A comprehensive genomic binding map of gene and chromatin regulatory proteins in Saccharomyces

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Highlights? Genomic maps of 200 yeast regulators in normal and stress conditions provide a compendium for discovery ? SAGA assembly pathway is associated with more regulation than the TFIID pathway ? SAGA-linked regulators are distal, and TFIID-linked regulators are proximal to the promoter ? During heat shock, SAGA- and TFIID-linked regulators displayed distinct mobilization patterns     

Comprehensive Analysis of Silencing Mutants Reveals Complex Regulation of the Arabidopsis Methylome

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Highlights? Genome-wide single-nucleotide resolution methylation maps in 86 silencing mutants ? Complex interplays between different DNA methylation pathways ? Identification of novel regulators of DNA methylation     

Sculpting of DNA at Abasic Sites by DNA Glycosylase Homolog Mag2

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Highlights? Unflipped AP site stabilized by helix-hairpin-helix DNA glycosylase homolog Mag2 ? Nonenzymatic AP site recognition and DNA sculpting ? Sculpting of DNA conformation enhances substrate transfer between proteins     

Kinetic,Energetic, and Mechanical Differences between Dark-State Rhodopsin and Opsin

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Highlights? Mapping the stability of opsin from the rod outer segment of the mouse eye ? Compared to dark-state rhodopsin opsin increases mechanical stability and rigidity ? Compared to dark-state rhodopsin opsin reduces lifetime and free energy ? Compared to dark-state rhodopsin opsin is pliable and adopts alternate conformations     

Solution structure of the ESCRT-I and -II supercomplex: implications for membrane budding and scission

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Highlights? Solution structures of yeast ESCRT-II complex and ESCRT-I-II supercomplex ? ESCRT-I-II has compact, crescent-shaped, and highly extended conformations ? ESCRT-I-II crescent shapes can be docked into a model vesicle bud neck ? Model for coupling of cargo sorting, membrane budding, and membrane scission     

Dissection of DNA Damage Responses Using Multiconditional Genetic Interaction Maps

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Highlights? A resource of genetic modules and networks induced by distinct types of DNA damage ? Networks distinguish DNA damage response pathways with high statistical power ? Rtt109, a histone acetyltransferase, affects the mutagenic bypass of DNA lesions ? The neddylation machinery and Irc21 affect cell-cycle control and genome stability     

Tet Proteins Connect the O-Linked N-acetylglucosamine Transferase Ogt to Chromatin in Embryonic Stem Cells

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Highlights? Ogt forms a complex with Tet1 and Tet2 in the nucleus of embryonic stem cells ? Ogt preferentially associates with promoter regions in proximity of TSS ? Ogt shows >90% of colocalization with Tet1 at methylation-free CpG-rich elements ? Tet1 is required for global Ogt chromatin recruitment regulating its activity     

ATP alters the diffusion mechanics of MutS on mismatched DNA

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Highlights? The development and use of smFlow-FRET and smPolarization-TIRF microscopy ? Lesion-searching MutS rotationally diffuses in continuous contact with the DNA ? ATP-bound MutS spins freely and in discontinuous contact with the DNA backbone ? Direct visualization of multiple ATP-bound MutS clamps that diffuse along the DNA     

Towards a structural understanding of PARP1 activation and related signalling ADP-ribosyl-transferases

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Highlights? PARP1 recognizes DNA strand breaks through substrate-assisted dimerization. ? PARP1 ZFIII and WGR domains link DNA break recognition to enzyme activation. ? Tankyrase-dependent PARylation regulates Wnt signalling and Cherubism syndrome.     

Stage-Specific Roles for Tet1 and Tet2 in DNA Demethylation in Primordial Germ Cells

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Highlights? PGCs differentiated from ESCs undergo genome-wide DNA demethylation ? Tet1 and Tet2 do not regulate genome-wide DNA demethylation in PGCs ? Tet1 and Tet2 regulate locus-specific demethylation in PGCs     

The prereplication complex recruits XEco2 to chromatin to promote cohesin acetylation in Xenopus egg extracts

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Highlights? XEco2 loading and cohesin acetylation require pre-RC assembly but not DNA synthesis ? Two N-terminal motifs in XEco2 are essential for XEco2 loading and cohesion ? The PIP box in XEco2 contributes to cohesion ? Interaction of acetylated cohesin with DNA is stabilized after DNA replication     

FANCM and FAAP24 Maintain Genome Stability via Cooperative as Well as Unique Functions

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Highlights? FANCM and FAAP24 exhibit nonepistatic functions in cell survival upon DNA damage ? FAAP24 confers unique lesion specificity in DNA damage cell-cycle checkpoint ? FANCM translocase activity is involved in recombination-independent ICL repair     

Structural Characterization of a Mouse Ortholog of Human NEIL3 with a Marked Preference for Single-Stranded DNA

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Highlights? Neil3 is an Fpg/Nei DNA glycosylase of the base excision repair pathway ? Neil3 excises a broad spectrum of base lesions, with a marked preference for ssDNA ? We report a crystal structure of Neil3 DNA glycosylase ? The structure provides valuable insights into Neil3′s unusual substrate specificity     

Proliferation-Dependent Alterations of the DNA Methylation Landscape Underlie Hematopoietic Stem Cell Aging

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Highlights? Locus-specific alterations of the DNA methylome accompany HSC aging ? Methylation changes target genes expressed downstream of HSCs to alter HSC potential ? HSC potential, DNA methylation, and replicative limits depend on divisional history ? Aging and forced proliferation of HSC results in DNA hypermethylation of PRC2 targets     

Short Telomeres in ESCs Lead to Unstable Differentiation

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Highlights? ESCs with short telomeres do not stably differentiate and can resume proliferation ? Critically short telomeres impair Nanog regulation during ESC differentiation ? Short telomeres elicit genome-wide DNA hypomethylation and altered H3K27me3 levels ? Impaired DNA methylation and differentiation are rescued by Dnmt3b or telomere elongation     

Solution Conformations of Prototype Foamy Virus Integrase and Its Stable Synaptic Complex with U5 Viral DNA

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Highlights? Missing domains in PFV intasome revealed by SAXS/SANS ? PFV IN undergoes dramatic changes in conformation and oligomerization upon binding DNA ? Strand transfer inhibitors do not alter quaternary structure of PFV intasome     

DNA Quality Control by a Lesion Sensor Pocket of the Xeroderma Pigmentosum Group D Helicase Subunit of TFIIH

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Highlights? Amino acid changes near the central pore of XPD confer defective excision repair ? These mutants retain DNA helicase activity when tested in an archaeal framework ? The mutants are unable to sense lesions during their ATP-driven tracking movement ? The mutants are unable to build a stable demarcation complex at DNA lesion sites