Two Types of scnRNAs
(A) A Tetrahymena cell contains a macronucleus (MAC) and a micronucleus (MIC). During vegetative growth, both the MAC and the MIC divide and segregate to daughter cells. Mixing starved cells of different mating types induces conjugation (i). The MICs undergo meiosis (ii), and one of the selected products divides mitotically to form two pronuclei (iii). One of the pronuclei crosses the conjugation bridge (iv) and fuses with the stationary pronucleus to produce the zygotic nucleus (v), which then divides twice (vi) to form two new MACs and two MICs (vii). The parental MAC is degraded, and the pair is dissolved (viii). The exconjugants resume vegetative growth when the nutrient supply is restored (ix). The approximate time when each event occurs is indicated (hpm, hours post-mixing).
(B) 1,464 MIC genome supercontigs (SCs, blue bars) were ordered by their lengths (longest to shortest) and concatenated. Normalized numbers (reads per kilobase per million reads [RPKM]) of sequenced 26- to 32-nt RNAs from WT cells at the indicated time points that map uniquely to the MIC genome are shown as histograms with 50-kb bins. The densities of IESs and mappable (unique) sequences are also shown. The drop in IES density in the region containing very short SCs is probably because these SCs are shorter than most of the IESs, and the prediction of IESs from them failed. The regions enlarged in (C and D) are marked with green lines. Longer (1–50) and shorter (51–1,464) MIC SCs represent B- and A-regions of the MIC genome, respectively.
(C and D) Small RNA expression from the indicated 300-kb windows (shown and analyzed as in B, except with 100-nt bins). Colored boxes indicate the positions of IESs (magenta, type A; sky blue, type B; see for the IES classification). In (D), the arrows mark MAC-destined regions that are the origins of Early-scnRNAs that accumulated prominently at early stages (3 hpm) but were degraded later.