An assessment of histone-modification antibody quality

We have tested the specificity and utility of more than 200 antibodies raised against 57 different histone modifications in Drosophila melanogaster, Caenorhabditis elegans and human cells. Although most antibodies performed well, more than 25% failed specificity tests by dot blot or western blot. Among specific antibodies, more than 20% failed in chromatin immunoprecipitation experiments. We advise rigorous testing of histone-modification antibodies before use, and we provide a website for posting new test results (http://compbio.med.harvard.edu/antibodies/)

An assessment of histone-modification antibody quality

We have tested the specificity and utility of more than 200 antibodies raised against 57 different histone modifications in Drosophila melanogaster, Caenorhabditis elegans and human cells. Although most antibodies performed well, more than 25% failed specificity tests by dot blot or western blot. Among specific antibodies, more than 20% failed in chromatin immunoprecipitation experiments. We advise rigorous testing of histone-modification antibodies before use, and we provide a website for posting new test results (http://compbio.med.harvard.edu/antibodies/)

Identification of functional elements and regulatory circuits by Drosophila modENCODE

To gain insight into how genomic information is translated into cellular and developmental programs, the Drosophila model organism Encyclopedia of DNA Elements (modENCODE) project is comprehensively mapping transcripts, histone modifications, chromosomal proteins, transcription factors, replication proteins and intermediates, and nucleosome properties across a developmental time course and in multiple cell lines. We have generated more than 700 data sets and discovered protein-coding, noncoding, RNA regulatory, replication, and chromatin elements, more than tripling the annotated portion of the Drosophila genome. Correlated activity patterns of these elements reveal a functional regulatory network, which predicts putative new functions for genes, reveals stage- and tissue-specific regulators, and enables gene-expression prediction. Our results provide a foundation for directed experimental and computational studies in Drosophila and related species and also a model for systematic data integration toward comprehensive genomic and functional annotation

A Twice-As-Smart Synthetic G-Quartet: PyroTASQ Is Both a Smart Quadruplex Ligand and a Smart Fluorescent Probe

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Cationic azacryptands as selective three-way DNA junction binding agents

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Synthetic G-Quartets as Versatile Nanotools for the Luminescent Detection of G-Quadruplexes

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Surface-promoted aggregation of amphiphilic quadruplex ligands drives their selectivity for alternative DNA structures

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TWJ-Screen: an isothermal screening assay to assess ligand/DNA junction interactions in vitro

International audienceThe quest for chemicals able to operate at selected genomic loci in a spatiotemporally controlled manner is desirable to create manageable DNA damages. Mounting evidence now shows that alternative DNA structures, including G-quadruplexes and branched DNA (or DNA junctions), might hamper proper progression of replication fork, thus triggering DNA damages and genomic instability. Therefore, small molecules that stabilize these DNA structures are currently scrutinized as a promising way to create genomic defects that cannot be dealt with properly by cancer cells. While much emphasis has been recently given to G-quadruplexes and related ligands, we report herein on three-way DNA junctions (TWJ) and related ligands. We first highlight the biological implications of TWJ and their strategic relevance as triggers for replicative stress. Then, we describe a new in vitro high-throughput screening assay, TWJ-Screen, which allows for identifying TWJ ligands with both high affinity and selectivity for TWJ over other DNA structures (duplexes and quadruplexes), in a convenient and unbiased manner as demonstrated by the screening of a library of 25 compounds from different chemical families. TWJ-Screen thus represents a reliable mean to uncover molecular tools able to foster replicative stress through an innovative approach , thus providing new strategic opportunities to combat cancers

Pharmacomodulation of G-quadruplexes in long non-coding RNAs dysregulated in colorectal cancer

International audienceBackground: Non-coding RNAs (ncRNAs) in human cells constitute a substantial portion of the transcriptome but do not lead to protein synthesis. Among them, long non-coding RNAs (lncRNAs, > 200 nucleotides long) are fascinating in their ability to orchestrate critical cellular functions that govern cell development, differentiation, and metabolism. Therefore, the dysregulation of lncRNAs has been linked with several diseases, chiefly cancers.Results: We focused here on colorectal cancer (CRC), the second-highest cause of mortalities related to cancer worldwide, and more particularly on three lncRNAs, i.e., LINC01589, MELTF-AS1, and UXT-AS1, known to be dysregulated in CRC. We identified a vulnerability in these lncRNAs that could be exploited from a therapeutic point of view: a part of their sequence folds into a secondary structure referred to as G-quadruplex (G4), which is suspected to play active roles in the lncRNA functions. We demonstrate here that these sequences do fold into G4s both in vitro and in CRC cells, and that these G4s can be modulated using PhpC, a prototype molecule for destabilizing G4s.Conclusion: We describe an innovative anticancer strategy that fully abides by the rules of chemical biology. We indeed modulate the formation of G4s in cells using ad hoc molecular tools in the aim of disturbing the homeostasis and inner functioning of lncRNAs. By exploiting cellular outcomes, we infer how this pharmacomodulation affects CRC biology and, beyond this, the fate of CRC cells owing to the flawed repertoire of correction and/or compensatory mechanisms in cancer cells