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      5-Formylcytosine does not change the global structure of DNA

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          Abstract

          X-ray crystallography and NMR analysis demonstrate that, contrary to previous observations, fC does not significantly alter DNA structure, thus suggesting an alternative basis for recognition of fC-DNA by epigenome-modifying enzymes.

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          Conformational analysis of nucleic acids revisited: Curves+

          R. Lavery, M. Moakher, J. H. Maddocks … (2009)
          We describe Curves+, a new nucleic acid conformational analysis program which is applicable to a wide range of nucleic acid structures, including those with up to four strands and with either canonical or modified bases and backbones. The program is algorithmically simpler and computationally much faster than the earlier Curves approach, although it still provides both helical and backbone parameters, including a curvilinear axis and parameters relating the position of the bases to this axis. It additionally provides a full analysis of groove widths and depths. Curves+ can also be used to analyse molecular dynamics trajectories. With the help of the accompanying program Canal, it is possible to produce a variety of graphical output including parameter variations along a given structure and time series or histograms of parameter variations during dynamics.
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            The discovery of 5-formylcytosine in embryonic stem cell DNA.

            Toni Pfaffeneder, Benjamin Hackner, Matthias Truß … (2011)
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              A screen for hydroxymethylcytosine and formylcytosine binding proteins suggests functions in transcription and chromatin regulation

              Mario Iurlaro, Gabriella Ficz, David Oxley … (2013)
              Background DNA methylation (5mC) plays important roles in epigenetic regulation of genome function. Recently, TET hydroxylases have been found to oxidise 5mC to hydroxymethylcytosine (5hmC), formylcytosine (5fC) and carboxylcytosine (5caC) in DNA. These derivatives have a role in demethylation of DNA but in addition may have epigenetic signaling functions in their own right. A recent study identified proteins which showed preferential binding to 5-methylcytosine (5mC) and its oxidised forms, where readers for 5mC and 5hmC showed little overlap, and proteins bound to further oxidation forms were enriched for repair proteins and transcription regulators. We extend this study by using promoter sequences as baits and compare protein binding patterns to unmodified or modified cytosine using DNA from mouse embryonic stem cell extracts. Results We compared protein enrichments from two DNA probes with different CpG composition and show that, whereas some of the enriched proteins show specificity to cytosine modifications, others are selective for both modification and target sequences. Only a few proteins were identified with a preference for 5hmC (such as RPL26, PRP8 and the DNA mismatch repair protein MHS6), but proteins with a strong preference for 5fC were more numerous, including transcriptional regulators (FOXK1, FOXK2, FOXP1, FOXP4 and FOXI3), DNA repair factors (TDG and MPG) and chromatin regulators (EHMT1, L3MBTL2 and all components of the NuRD complex). Conclusions 0ur screen has identified novel proteins that bind to 5fC in genomic sequences with different CpG composition and suggests they regulate transcription and chromatin, hence opening up functional investigations of 5fC readers.
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                Author and article information

                Journal
                Title: Nature Structural & Molecular Biology
                Abbreviated Title: Nat Struct Mol Biol
                Publisher: Springer Nature
                ISSN (Print): 1545-9993
                ISSN (Electronic): 1545-9985
                Publication date Created: May 15 2017
                Publication date (Print): May 15 2017
                Volume:
                Issue:
                Article
                DOI: 10.1038/nsmb.3411
                PMC ID: 5747368
                PubMed ID: 28504696
                SO-VID: 9202513a-06c1-4eed-942f-d51d6656074a
                Copyright © © 2017
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