28]. This raises the question of whether there are further structural features of the DNA molecule, which determine the order of recombination. It is this question that the log-periodic nature of the TCR locus elucidated in our analysis may help answer. In nature there is a tendency for organizational patterns to be repeated over different scales of measurement and for such patterns to be observed across different systems. Fractal organization in the VDJ segment usage in the T-cell repertoire of normal individuals has been observed with the diversity, joining and variable gene segment usage defining a virtual `structure’ that results from recombination of the T-cell b receptor locus [10,20,29]. With this background, the proportions between the V and J segment size and intergenic segment lengths between adjacent LM22A-4MedChemExpress LM22A-4 segments were examined relative to each other and found to be similar, demonstrating spatial symmetry between the TCR regions harbouring the V and J segments. It is likely that the proportional distribution of V and J segment size and spacing between individual segments (fractal organization) in this instance serves to order the ensuing rearrangement process. This may in part explain why in the order of gene segment rearrangement, Db to Jb and DJb or Ja to Vb/a segments, RAG complexes are Lumicitabine site always directed from the shorter, closely spaced J segments to the longer, more dispersed V segments, such that the reverse does not transpire in the course of normal recombination. Further, the logarithmic scaling implies that the distribution of these size-ordered segments is always similar in their respective sections of the TCR locus, which ensures that RAG complexes do not have to `scan’ an entire sequence of nucleotides to randomly encounter a coding segment, but can potentially align with relevant segments, skipping over given lengths of intergenic material. This would then provide an additional mechanism to complement the 12/23 rule and ensure fidelity of recombination. Epigenetic mechanisms such as RAG2 interacting with methylated histone H3-K4, further facilitates the VDJ recombination [30]. Other sequence motifs critical in terms of facilitating VDJ recombination are the ubiquitous CTCF-cohesin-binding GC-rich consensus sequences [31,32]. These trans-acting factors help bring about conformational changes in the locus, which bring V segments in apposition to J segments allowing successful recombination. However, while they give important mechanistic insights, the sequence motifs and chromatin-based landmarks for recombination still require appropriate scaling–logarithmic–as in the measurements presented here, to yield a quantifiable effect on the TCR recombination process. This hypothesis, if true, suggests that the origin of the fractal properties of the T-cell repertoire clonal distribution is within the arrangement of the TCR loci resulting in an ordered recombination process. The log-periodic nature of other fractal phenomenon encountered in nature supports this postulate [33,34].High-throughput sequencing of TRB has demonstrated a differential representation of the different gene segments in the T-cell clonal repertoire, indicating that some sequences are used at a higher frequency than others [4,5,10]. This has been observed for TCRg as well as TCRb and has been seen for both J and V segments [35]. This recombination bias affects both in-frame and out-of-frame recombined sequences, suggesting that it is not a consequence of thy.28]. This raises the question of whether there are further structural features of the DNA molecule, which determine the order of recombination. It is this question that the log-periodic nature of the TCR locus elucidated in our analysis may help answer. In nature there is a tendency for organizational patterns to be repeated over different scales of measurement and for such patterns to be observed across different systems. Fractal organization in the VDJ segment usage in the T-cell repertoire of normal individuals has been observed with the diversity, joining and variable gene segment usage defining a virtual `structure’ that results from recombination of the T-cell b receptor locus [10,20,29]. With this background, the proportions between the V and J segment size and intergenic segment lengths between adjacent segments were examined relative to each other and found to be similar, demonstrating spatial symmetry between the TCR regions harbouring the V and J segments. It is likely that the proportional distribution of V and J segment size and spacing between individual segments (fractal organization) in this instance serves to order the ensuing rearrangement process. This may in part explain why in the order of gene segment rearrangement, Db to Jb and DJb or Ja to Vb/a segments, RAG complexes are always directed from the shorter, closely spaced J segments to the longer, more dispersed V segments, such that the reverse does not transpire in the course of normal recombination. Further, the logarithmic scaling implies that the distribution of these size-ordered segments is always similar in their respective sections of the TCR locus, which ensures that RAG complexes do not have to `scan’ an entire sequence of nucleotides to randomly encounter a coding segment, but can potentially align with relevant segments, skipping over given lengths of intergenic material. This would then provide an additional mechanism to complement the 12/23 rule and ensure fidelity of recombination. Epigenetic mechanisms such as RAG2 interacting with methylated histone H3-K4, further facilitates the VDJ recombination [30]. Other sequence motifs critical in terms of facilitating VDJ recombination are the ubiquitous CTCF-cohesin-binding GC-rich consensus sequences [31,32]. These trans-acting factors help bring about conformational changes in the locus, which bring V segments in apposition to J segments allowing successful recombination. However, while they give important mechanistic insights, the sequence motifs and chromatin-based landmarks for recombination still require appropriate scaling–logarithmic–as in the measurements presented here, to yield a quantifiable effect on the TCR recombination process. This hypothesis, if true, suggests that the origin of the fractal properties of the T-cell repertoire clonal distribution is within the arrangement of the TCR loci resulting in an ordered recombination process. The log-periodic nature of other fractal phenomenon encountered in nature supports this postulate [33,34].High-throughput sequencing of TRB has demonstrated a differential representation of the different gene segments in the T-cell clonal repertoire, indicating that some sequences are used at a higher frequency than others [4,5,10]. This has been observed for TCRg as well as TCRb and has been seen for both J and V segments [35]. This recombination bias affects both in-frame and out-of-frame recombined sequences, suggesting that it is not a consequence of thy.
