Table S1. All regions of WCC enrichment at p<0.001 and z score >3.09
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1 Table S. All regions of WCC enrichment at p<. and z score >3.9 N. crassa contig start nt # of reads z score promoter coding region intergenic chrvii_contig frq chrvi_contig vvd chri_contig cry chrii_contig bli- chrii_contig bli- chri_contig os-/ncu37 chrvii_contig frq AS/NCU6 chriv_contig none chrv_contig sah- chrv_contig NCU63 chrvi_contig NCU chrii_contig NCU58/NCU55 chrii_contig NCU58/NCU55 chrvi_contig NCU559 chri_contig NCU8/NCU8 chri_contig NCU8/NCU8 chrvii_contig wc- chrv_contig NCU95 chriii_contig NCU75 chri_contig al- chrvi_contig NCU3968 chrvii_contig NCU3/NCU67 chrii_contig NCU965 chri_contig al-/ncu58 chriii_contig NCU57 chriii_contig NCU9 chrii_contig NCU353 chri_contig tca- chri_contig NCU75 chri_contig nit- chri_contig NCU35/ chrvi_contig NCU596 chrii_contig NCU9335 chri_contig NCU997/ prr-5 chrv_contig NCU989 chrvii_contig NCU695 chrvi_contig NCU3865 chriv_contig NCU5 chrvii_contig NCU395 chrv_contig NCU568 chrv_contig NCU/NCU3 chrii_contig NCU53/NCU5338 chriv_contig crf5-/ncu637 chri_contig NCU87 chriii_contig nst-5/ncu chriii_contig cdc-7/ncu6 chrii_contig hsf- chrv_contig tre- chrvi_contig NCU3967/vvd chri_contig NCU89 chrii_contig NCU8 chriv_contig NCU655/NCU6553 chrvi_contig NCU3866 chriii_contig NCU75
2 chri_contig msh- chriv_contig mus-5 chrv_contig NCU983 chrii_contig NCU333 chrii_contig NCU333 chrvi_contig NCU78 chriv_contig rhp-55 chri_contig NCU9 chri_contig NCU866 chrvi_contig prk-7/ylo- chri_contig csp- chrv_contig sah- chrii_contig rpn- chriv_contig cre- chriv_contig NCU773 chrvi_contig NCU53 chrv_contig NCU76/spr-7 chrvi_contig NCU3968/NCU3969 chrvi_contig NCU3968/NCU3969 chriii_contig NCU359/NCU36 chri_contig NCU939 chrv_contig NCU953/NCU9535 chrii_contig NCU5373/NCU5375 chri_contig phr chri_contig adv- chriii_contig bek- chrii_contig NCU935/NCU935 chriii_contig NCU68/NCU69 chri_contig cr-/ncu7378 chri_contig cr-/ncu7378 chrv_contig NCU7/7 chriii_contig NCU68/NCU69 chri_contig dtn- chrv_contig NCU76 PP chrv_contig NCU779 PP chrii_contig NCU83 chrvii_contig NCU9 chriv_contig NCU9/NCU9 chriii_contig NCU6/NCU6 chri_contig NCU933/con-8 chrv_contig ccg-3 chri_contig NCU89/3 chri_contig NCU7/ (PP/CH) chri_contig NCU86 chrvi_contig NCU59 chriii_contig NCU6 chri_contig NCU69 chrii_contig NCU3388 chriv_contig erg- chri_contig gh38- chriv_contig NCU775 chrvii_contig NCU867 chrvii_contig NCU867 chriv_contig os- chri_contig NCU9 chrv_contig NCU8883 PP chrvi_contig ubi chriv_contig NCU736
