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Supp. Figure S1. The deletion breakpoints map to locally GC-rich regions. The GC content of the entire FOXF1 intron is shown. Deleted region is in red frame.

Supp. Figure S2. Maternal origin of the FOXF1 intronic deletion. Chromatopherograms across informative SNPs are shown.

Supp. Figure S3. FOXF1 mRNA levels in ACDMPV and normal fetal lungs, and normal fetal lung fibroblasts, IMR-90. The red bar within each box represents the median. Mann-Whitney P values are indicated for relevant comparisons.

Supp. Figure S4. Splicing pattern in periferal blood lymphoblasts of FOXF1 minigenes bearing normal and truncated copies of the FOXF1 intron. Boxes 1 and 2 represent intron-flanking regions of the FOXF1 exon 1 and 2, respectively. The predominant 0.4 kb band represents RT-PCR product of correctly spliced mRNA of minigenes from plasmids transfected into cells.

Supp. Figure S5. Location of selected regulatory elements within the deletion region of the FOXF1 intron. The part of the intron deleted in ACDMPV case (chr16:86,545,491-86,546,265) is highlighted red. The remaining parts of the intron are marked green. Sequences corresponding to primers used to amplify the intron for mini-gene constructs are in lower case letters and in italics. (A) In silico predicted CTCF binding sites are highlighted black (CTCFBSDB 2.0, http://insulatordb.uthsc.edu/home_new.php, score > 5). CTCF binding sites identified by ChIP-seq in fetal lung fibroblasts, IMR-90 (UCSC Genome Browser), are highlighted gray. (B) The in silico identified CAAT boxes for binding of CEBPB are highlighted yellow. CEBPB binding sites identified by ChIP-seq in IMR-90 cells (UCSC Genome Browser) are highlighted gray.

Supp. Figure S6. A model of interactions between the FOXF1 promoter and its intronic enhancer.

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