Additional file 1 of Discovering candidate imprinted genes and imprinting control regions in the human genome
Creators: name: Minou Bina
Publisher: name: figshare
Year: 2020
Subjects: subject: Genetics
subject: FOS: Biological sciences
subject: FOS: Biological sciences

description: Additional file 1 Figure S1. A candidate ICR for PRDM8. Large scale experimental studies listed PRDM8 as acandidate imprinted gene [15]. Due to its vicinity to a robust density peak, my strategy also predicts that PRDM8 is potential imprinted gene. Figure S2. A candidate ICR for PCNT. Large scale experimental studies listed PCNT as a candidate imprinted gene [15]. Since PCNT includes 2 intragenic robust density peaks, my strategy predicts that PCNT is a potential imprinted gene. Figure S3. A density peak in the vicinity of WDR60. Results of large-scale experimental studies listed WDR60 as a candidate imprinted gene [15]. within WDR60, I noticed a peak covering 2 ZFBS-morph overlaps. This peak could be a false or a true-positive. If false-positive, then another peak -far upstream of (WDR60)- could be a candidate ICR for regulating parent-of-origin specific expression of both WDR60 and ESYT2. The latter gene encodes a protein (synaptotagmin-like protein 2) that belongs to a family of membranous Ca2 + −sensors. Figure S4. The positions of density peaks with respect to the ICR of H19 – IGF2 imprinted domain. In a few cases, an ICR encompasses two density peaks. The figure below includes a track displaying “Updated CTCF Binding sites predictions”. See references [25, 26] for updated positions of the unique repeats and CTCF sites upstream of H19 TSS. Results of the ENCODE ChIPs do not support the existence of the predicted CTCF site 5 described previously [24]. Furthermore, in results of ChIPs displayed at the UCSC genome browser, I noticed a chromatin boundary consisting of CTCF, RAD21, and SMC3 in a CpG island upstream of H19 TSS [25]. I named the predicted site in that island CTCF site 8. Figure S5. A peak in the density plots correctly locating the KvDMR in the KCNQ1 imprinted domain. Figure S6. A candidate ICR for a potential imprinted gene (CITED2). This gene encodes a regulator of transcription. Absence of Cited2 in mouse embryos caused congenital heart disease by perturbing left-right patterning of the body axis [31]. Deleterious mutations in CITED2 cause VSD2 –ventricular septal defect 2 [75]. Figure S7. A candidate ICR for a potential imprinted gene (FUCA2). Note the position of the candidate ICR with respect to the SNP (rs72992630) and primers used to deduce that FUCA2 is biallelically expressed gene [19]. The SNP and primers are not in the vicinity of the 1st exon of the transcript that is associated with a candidate ICR. Figure S8. A candidate ICR for a potential imprinted gene (SAMD5). A study found that SAMD5 was overexpressed in prostate cancer and had powerful prognostic ability for predicting postoperative biochemical recurrence after radical prostatectomy [33]. Figure S9. A density peak predicted a candidate ICR for a potential imprinted gene (ZBTB2). In mouse embryonic stem cells, ZBTB2 dynamically interacted with nonmethylated CpG island promoters and regulated differentiation [35]. In colorectal cancer, the abnormal forms of ZBTB2 increased cell proliferation [36]. Figure S10. Density peaks mapping to known parent-of-origin specific transcripts. One peak correctly located the ICR at the MEST locus. This ICR is intragenic and encompasses the TSSs of MESTIT1 (a noncoding RNA gene) and a subset of MEST transcripts. KLF14 is a known imprinted gene [30]. Density-plots predicted a candidate ICR regulating its imprinted expression. Figure S11. In density-plots, a peak correctly located the ICR regulating the expression of INPP5_v2.