125,483 research outputs found
Coding limits on the number of transcription factors
Transcription factor proteins bind specific DNA sequences to control the
expression of genes. They contain DNA binding domains which belong to several
super-families, each with a specific mechanism of DNA binding. The total number
of transcription factors encoded in a genome increases with the number of genes
in the genome. Here, we examined the number of transcription factors from each
super-family in diverse organisms.
We find that the number of transcription factors from most super-families
appears to be bounded. For example, the number of winged helix factors does not
generally exceed 300, even in very large genomes. The magnitude of the maximal
number of transcription factors from each super-family seems to correlate with
the number of DNA bases effectively recognized by the binding mechanism of that
super-family. Coding theory predicts that such upper bounds on the number of
transcription factors should exist, in order to minimize cross-binding errors
between transcription factors. This theory further predicts that factors with
similar binding sequences should tend to have similar biological effect, so
that errors based on mis-recognition are minimal. We present evidence that
transcription factors with similar binding sequences tend to regulate genes
with similar biological functions, supporting this prediction.
The present study suggests limits on the transcription factor repertoire of
cells, and suggests coding constraints that might apply more generally to the
mapping between binding sites and biological function.Comment: http://www.weizmann.ac.il/complex/tlusty/papers/BMCGenomics2006.pdf
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1590034/
http://www.biomedcentral.com/1471-2164/7/23
Invariance: a Theoretical Approach for Coding Sets of Words Modulo Literal (Anti)Morphisms
Let be a finite or countable alphabet and let be literal
(anti)morphism onto (by definition, such a correspondence is determinated
by a permutation of the alphabet). This paper deals with sets which are
invariant under (-invariant for short).We establish an
extension of the famous defect theorem. Moreover, we prove that for the
so-called thin -invariant codes, maximality and completeness are two
equivalent notions. We prove that a similar property holds in the framework of
some special families of -invariant codes such as prefix (bifix) codes,
codes with a finite deciphering delay, uniformly synchronized codes and
circular codes. For a special class of involutive antimorphisms, we prove that
any regular -invariant code may be embedded into a complete one.Comment: To appear in Acts of WORDS 201
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