SUPPORTING INFORMATION FULL LEGENDS
Figure S1. Peptide-specific antibodies used for transcription factors ChIP-seq.
(a)-(c) Protein gel stained with GelCode Blue showing protein induction in E.coli cells for
recombinant ARK1a, ARK1b, ARK2, BLR, PCN, and PRE proteins. (d)-(g) Western blot
with ARK2, BLR, PCN, and PRE antibodies, respectively, showing that each antibody
specifically recognizes the corresponding protein. The colored arrows indicate the expected
protein size as labeled.
Figure S2. Cross-correlation analysis for evaluating the quality of ChIP-seq replicates.
(a)-(d) Evaluation of
ChIP-seq replicates of ARK2, BLR, PCN, and PRE with cross-
correlation analysis, respectively. (e)-(h) Evaluation of the pooled ChIP-seq sample of ARK2,
BLR, PCN, and PRE with cross-correlation analysis, respectively. NSC, normalized strand
coefficient; RSC, relative strand correlation.
Figure S3. Genome-wide distribution of ARK1 and BLR binding regions relative to the nonoverlapping putative target genes.
(a) and (b) show the distribution of ARK1 binding regions associated with ARK1_unique
and BLR binding regions associated with BLR_unique, respectively. The left plot shows the
distribution of binding regions relative to the transcriptional start site (TSS) of genes. The pie
chart on the right shows the distribution of binding regions relative to gene features.
ARK1_unique, ARK1 putative target genes that were not bound by BLR; BLR_unique, BLR
putative target genes that were not bound by ARK1.
Table S1. Summary of transcription factor ChIP-seq replicates.
Table S2. List of ChIP-seq peaks and putative target genes for all transcription factors.
Table S3. GO enrichment of ARK2, BLR, PCN, and PRE putative target genes. “GOBPID”, “GOMFID”,
and “GOCCID” stand for the over-represented GO categories in biological process, molecular
function, and cellular component, respectively.
Table S4. GO enrichment of ARK1/BLR_overlap. “GOBPID”, “GOMFID”, and “GOCCID”
stand for the over-represented GO categories in biological process, molecular function, and
cellular component, respectively. ARK1/BLR_overlap, ARK1 and BLR overlapping putative
target genes which were bound by their overlapping binding regions.
Table S5. GO enrichment of ARK1/BLR_non-overlap. “GOBPID”, “GOMFID”, and
“GOCCID” stand for the over-represented GO categories in biological process, molecular
function, and cellular component, respectively. ARK1/BLR_non-overlap, ARK1 and BLR
overlapping putative target genes which were bound by their non-overlapping binding
regions.
Table S6. Annotations from Populus Phytozome V3.0 and Arabidopsis orthologs for genes
included in co-expression network presented in Figure 6.
Table S7. Primers used for cloning and PCR verification.