3 chri_contig gh5-/ncu397 chriv_contig NCU59 PP chrvi_contig NCU557 PP chriv_contig bdp- chrvi_contig NCU56 chrv_contig NCU6/gh7-3 chri_contig NCU77/NCU77 chrii_contig NCU539/NCU5395 chrvii_contig NCU687 chriv_contig NCU885 PP chrv_contig nup-/ncu87 chriv_contig NCU53 chrii_contig NCU537/NCU5373 chriii_contig NCU755 chriv_contig NCU983 contig none contig none chrii_contig NCU536 chrii_contig NCU/NCU63 chriii_contig csb/pan-3 chriii_contig csb/pan-3 chrv_contig gt- chri_contig NCU76 PP chrii_contig NCU788 chriv_contig NCU66 CH chriv_contig NCU97 chri_contig NCU97/NCU97 (CH/CH) chriv_contig NCU7 chriii_contig NCU69 chrii_contig NCU8/NCU83 chriii_contig NCU chri_contig NCU3/NCU33 chrv_contig NCU793 chriv_contig NCU3 chri_contig NCU9 chrv_contig NCU77 chri_contig NCU369 chrvi_contig NCU559 chrv_contig NCU6655 chrv_contig NCU775 PP chrv_contig NCU6 contig none chri_contig NCU8/NCU8 chrvi_contig mus-5/ncu73 chri_contig NCU/NCU3 chriv_contig NCU5 chrv_contig NCU983 contig none chrv_contig NCU8956 chrii_contig NCU87 chrvii_contig NCU6888 PP chriv_contig NCU PP chrv_contig sub- chri_contig NCU59 chrvii_contig NCU9 chri_contig NCU33/NCU3 chrvii_contig NCU5897 chrvii_contig NCU5897
4 chrv_contig NCU7 chriii_contig NCU996 chri_contig NCU6 chri_contig NCU593/NCU59 chri_contig hda-/ncu897 chriv_contig NCU776/NCU777 chrv_contig NCU76 chrvi_contig mrp-7 contig none chriv_contig trm- chrv_contig NCU36/NCU36 chrii_contig chrii_contig hda-/gpd- (ccg-7) chriii_contig NCU36 chrii_contig NCU76/NCU78 chri_contig NCU66 chri_contig NCU336/nca- chrv_contig NCU376 chrv_contig NCU37/NCU37 chrvi_contig NCU3865 chrv_contig NCU8 chrv_contig NCU639 PP chrvi_contig NCU765 PP chrvi_contig NCU8 CH chriv_contig NCU76 PP chriii_contig NCU783 chriii_contig NCU7869 chriii_contig NCU8797 PP chriii_contig NCU959/NCU95 chrv_contig NCU6/NCU376 chrv_contig NCU56/sub- chri_contig NCU77/NCU78 chriv_contig asn- chrvi_contig NCU78 chriv_contig NCU969 chrvi_contig NCU387 chrvi_contig NCU55/NCU56 PPs chriv_contig NCU539/NCU53 chriv_contig trm- chri_contig NCU59 chri_contig NCU33/msp- chrii_contig un- chrv_contig NCU389 chrv_contig NCU389 chrv_contig NCU79/NCU79 chrv_contig NCU7786/ccg- chrii_contig none chrv_contig NCU3586 chrvi_contig NCU59 chriii_contig NCU683 chriv_contig NCU653/NCU6536 chri_contig NCU99 PP contig none contig none chrvi_contig NCU598/NCU599 chrv_contig mbf-/ncu chrvi_contig nuo.6/ilv-6 chrv_contig NCU8
5 chrii_contig NCU6785 chrii_contig NCU355 chri_contig cea- chri_contig ck- chrv_contig gh63- chri_contig msr-7/ad-5 chri_contig NCU9 PP chrvi_contig NCU55 chri_contig NCU75 chriv_contig NCU7635 PP chrvii_contig NCU936/7 contig none chrii_contig vph- chrii_contig vph- chri_contig hom- chri_contig NCU979 chrii_contig NCU3375 chriii_contig NCU667/NCU668 chrii_contig NCU678/mrp-9 chriv_contig NCU7/NCU7 chri_contig prm-/chi-3 chri_contig prm-/chi-3 contig NCU576 chrvi_contig sah- chriii_contig gh6-5 chrv_contig NCU9/NCU9 chri_contig NCU665 chriv_contig NCU98 chriii_contig NCU5688 PP chrvii_contig NCU585 CH/NCU5855 chri_contig NCU838 chriii_contig NCU956 chrii_contig nmt- contig none chriv_contig sre