Additional file 11: of Genome-wide mapping of Hif-1α binding sites in zebrafish
Creators: name: Greenald, David
name: Jeyakani, Justin
name: Pelster, Bernd
name: Sealy, Ian
name: Sinnakaruppan Mathavan
name: Fredericus Van Eeden
Publisher: name: Figshare
Year: 2015
Subjects: subject: Biophysics
subject: Biochemistry
subject: Medicine
subject: Microbiology
subject: FOS: Biological sciences
subject: FOS: Biological sciences
subject: Cell Biology
subject: Genetics
subject: Molecular Biology
subject: Evolutionary Biology
subject: 20199 Astronomical and Space Sciences not elsewhere classified
subject: FOS: Physical sciences
subject: FOS: Physical sciences
subject: 69999 Biological Sciences not elsewhere classified
subject: Developmental Biology
subject: Cancer
subject: 111714 Mental Health
subject: FOS: Health sciences
subject: FOS: Health sciences
subject: 110309 Infectious Diseases
subject: Plant Biology
subject: 60506 Virology
subject: Computational Biology

description: Examples of Hif-1α binding in proximity to hypoxia response genes. In all panels the red vertical bar shows the region of the chromosome that is enlarged in the window below. The introns and exons of known genes in the enlarged region are annotated in dark blue, the small chevrons on the genes show the orientation of transcription. The window shows mapped significant peaks for WT and VHL mutants. Peaks appear as black vertical bars. ‘VHL all peaks’ refers to all the peaks found using MACS in the vhl mutant samples, ‘VHL HRE only’ refers to the peaks found in vhl mutants containing the RCGTG motif in the surrounding 100 bp and thus show a subset of the black vertical bars of “VHL all peaks”, ‘WT all peaks’ refers to all the peaks found in wild-type samples using MACS, and ‘WT HRE only’ refers to the peaks found in the wild-type sample containing RCGTG motif in the surrounding 100 bp. A: A HRE-containing peak −57 bp upstream of Prolyl 4-hydroxylase α1b (p4ha1b), a known hypoxia response gene involved in extracellular matrix remodelling which is found to be up-regulated in the vhl mutant by FC 34.0 in the microarray [55]. Given that this peak is highly significant, and in the close vicinity to the TSS of a highly expressed gene, it may represent a functional HRE for this gene. B: Screenshot showing a number of Hif-1α binding sites in both vhl mutant and wild-type samples surrounding egln3. Egln3 (phd3) is a gene which is seen to be strongly activated in response to hypoxia in zebrafish [49], and is up-regulated with a FC of 151 in our microarrays. In vhl mutants there is are two strong HRE-containing peak residing within intron 1. Additionally, there are a number of peaks upstream of the gene. Interestingly, there are a number of peaks found in the wild-type sample, suggesting that there is Hif-1α binding, and possible transcription in normoxic environments. Furthermore, these peaks are not at the same sites as found in vhl mutants, suggesting that control of egln3 expression under normoxic environments may be influenced by more factors that Hif-1α binding alone. It would be interesting to discover if these HRE-containing peaks in vhl mutants control egln3 expression, and to what extent the other peaks and “wild-type peaks” contribute to this. We suspect high Hif-1α binding as there is an extremely high fold change found in the microarray and the high fold enrichment of one of the HREcontaining ChIP peaks (28.6). C: Screenshot showing Hif-1α binding in vhl mutants surrounding the gene tiparp. The data presented here may also be useful for investigating lesser or previously unknown Hifresponsive genes. For instance, TCDD-inducible poly (ADP-ribose) polymerase (tiparp), is a gene not previously associated with the Hif response but seen to be up-regulated in the microarray by FC 3.49 which has multiple Hif-1α peaks in its vicinity, some containing HREs. TIPARP was not recognised as being associated with the hypoxic response by gene ontology software such as DAVID or manual literature searches. Interestingly for tiparp a xenopbiotic response element has been defined in mouse in the first half of intron 1 [82]. One of the two HRE containing HIF peaks in zebrafish associated with tiparp also maps to the first half of intron 1. As HRE and XRE consensus sequence are essentially identical, this might in fact represent the same enhancer responding to two different inputs. D: Screenshot showing a Hif-1α binding site found in vhl mutants in the vicinity of mir22a-1 Despite not being included in the microarray analysis, there is evidence of Hif-1α binding in close proximity to three microRNAs involved in the regulation of the hypoxic response. Hif-1a binds in close proximity to mir22a-1, a microRNA that suppresses HIF-1α regulated transcription in human colon cancer cells [83]. We also find sites close to mir210 and mir-132/212 which may be involved in the hypoxic response. E: Screenshot showing Chip-seq peaks near pfkfb3, which is unique in the genome, as it has several exonic peaks. It also shows several peaks in the surrounding genomic DNA. (PDF 1480 kb)