Instruct: Identify the main and secondary category of Arxiv papers based on the titles and abstracts
Query: RNA structure generates natural cooperativity between single-stranded
  RNA binding proteins targeting 5' and 3'UTRs   In post-transcriptional regulation, an mRNA molecule is bound by many
proteins and/or miRNAs to modulate its function. To enable combinatorial gene
regulation, these binding partners of an RNA must communicate with each other,
exhibiting cooperativity. Even in the absence of direct physical interactions
between the binding partners, such cooperativity can be mediated through RNA
secondary structures, since they affect the accessibility of the binding sites.
Here we propose a quantitative measure of this structure-mediated cooperativity
that can be numerically calculated for an arbitrary RNA sequence. Focusing on
an RNA with two binding sites, we derive a characteristic difference of free
energy differences, i.e. \Delta\Delta G, as a measure of the effect of the
occupancy of one binding site on the binding strength of another. We apply this
measure to a large number of human and C. elegans mRNAs, and find that
structure-mediated cooperativity is a generic feature. Interestingly, this
cooperativity not only affects binding sites in close proximity along the
sequence but also configurations in which one binding site is located in the
5'UTR and the other is located in the 3'UTR of the mRNA. Furthermore, we find
that this end-to-end cooperativity is determined by the UTR sequences while the
sequences of the coding regions are irrelevant.

16
The categories of this paper are: stat
34
The categories of this paper are: chem-ph
17
The categories of this paper are: q-fin
7
The categories of this paper are: hep-th
25
The categories of this paper are: patt-sol
35
The categories of this paper are: mtrl-th
15
The categories of this paper are: nucl-ex
5
The categories of this paper are: gr-qc
33
The categories of this paper are: plasm-ph
8
The categories of this paper are: hep-ex
14
The categories of this paper are: math-ph
20
The categories of this paper are: acc-phys
0
The categories of this paper are: hep-ph
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The categories of this paper are: hep-lat
23
The categories of this paper are: solv-int
2
The categories of this paper are: math