chriv_contig sre chri_contig arg- chri_contig gh7- chriv_contig NCU536/gh8-6 chriii_contig NCU chriii_contig NCU chrv_contig NCU78 chrv_contig NCU78 chriv_contig NCU567 chriii_contig NCU6 chrv_contig NCU669 PP chriii_contig NCU786 chriii_contig NCU8533 PP chri_contig NCU9 chri_contig NCU9 chrv_contig prk- chriv_contig pyr-3/ncu883 chriv_contig pyr-3/ncu883 chri_contig trm- chriii_contig mrp-35 chri_contig NCU596 chri_contig NCU687/8 chri_contig NCU687/8
6 chrii_contig NCU598/NCU599 chrv_contig NCU59/3678 chrv_contig NCU6 chriii_contig ptr-/ncu8 chriii_contig ptr-/ncu8 chriii_contig NCU63/ chriv_contig NCU738 chriv_contig NCU7995 chri_contig cyt-/gh6- chrvii_contig NCU93 chrii_contig none contig none chriii_contig NCU39 chri_contig NCU667/NCU668 chrvi_contig NCU5/NCU53 chriv_contig NCU659 chriv_contig NCU6597 PP chri_contig NCU936 CH chri_contig NCU7/NCU73 chri_contig NCU33/msp- chri_contig NCU386/NCU6 chri_contig NCU839/NCU839 chri_contig NCU93/NCU933 chriii_contig NCU566 contig NCU999 chrii_contig eas chrvi_contig gh7-5 chriii_contig NCU75/mip- chri_contig NCU857/NCU859 chriv_contig NCU796 chrv_contig NCU887 PP chrv_contig NCU95 CH chrv_contig NCU9678/NCU9679 chrii_contig nup-3 chriii_contig NCU3 chrv_contig NCU3689/NCU369 chrv_contig NCU3/NCU3 chriv_contig NCU638/NCU639 chriv_contig NCU698/NCU698 chriv_contig vsp-/ncu8 chriv_contig vsp-/ncu8 chrii_contig NCU538 chriv_contig NCU983 chriv_contig NCU698 chri_contig crf9- chrv_contig mrp-33/ad-6 chri_contig NCU889/NCU89 PPs chrvi_contig NCU83 chriv_contig NCU983 chrvi_contig NCU53 PP chrvi_contig NCU599 chrv_contig NCU7778 chrv_contig NCU7778 chrv_contig NCU9685 CH chriv_contig NCU977 contig NCU988/NCU988 chriii_contig NCU387 chrii_contig none
7 chri_contig rpn-5 chri_contig vad-/ncu95 chriii_contig NCU5 chri_contig NCU688 chrii_contig NCU8 chrii_contig NCU8 chrvi_contig nuo3./ncu75 chrv_contig NCU65/NCU653 chriii_contig NCU63/NCU6 chriv_contig NCU83/NCU835 chrvi_contig NCU77 chrii_contig NCU5388 PP chri_contig NCU838/NCU838 chri_contig efr-3 chriii_contig NCU CH chri_contig NCU786/NCU787 chrii_contig NCU653/NCU65 chri_contig NCU33 chri_contig NCU335 chri_contig NCU373/NCU37 chrv_contig NCU9 CH chrvi_contig NCU5563 PP chriii_contig NCU5737 chri_contig NCU7359 CH chriv_contig NCU83 PP chrv_contig NCU8966 PP chrvi_contig NCU78 PP chriii_contig NCU878 chri_contig vma-/ncu668 chriii_contig NCU/mrp-35 chriii_contig NCU6 chri_contig nuo9.5 chrvi_contig gh7-/ncu69 chri_contig NCU355 chrvii_contig NCU33 chriv_contig NCU53/NCU533 chriii_contig NCU68/NCU69 chrv_contig NCU65/NCU66 chrv_contig NCU65/NCU66 chriii_contig NCU753 chrii_contig NCU89/NCU89 chri_contig NCU38 chrvii_contig none chri_contig NCU79 chri_contig gh7-7 chri_contig NCU79 chri_contig NCU3 chrii_contig NCU358 chrv_contig NCU375 ccg- chrvi_contig NCU389/NCU385 chriii_contig NCU635/NCU636 chriii_contig NCU683 chri_contig NCU7353 PP chriv_contig NCU8 chrii_contig NCU859 PP chriii_contig NCU8779 chri_contig NCU978 chrii_contig NCU5
