereas destabilization enhances translation, suggesting that these RNA elements are cis-acting translational regulators of proteins involved in viral latency.

The natural product thiostrepton is known to have anticancer properties but its mechanism of action is not known. Here, it is shown that thiostrepton binds to the protein FOXM1, preventing its interaction with several gene promoters and inhibits their expression. This illustrates the druggability of transcription factors, and provides a molecular basis for targeting FOXM1.

Abasic sites are amongst the most common forms of DNA damage. Despite their biological significance, little is known regarding the distribution of these sites within DNA. Now a method to sequence abasic sites at single-nucleotide resolution has been developed. This method allows the ___location of abasic sites to be mapped genome-wide.

Quantitative ChIP–seq analysis maps G-quadruplex (G4) DNA structures in breast cancer patient-derived tumor xenograft (PDTX) models. G4-based subtypes highlight additional tumor heterogeneity in the integrative cluster (IC) system.

Guanine-rich DNA can form four-stranded structures called G-quadruplexes, which are thought to influence DNA replication, transcription and repair; their stability and prevalence in the genome is in need of further elucidation. Here the authors employ an antibody-based approach to sensitively map G-quadruplexes in the genome.

Overexpression of the FOXM1 transcription factor occurs in several cancer and correlates with poor prognoses. Here, the authors identify a novel small molecule capable of displacing FOXM1 from its DNA consensus motif in vitro, displace it from target promoters and downregulate the expression of its target genes cancer cells.

Three studies identify a transcription-coupled DNA–protein cross-link repair pathway that depends on the Cockayne syndrome proteins and the proteasome.

Research into naturally occurring chemically modified DNA bases has been invigorated by new chemical and enzymatic methods that, when coupled with sequencing approaches, enable us to detect and decode them. These techniques will support a better understanding of the role of chemically modified DNA bases in normal physiology and disease.

How small molecules bind chromatin and DNA is determined by Chem-map.

A six-letter sequencing workflow can simultaneously detect genetic and epigenetic bases.

5-Formylcytosine (5fC), produced by TET-mediated oxidation of 5-methylcytosine, is considered an intermediate in active DNA demethylation. Labeling studies and LC/MS analysis across mouse developmental stages reveals that 5fC modifications are more persistent in the genome and may have other functional roles.

A series of in vitro and in vivo studies has now shown that 5fC is linked to increased nucleosome occupancy and stability. Moreover, there is evidence that Schiff base formation between histones and 5fC impacts RNA polymerase II transcription activity in mouse embryonic stem cells.

Guanine-rich sequences with a tendency to form G4 structures are a hallmark of hominoid-specific L1 retrotransposons, and their stabilization increases L1 mobility, thus potentially affecting genome evolution.

Delayed resolution of G-quadruplexes during replication can induce localized loss of epigenetic information and changes in gene expression. Now, this effect has been used to discover biologically potent G-quadruplex ligands and to demonstrate that G-quadruplex stabilization can induce epigenetic changes that are heritable across cell divisions even after the ligand is removed.

Stabilization of DNA quadruplex structures (G4) is lethal for cells with a compromised DNA repair pathway. Here, the authors show that CX-5461, a small molecule in clinical trials as RNA polymerase inhibitor, has G4-stablization properties and can be repurposed to target DNA repair-defective cancers cells.

DNA–protein interactions are essential to genome function, but they are challenging to map in a cellular environment. Now, a chemical proteomics approach, which uses DNA G-quadruplex-specific ligands containing a photocrosslinking motif, has enabled the systematic identification of DNA G-quadruplex-binding proteins in live cells.

Biochemical and genome-wide analyses reveal that G4 structures sequester and inhibit the activity of DNMT1, thereby protecting CpG islands from methylation in human cells.

Visualization of endogenous G-quadruplexes (G4s) in living cells by fluorescence microscopy has been hampered by the high concentrations of G4-binding probes required, which can artificially induce additional G4 formation. Now, a G4-specific fluorescent probe (SiR-PyPDS) has been developed that enables single-molecule and real-time detection of individual G4 structures in living cells without perturbing G4 formation and dynamics.

G-quadruplexes are four-stranded DNA structures that appear to be over-represented in the promoter region of various genes, including oncogenes such asMYC and KRAS. This article discusses evidence indicating the possibility of therapeutically modulating the transcription of such genes through the targeting of G-quadruplexes with small molecules, and considers challenges and opportunities for the development of such molecules as anticancer drugs.

The history and future potential of DNA sequencing, including the development of the underlying technologies and the expansion of its areas of application, are reviewed.

Developmental expression of the microRNA let-7 is tightly regulated in many animals, and turnover has been linked to LIN-28 and uridylation in mammals. This regulation is now shown to be conserved in Caenorhabditis elegans, and PUP-2 is shown to be a uridylase that is specifically recruited to let-7 in a LIN-28–dependent manner.

G-quadruplex structures in telomeric DNA inhibit the action of telomerase — an enzyme over-expressed in many cancer cells. Small molecules that stabilize the formation of G-quadruplex structures are therefore of interest as potential cancer treatments. Here, a platform is described that allows the interactions between small-molecule ligands and human telomeric G-quadruplexes to be measured at the single-molecule level.

Notch can drive senescence in a cell contact dependent manner. Here the authors show that NOTCH signalling can modulate chromatin structure autonomously and non-autonomously via the JAG1-NOTCH-HMGA1 interplay during senescence.

Telomere capping is essential for genomic integrity. In yeast, a capping complex containing protein Cdc13 protects telomeres from degradation and from the DNA damage repair system. Yeast telomeric repeats can form G-quadruplexes, whose potential capping role is now revealed using Cdc13-impaired strains.

Various small molecules, including numerous anticancer agents, act by targeting DNA or protein components of chromatin. This Review describes how various complementary technologies use high-throughput sequencing to delineate drug responses, from identifying the genomic binding sites of drugs or their targets, to the ensuing changes to chromatin states and gene expression. These insights should facilitate the rational use of these therapies.

Details of the activity of promising anticancer drugs known as BET inhibitors remain elusive. An approach called click chemistry enables in-depth analysis of how these drugs modulate the function of a crucial target protein, BRD4.