As slow-evolving sites of stem regions have globally higher G + C contents than fast-evolving ones (see the electronic supplementary material, figure S4), this simulation result is in agreement with the bias of Gowri-Shankar & Rattray [ 17].
For example, different sites of stem in pri-miRNA may have different numbers of unpaired nucleotides, and the length of terminal loop by bioinformatic prediction could range from 3-nt to more than 10-nt [ 5- 7].
21 Leptomeninges have been recently identified as sites of stem cell recruitment in response to ischemia 22, 23 or brain damage 21, 24, 25 suggesting that they also serve as a niche for neural precursors in adulthood during periods of CNS distress.
Sites of stem-loop structure are particularly vulnerable to both degradation and to polymerase stalling [ 25- 27] both of which generate noise in BPCR.
In situ hybridization analysis of adult Clytia medusae (Figure 2A) revealed that as in Xenopus [8], Poc1 mRNA is predominantly expressed in the gonads with only low expression detectable in other tissues (including at the base of the tentacle bulbs, a site of intense stem cell division [12]).
Yoshimoto, M., Porayette, P. & Yoder, M. C. Overcoming obstacles in the search for the site of hematopoietic stem cell emergence.
The matching PARE tags were mainly mapped to precursors in one of two places: either the lower or upper cleavage site of the stem-loop 3′ arm.
Local separation criterion is intended for this purpose and is equal to the length (i.e. expected number of substitutions per site) of the stemming branch of the phylotype.
As shown in Fig. 4c, in contrast, matching PARE tags were mainly mapped to nov-sit-miR14, sit-miR156b-2, sit-miR319-1 and sit-miR535 precursors at the upper cleavage site of the stem-loop 3′ arm.