8 chrvi_contig phy- chriii_contig NCU5 chriii_contig NCU/NCU86 chrii_contig hh- chrii_contig NCU66/NCU66 chri_contig NCU598/NCU597 chri_contig NCU869 chri_contig NCU36 chrv_contig NCU36/NCU365 chrv_contig NCU36/NCU365 chrv_contig NCU76/fpp chriii_contig NCU687/crf3- chrii_contig NCU6775 chrii_contig NCU683 chriv_contig trm-9/ncu77 chri_contig contig NCU573 chrii_contig NCU989/NCU99 chri_contig NCU775 PP chrv_contig NCU3/hsp-8 chrvii_contig NCU5793/NCU579 chrii_contig crp-/ncu85 chriv_contig cys- chriii_contig NCU/NCU chriii_contig NCU/NCU chrv_contig NCU7 chri_contig NCU773/NCU77 PPs chri_contig NCU79 CH chri_contig NCU36/NCU365 chri_contig NCU36/NCU365 chrii_contig NCU36/NCU38 PPs chriv_contig NCU79/NCU8 chrvi_contig NCU8 PP chrvi_contig NCU58 PP chriii_contig NCU573 PP chrvii_contig NCU695 chriii_contig NCU63 chriii_contig NCU63 chriv_contig NCU6375 chriv_contig NCU789 chrii_contig NCU878/NCU879 chri_contig NCU93 chriv_contig NCU9657 chriv_contig NCU9657 contig NCU996 chrv_contig NCU57 PP chriv_contig xdh- chri_contig NCU3/NCU68 chri_contig NCU88 chrvi_contig coq-3/ncu598 chrvi_contig NCU5978 chrii_contig NCU557 chrii_contig NCU633 chrv_contig tah-3 chrvi_contig NCU399 chrv_contig apr-6 chriii_contig cat- chrvii_contig NCU63
9 chrii_contig NCU675 chrii_contig NCU6769 chriii_contig cyp5- chriv_contig NCU979/NCU973 chriv_contig gh6- chrv_contig NCU chrii_contig NCU675 chri_contig NCU75 chrvii_contig NCU859 chrii_contig NCU9336 chri_contig NCU33/NCU3 chriii_contig ncw-3 contig NCU57 See Experimental Procedures for details. PP denotes predicted protein, CH denotes conserved hypothetical protein. Promoter denotes WC- binding sites close to known or predicted transcriptional start sites, coding region denotes peaks found only in coding regions of genes but not also in the promoter, and intergenic denotes peaks that are in gene-poor non-coding regions. A z score of 3.9 or greater means significance at p<..
10 Table S. Oligonucleotide primers. A. Primers used for ChIP-PCR. Name Sequence (5 to 3 ) expected size (bp) frq_plref GCAGAGGACCCTGAACTTTTC frq_plrer TCTCTTGCTCACTTTCCCACAG frq_dlref GGTCGGGTTGCCGTGACT frq_dlrer GTCATCGGTCTTGCAGCGG vvdf CGCACCCAAGATTACTGTTTCCACC vvdr TAGAGTCGAGGATGAGATGGAG 8 al-3f CTCAGCAGGCAAGCAGGGCAAATC al-3r CTAACCCCGTGCGTCGTCTGATCC 5 hh-f AACCACCGAAACCGTAGAGGGTAC hh-r ATCGCCGACACCGTGTGTTGTAAC B. Primers used for isolation of cdna. Name Sequence (5 to 3 ) act CTTGATGTCACGAACGATTTCG frq AAGACGAAATCCTCGTCATTC frq antisense GTATCTCAATCTGCTTTGTAACCTGGC C. Primers used for Taqman probe realtime PCR. Name Sequence (5 to 3 ) NCUf TCCGCACCGGTCAAGAAA NCUr GGAAGTGGGCGCATGAGAT NCUprobe CGACCAACGTATACCGCGACAACAAAGTC NCU73f TCCTGCAGCGAACATCCACTA NCU73r GTCATCACAGTCCTGCTCGAGAA