Non‐canonical Bases in the Genome: The Regulatory Information Layer in DNA

Abstract

Multicellular organisms developed the concept of specialized cells that perform specific functions. Examples are neurons and fibroblast to name just two out of more than 200. These cellular differences are established based on the same sequence information stored in the cell nucleus of all cells of an organism. The sequence information needs consequently different interpretations by the different cell types. During cellular development this interpretation of the genetic code has to be tightly regulated in space and time. Interpretation of the sequence information involves the controlled activation and silencing of specific genes so that certain proteins are made in one cell type but not in others. This involves an additional regulatory information layer beyond the pure base sequence. One aspect of this regulatory information layer relies on functional groups that are attached to the C(5) position of the canonical base dC. Currently four regulatory, non-canonical bases with a methyl (CH )-, a hydroxymethyl (CH OH)-, a formyl (CHO)- and a carboxyl (COOH)- group are known. While 5-methyl-cytidine is long recognised to be a regulatory base in the genome, the other three bases and the enzymes responsible for generating them, were just recently discovered.

5‐Methylcytosine is Oxidized to the Natural Metabolites of TET Enzymes by a Biomimetic Iron(IV)‐Oxo Complex

“…[4,5] Surprisingly,5 hmC is ten-and 100-fold more abundant than 5fCa nd 5cC, respectively. [7][8][9] Additionally,5 fC und 5cC can be removed through the base excisionr epair (BER) pathway. [7][8][9] Additionally,5 fC und 5cC can be removed through the base excisionr epair (BER) pathway.…”

“…[13][14][15] Surprisingly,T ET2 shows as ubstrate preference and fastert urnover for 5mC, and not 5hmC/5fC, in contrast to the calculated bond dissociation energies of the CÀHb onds in these substrates. [7,27] The red oxygen atomss temfrom molecular dioxygen, which coordinates to the respective iron(II) precursor with formation of an iron(III)-superoxo intermediate,w hich then reactsv ia an iron(IV)-peroxo intermediate to the proposed active iron(IV)-oxo species with CO 2 formation. Proposed methylation and demethylation cycle of cytosine residues in DNA.…”

Analytical epigenetics: single-molecule optical detection of DNA and histone modifications

“…Considering the multitude of possible epigenetic marks and, in part, their high abundance (up to 80 % of all CpG dinucleotides are methylated) [31], the interrogation of non-modified nucleobases becomes an important task in its own right. In the case of unmodified CpGs, a selective labeling with alkyne or amine groups can be achieved by ‘methyltransferase-directed transfer of activated groups’ (mTAG) [32–34].…”

“…Selectivity towards the aldehyde group of 5fC can be achieved through fine-tuning of reaction conditions. Still, considering the low abundance of 5fC in natural samples, even low levels of background noise are problematic [31]. An elegant strategy to increase selectivity and sensitivity is to form a fluorophore with the nucleobase of interest in situ .…”

Adventures in Defining Roles of Oxygenases in the Regulation of Protein Biosynthesis

“…TET catalysed modification of 5‐methylcytosine has been associated with either direct or indirect 5‐methylcytosine demethylation (via excision by thymine DNA glycosylase and subsequent base excision repair) ,. Given the importance of 5‐methylcytosine in epigenetic regulation, the discovery of the TET reaction was of substantial interest; more recently it has become apparent that 5hmC, 5fC and 5caC may also have signalling or regulatory functions in their own right ,. As has been found for JmjC KDMs, the TET proteins are frequently mutated in cancers and as such a better understanding of their full biological roles may be important for the treatment of human diseases, including cancer and developmental disorders …”