Global expression profile of differentially expressed ncRNAs. Each line corresponds to an annotated segment, and each column represents the averaged values (computed for each segment) observed in duplicate samples. (A) Antisense rsSUTs or (B) MUTs and differentially expressed sense mRNAs showing opposed expression patterns. (C) rsSUTs or (D) MUTs and differentially expressed antisense mRNAs showing similar patterns. (E and F) Sense/antisense pairs of rsSUTs and MUTs and known ncRNAs. (G and H) Sense/antisense pairs of rsSUTs and MUTs. (I and J) rsSUTs or MUTs not overlapping with any transcript. MATa/α cells were cultured in YPD, YPA (black bar), and sporulation medium (SPII, hourly samples from 1 to 12 h; light green bar). The MATα/α strain was incubated in YPA (black bar) and SPII (6 and 10 h; dark green bar). MATa cells were grown in rich medium (YPD, samples were taken every 5 min from 0 to 135 min covering two cycles; black bars). Right: Scale for log2-transformed values, containing 20 colors corresponding to increments of 5 percentiles each.

Genomic ncRNA heatmaps. (A and B) Opposed sense/antisense profiles are shown for CSH2/MUT70 and CLN3/MUT30. (C) Correlated induction profiles for HUG1/MUT1091. (D) CLN2 mRNA and MUT1465 covering CLN2’s regulatory region. (E) Bidirectional promoter mediating expression of DER1 and MUT100 covering ARS220. (F) Bidirectional promoter of PES4 and MUT523 covering ARS607. Blue, purple, and gray boxes symbolize genes, MUTs, and ARS elements, respectively. Arrows indicate the direction of transcription. Averaged, normalized, and log2-transformed data at the oligonucleotide probe level covering the top (+) and bottom (−) strands are shown. Media, samples, and scale are as in .

Rrp6 control of meiotic and mitotic ncRNAs. (A) Differentially expressed CUTs, rsSUTs, and MUTs in RRP6 vs. rrp6 strains. A scale for percentiles and log2-transformed data is given. (B) MUT concentrations determined by RT-PCR in fermenting (YPD), respiring (YPA), and sporulating (SPII, 2–12 h) cells. ACT1 was used as a standard. (C) Expression data for Rrp6-dependent MUTs, rsSUTs, and CUTs in sporulating (MATa/α) and starving (MATα/α) diploid cells and in a growing haploid strain (MATa). The scale is as in .

Rrp6 regulation and function. (A) Genomic heatmap of expression data for RRP6/MUT1312 from strains and samples as given. The layout is as in , and the scale is as in . (B) RT-PCR expression data for RRP6/MUT1312 using samples as in . (C) Western blot data for Rrp6 and Pgk1 detected in extracts prepared from a diploid rrp6 mutant (rrp6) and diploid growing (YPD, YPA) and sporulating wild-type cells (time points taken every 2 h from 2 to 10 h). Histogram below the bands shows relative Rrp6 protein amounts on the y-axis detected in the samples given on the x-axis. (D) DNA replication dynamics analyzed by fluorescence-activated cell sorting in diploid strains containing wild-type (RRP6) and mutant (rrp6, pap2) alleles. Respiring cells (YPA) were compared with hourly samples from sporulating cells (SPII, 1–12 h). DNA content is given at the bottom. (E) Wild-type (RRP6) and mutant (rrp6) strains undergoing MI, MI+II, and ascus formation. The x-axis shows the time of incubation in SPII sporulation medium in hours, and the y-axis displays the percentage of cells within the population that have completed landmark events. The average of three independent sporulation assays is shown.