NCU73probe ATGTCCTCCCGGAGCATCTTGCCA NCU87f CCACGACAACACAAGACCTTAACTT NCU87r CATCCATGACTTGAGACTGGAACA NCU87probe TCGAAGGCACAAATACCAACTCGCCA NCU3f CAATGCCGATGATGAGGAGAA NCU3r GGGAGAGGGACTGCGGAAT NCU3probe TCCAGACCCCCTCTGCGAACATCA NCU95f TCTTGTTGAGGCTCCCGAGTT NCU95r CGAGCCGCTCTGGAAGAAG NCU95probe CTCAGTCCAGCAGCGTTACCCGTTGA NCU3968f CATCTTTCCAAATCCGCTACCTACT NCU3968r CCCGTCAGCTGTGATTTACGA NCU3968probe TGGCGCCATCAACGATACCCTGTTT NCU58f CAGAGACCGTCAGAATGGAACTCT NCU58r GCGGAAAAGCTTGTCACCATAC NCU58probe TGGCGCGATTACATGAGGTTGTGTCA NCU37f TGCAGCATGAATGGATCATGA
11 NCU37r CGCCTTGACTCGTCGTTGA NCU37probe TCGAGC CTGCCACCCCTAGTAGCG NCU37f CGATGGTGGGTGACTCACAAG NCU37r AGCCGAGATGTGGTGTTTGG NCU37probe CAAGAGGATGAGAAAATGGTCGCGGC NCU67f AGCTATGGATCGAGGAGGGT NCU67r GTCCTCATTCATCTCGGGAA NCU67probe CGTCCAGACGTTTCCGGATTCG NCU7389f ACGTTCGCCAATTTCTTGAC NCU7389r GAGCACGTAATCTCGCATGA NCU7389probe CCAACACCGCCGTTCGAGCT NCU95f TTGATGCGCGTAAAGTCTTG NCU95r AGCTCTTGTCGTTTCTCCCA NCU95probe TCCATCTCCTCTTCGTATCTGCGCTC NCU37f CATCGATTTGCTTCCGTACA NCU37r AAACCCGTGAATGTGAATGG NCU37probe CGCTGCGCCATTCTTCACGA NCU8f CGATGCCTACAAGGAAGAGC NCU8r TTTCTGGGACATAGCGTTCC NCU8probe TCAGGCCAAGATGGCACAAACG NCU873f GAGTCTGTGGCAGTTCACGA NCU873r GATTGCGATTCGGAAGGTTA NCU873probe CGCCGAAACTGGCCTCACCT NCU6536f ACGAGACAGAATTGGGCAAG NCU6536r CTTGTACTTGCCATCGGGTT NCU6536probe TATGGCGCAGTCCGCAGCC NCU968f GCGGAATGGACGTTGATAGT NCU968r GTTGAAGGTGGGCATTGTTT NCU968probe CCCGCCAACTCGACAGGATCT NCU596f ATGCGCCATCAAATACACAA NCU596r CATCGTCGTGCTCGGTACTA NCU596probe CGTTTGCAAGCTTGTCGCTCCA NCU989f AAACAGACGTTGGATTTGGC NCU989r ACCGACAGGAAAGCAAACAC NCU989probe AGATCACCGCCAAGGCGTGC NCU97f CCAACACCAGCCCATATACC NCU97r GCCCATGACGGTGTTCTAGT NCU97probe CCCTCCTCACGGGTATCCTCAAGA NCU775f TGGACCTCTCCAACACTTCC NCU775r CGATAGTGGCTCCTCCATGT NCU775probe CAGGCGTACCAAACGTTGACACGA NCU653f GCTGATCCAGTCCTTGCTTC NCU653r GTAGCCATGCACGCTCACTA NCU653probe CGCATCCAAGGCCCTCACTGA Ncu778f AACCGTTGTTATTGCTTGCC Ncu778r CGCATTGCAAATGGTATGAC
12 Ncu778probe TTCGTCCCTTCGCCAGAGCG NCU75f CGACAATTTCATGGATGTGG NCU75r CTAGGCTTCGCTCGCATACT NCU75probe CGGGCACCTCTTCCGTATCCG NCU9f TATACCGAACCTTGGCCTTG NCU9r CCACCCATGGTAGTTGATCC NCU9probe CCGCCTCGAACGGATCCATC NCU599f AGGCACGCAACTCGTACTCT NCU599r GCGCTTTGAAAGGTTGAGTC NCU599probe CCGAGTCAGGCAACCCGCTG NCU373f AACGTCAACTGGTCCCAGAC NCU373r GGCTAGACTGTGCAGGAAGG NCU373probe CGCCCGACGAGAAGCGTCTC NCU38f TAGTCCTCCCATGTCTTCGG NCU38r AGTAGTTGGAGCTGCCCTGA NCU38probe TCGAGCAAGCCAGCAAGCCA NCU8f GTGGAAGCGTATCTGGTGGT NCU8r ATATGACAAGGTCGCCCAAG NCU8probe ACCGATCGACAGCTGTCGCG NCU859f TTTCCAATGGAGGAGACGAC NCU859r CAAGACCCGCTCTCTGTTTC NCU859probe CCCTCTGCCTTTCCCTCCACG NCU695f AGCACACCAGAGAGGAGGAA NCU695r GAGAAACCGTCAAACGAAGC NCU695probe CGATGCGCGTCCTCTTGTCG
