Table 3 Peaks in common to all four ChIP-seq experiments with over fourfold enrichment relative to controls
Gene(s) in Correct Orientation Relative to ChIP PeaksqPCR ResultaAIM SequencebAIM Summitc
NCU00576 (hypo)NdYN
NCU00577 (hypo)NdYN
NCU00682 (Ser-Thr protein kinase)NdYY
NCU00865 (oxalate decarboxylase)NdYY
NCU00866 (DUF 1275)NdYY
NCU01195 (gdh)No effectYY
NCU01224 (26S protease reg subunit)No effectNNa
NCU01225 (ubiquitin conj enzyme)No effectNNa
NCU01744 (glutamate synthase)NdYY
NCU01742 (hypo)NdYY
NCU01808 (cytochrome c)2+, 5+YY
NCU01807 (hypo)NdYY
NCU01834 (hypo)NdYY
NCU01944 (hypo)NdNNa
NCU02092 (hypo)NdYY
NCU02474 (Tom5)No effectYY
NCU02475 (glycine dehydrogenase)2+, 5+YY
NCU02496 (M phase inducer phosphatase 3)NdYY
NCU02497 (hypo)NdYY
NCU02514 (ATPase-1)No effectNdNa
NCU02549 (processing enhancing protease)NdYY
NCU02550 (α-galactosidase)NdYY
NCU02720 (hypo)NdYY
NCU02732 (hypo)No effectNNa
NCU03118 (hypo)NdYY
NCU03120 (hypo)NdYY
NCU03257 (ammonium transporter MEP1)NdYY
NCU03364 (DENN domain)NdYY
NCU03365 (hypo)NdYY
NCU03408 (hypo)2+, 5+YYe
NCU03409 (RNA lariat debranching)No effectYY
NCU03466 (hypo)NdYY
NCU03548 (hypo)NdYY
NCU03549 (hypo)NdYY
NCU03593 (kaleidoscope-1)NdYY
NCU03651 (NADP-dependent malic enzyme)2+, 5+YY
NCU03749 (hydroxyacyl glutathione hydrolase)2−NNa
NCU04307 (MSF1)No effectYY
NCU04569 (5-oxoprolinase)2+, 5+YY
NCU04730 (post-transcript silencing protein QDE-2)No effectYN
NCU04801 (hypo)NdYN
NCU04874 (aod-3)5−YY
NCU04953 (penicillopepsin)NdYN
NCU04954 (hypo)NdYN
NCU04986 (hypo)NdNNa
NCU11067 (hypo)NdNNa
NCU05202 (mt K+ H+ exchange)No effectYN
NCU05203 (hypo)No effectYN
NCU05299 (NADH-ubiquinone reductase 29.9)No effectNNa
NCU05390 (mt phosphate carrier)NdYY
NCU05391 (hypo)NdYY
NCU05477 (hypo)NdYY
NCU11913 (hypo)NdYY
NCU05616 (arsenite S-adenosyl methyl transferase)NdNfNa
NCU05989 (hypo)NdYY
NCU06083 (hypo)NdYN
NCU06230 (Ser/Thr kinase)2−, 5−YY
NCU06381 (cell wall endoglucanase)NdYY
NCU06382 (ABC transporter)2+, 5+YY
NCU06387 (hypo)NdYY
NCU06389 (DUF 625 domain)NdYY
NCU06424 (amino methyl transferase)NdYY
NCU06425 (hypo)NdYY
NCU06426 (hypo)NdYY
NCU06724 (glutamine synthase)NdYY
NCU06939 (endosome assoc ubiquitin isopeptidase)No effectYY
NCU06940 (hypo)2+, 5+YY
NCU07098 (hypo)NdYN
NCU07099 (hypo)NdYN
NCU07166 (hypo)NdYY
NCU07167 (isoflavone reductase)NdYY
NCU07327 (hypo)NdYY
NCU07530 (transporter Smf2)NdYN
NCU07531 (Cu transporting ATPase)NdYN
NCU07668 (MFS multidrug transporter)NdYN
NCU11717 (hypo)NdYN
NCU07676 (hypo)NdNNa
NCU07678 (hypo)No effectNNa
NCU07807 (fructose bisphophatase aldolase)No effectYY
NCU07941 (aspartate amino transferase)NdYY
NCU07942 (hypo)NdYY
NCU07953 (aod-1)2+, 5+YY
NCU07954 (hypo)NdYY
NCU08674 (pentatricopeptide repeat protein)2+, 5+YY
NCU08877 (glycine cleavage system H)No effectYY
NCU08878 (Tem1)No effectYY
NCU08940 (complex III protein)NdYY
NCU08941 (Ca binding mt carrier)NdYY
NCU08946 (hypo)No effectNNa
NCU08947 (complex III protein)2+, 5+NNa
NCU08976 (fatty acid elongase)NdYY
NCU08977 (long chain fatty alcohol oxidase)NdYY
NCU09656 (carboxymethyl butenelidase)NdYY
NCU11414 (plasma membrane Zn transporter)No effectYY
NCU09873 (PEPCK)2+, 5+YY
NCU10007 (malate synthase)2+, 5+YY
NCU10894 (hypo)NdYY
NCU12093 (phospholipase D)NdYY
  • Alternating gray and white rows indicate one or two genes in the correct orientation to a set of peaks found in all four experiments. NCU numbers are followed by known gene functions where applicable. General information about N. crassa genes is available at FungiDB (http://fungidb.org/fungidb/). hypo, hypothetical protein

  • a Nd, not determined. Numbers indicate either AOD2 or AOD5. The plus sign indicates that protein is a positive regulator of the gene. The minus sign indicates that protein is a negative regulator of the gene.

  • b Y (yes), one or more AIM sequences present in upstream intergenic region of gene(s). N (no), no AIM sequence present in upstream intergenic region.

  • c Alignment of at least one AIM sequence with at least one ChIP-seq summit. Y (yes), AIM sequence at or near ChIP-seq summit. N (no), AIM sequence not found at or near summit. Na, not applicable.

  • d No AIM sequence in intergenic region but AIM present in nearby coding region and does align with ChIP-seq peak summit.

  • e Summit and AIM match, but only for the AOD5 peaks. Summits of the AOD2 peaks match the repeat sequence consensus (see AOD2 binds to a repeat sequence in the genome).

  • f As footnote c, but aligns only with shoulders of summits.