13 Figure S. Validation of ChIP-seq libraries. After ChIP-seq library construction, PCR shows enrichment of four known WCC binding sites (frq plre and dlre, vvd and al-3) in the WC- library. Figure S. ChIP-seq reveals WCC regulation of TF genes. TFs with WCC peaks in their promoters and whose expression is: A. light induced and dependent on WC-, B. not light induced but dependent on WC-, and C. not light induced and independent of WC- (summarized in Table B; TF genes shown in Fig. are omitted). SOAP mapped sequence reads from the WC- ChIP library are plotted as a histogram of sequence coverage per base along fragments containing loci of interest. The y-axis has a maximum value of reads per base and regions with > reads are shown in black, others in grey. Gene annotations are based on known or predicted cdnas (UTRs are shown in light green, coding regions in dark green and introns are shown as thin lines). Quantitative RT-PCR was performed on RNA isolated from control (black bars) and Δwc- (white bars) strains grown in the dark (D) or following a 5-min light induction (L). Values shown are the average of two experiments (y-axis). Figure S3. Genes with WCC binding sites fall into diverse functional categories. The pie chart shows functional categories for all 58 regions. The tables show a comparison of the most significant 9 WC- binding sites (z-score >5, p<.9e-7) with all 58 regions (z-score 3.9, p<.). This comparison reveals enrichment for factors involved in cell cycle control, transcription, protein binding and interactions with the environment.
14 Smith et al., Figure S! WC- lib! Input DNA! hh! hh!
15 A! NCU95 TF! Smith et al., Figure S! 8 6 NCU965 TF! D D L L D D L! L! NCU596 TF! 8 6 NCU989 TF! NCU3 TF! NCU! NCU73 TF csp-! 6 8
16 A (continued)! Smith et al., Figure S (contʼd)! 6 NCU739 TF adv-! 8 6 NCU97 TF bek-! NCU775 TF! NCU5 TF sub-! 8 6 NCU73 TF sah-! NCU778 TF sre!
17 Smith et al., Figure S (contʼd)! A (continued)! NCU786 TF! NCU75 TF! NCU9 TF vad-! NCU95! NCU38 TF! NCU859 TF! 8 6 NCU695 TF ghh!
18 Smith et al., Figure S (contʼd)! B! NCU968 TF nit-! NCU653 TF! NCU6536! NCU8 TF!
19 Smith et al., Figure S (contʼd)! C! NCU886 rhp55! NCU887 cre-! NCU87 TF! NCU873! NCU599 TF! NCU373! NCU37!
20 Smith et al., Figure S3! All significant peaks (see above)! Functional category # % Metabolism 9 6% Energy 9 % Cell Cycle 7 5% Transcription 3 5% Protein Fate 3 5% Protein Binding % Transport % Cell Rescue % Environment 8 % Cellular Components % Unclassified 36 5% Not Near Gene 5 3% Cell Fate % Signal Transduction % Differentiation % Subcellular localization 3 % Protein Synthesis 7 % Regulation of Metabolism % Total 58 % Peaks with z score >5 (Fig. A)! Functional category # % Metabolism 8 7% Energy % Cell Cycle % Transcription 9 8% Protein fate 7 6% Protein Binding 7 6% Transport % Cell Rescue % Environment 3 3% Cellular Components 3 3% Unclassified 6 % Not Near Gene % Total 9 %
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