Genome-wide Association of Hypoxia-inducible Factor (HIF)-1α and HIF-2α DNA Binding with Expression Profiling of Hypoxia-inducible Transcripts

Mole, David R.; Blancher, Christine; Copley, Richard R.; Pollard, Patrick J.; Gleadle, Jonathan; Ragoussis, Jiannis; Ratcliffe, Peter J.

doi:10.1074/jbc.m901790200

Cited by 496 publications

(465 citation statements)

References 61 publications

(85 reference statements)

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“…We found that 441 (83%) and 413 (67%) regions contained the HRE motif in DLD-1 and in TIG-3 cells, respectively (fourth column, Table 1). These frequencies were similar to those reported in previous HIF-1a ChIP-chip studies (Mole et al 2009;), although the detected genomic regions containing the HIF-1a binding sites were shorter in length due to the improved resolution of the analysis (the lengths of the detected binding sites were more than threefold shorter than those detected in previous studies using ChIP-chip, which reflected the intervals of the designed DNA probes (Mole et al 2009); see also Supplementary Fig. 3a).…”

Section: Resultssupporting

confidence: 88%

“…When a RefSeq gene contained multiple transcript variant models, all of the variants were considered and counted redundantly. We found that approximately 70% of the binding sites were located within 1 kb of the 5 0 -ends of the RefSeq transcript models, which is consistent with previous estimations Mole et al 2009). …”

Section: Transcripts In the Proximal Regions Of The Identified Hif-1asupporting

confidence: 92%

“…The cels might memorize their histories with respect to the chromatin status. Such a prepared status of the cells via epigenetic regulation has been discussed in previous reports (Heintzman et al 2007;Kim et al 2008;Mole et al 2009); however, this is the first study to provide direct evidence supporting this possibility.…”

Section: Epigenetic Regulation In Regions Surrounding Hif-1a Bindingsupporting

confidence: 53%

“…These results indicated that only a part of HRE motifs had an open nucleosome structure suitable for subsequent transcriptional activation, although HRE motifs were present throughout the human genomic sequences. Previous HIF-1a ChIP-chip studies have reported that less than 1% of the HRE motifs within the genomic sequences that are located in regions used for the microarrays are bound by HIF-1a (Mole et al 2009;Wenger et al 1998Wenger et al , 2005. Epigenetic regulation of the human genome plays an essential role in specifying the binding sites of HIF-1a in addition to the consensus binding sequences.…”

Section: Epigenetic Regulation In Regions Surrounding Hif-1a Bindingmentioning

confidence: 99%

“…Although computational methods alone may still require further innovation due to the ambiguity of the HRE motif, the combination of computational methods and expression analyses using microarrays has proven to be a powerful approach (Benita et al 2009). More recently, several papers have reported the identification of HIF-1a binding sites based on chromatin immunoprecipitation and microarray (ChIP-chip) technology (Mole et al 2009;. These studies have reported that about 400-500 of the HIF-1a binding sites in the human genome and approximately 70% of the HIF-1a binding sequences contain HREs.…”

Section: Introductionmentioning

confidence: 99%

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Genome-wide identification and annotation of HIF-1α binding sites in two cell lines using massively parallel sequencing

Tanimoto

Tsuchihara

Kanai

et al. 2010

HUGO J

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We identified 531 and 616 putative HIF-1a target sites by ChIP-Seq in the cancerous cell line DLD-1 and the non-cancerous cell line TIG-3, respectively. We also examined the positions and expression levels of transcriptional start sites (TSSs) in these cell lines using our TSS-Seq method. We observed that 121 and 48 genes in DLD-1 and TIG-3 cells, respectively, had HIF-1a binding sites in proximal regions of the previously reported TSSs that were up-regulated at the transcriptional level. In addition, 193 and 123 of the HIF-1a target sites, respectively, were located in proximal regions of previously uncharacterized TSSs, namely, TSSs of putative alternative promoters of protein-coding genes or promoters of putative non-protein-coding transcripts. The hypoxic response of DLD-1 cells was more significant than that of TIG-3 cells with respect to both the number of target sites and the degree of induced changes in transcript expression. The Nucleosome-Seq and ChIP-Seq analyses of histone modifications revealed that the chromatin formed an open structure in regions surrounding the HIF-1a binding sites, but this event occurred prior to the actual binding of HIF1a. Different cellular histories may be encoded by chromatin structures and determine the activation of specific genes in response to hypoxic shock.

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Section: Resultssupporting

confidence: 88%

Section: Transcripts In the Proximal Regions Of The Identified Hif-1asupporting

confidence: 92%

Section: Epigenetic Regulation In Regions Surrounding Hif-1a Bindingsupporting

confidence: 53%

Section: Epigenetic Regulation In Regions Surrounding Hif-1a Bindingmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Genome-wide identification and annotation of HIF-1α binding sites in two cell lines using massively parallel sequencing

Tanimoto

Tsuchihara

Kanai

et al. 2010

HUGO J

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ERK signaling controls productive HIF‐1 binding to chromatin and cancer cell adaptation to hypoxia through HIF‐1α interaction with NPM1

et al. 2021

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LIST OF ABBREVIATIONS (in order cited) chromatin bound NPM1. In fact, as NPM1 expression has been previously shown to be induced by HIF-1 and hypoxia [28], a finding in agreement with our data (see Suppl. Fig. S6A,F), our results also suggest the operation of an ERK-controlled positive feed-forward mechanism, based on amplification of HIF-1 activity following upregulation of NPM1 expression by HIF-1 itself. NPM1 is required for the cellular transcriptional response to hypoxiaTo address the above hypothesis, we performed sequencing of RNA extracted from HeLa cells subjected or not to NPM1 silencing, both under normoxia or hypoxia, or HIF-1α silencing under hypoxia. In cells treated with control siRNAs (Nt), hypoxia heavily affected gene expression, with 1068 genes exhibiting altered mRNA levels (487 downregulated, 581 upregulated) when compared to normoxia (Suppl. Fig. S8A). These genes are mostly involved in transcriptional regulation, response to hypoxia or drugs and control of apoptosis, angiogenesis, cell cycle and metabolism (Suppl. Fig. S8B). Knocking-down NPM1 in normoxic cells resulted in the differential expression of a limited number of genes, 114 in total (68 down-, 46 up-regulated), which are mainly implicated in functions related to the immune response (Fig. 4A left panel; Suppl. Fig. S8C,D) a subset of which (33 genes) were also regulated by HIF-1 (Suppl. Fig. S8C,E). In contrast, when NPM1 silencing was performed in hypoxic cells (Fig. 4A, right panel), it had a profound effect on gene expression with 761 deregulated genes (320 down-, 441 up-regulated), 123 of which were common with the ones affected by the hypoxic shift (Fig. 4B). A similar, strong, effect on differential gene expression was also observed when HIF-1α was silenced under hypoxia with 844 deregulated genes (561 down-, 283 up-regulated) (Fig. 4A, middle panel), 257 of which were common with the ones affected by hypoxia (as compared to normoxia) (Fig. 4B). Analysis of those results revealed a significant number of genes commonly regulated by HIF-1α and NPM1 (130 genes in total, out of which 36 also deregulated during the hypoxic shift) (Fig. 4B). These common genes were involved in processes known to rely on HIF-1 and hypoxia-mediated reprogramming, such as cell adhesion, migration and ECM organization, redox and apoptosis control, metabolism and angiogenesis (Suppl. Fig. S8F). From the 67 genes that were upregulated by hypoxia and repressed by both NPM1 and HIF-1α knockdown (Suppl. Fig. S9), marker genes were selected as typical examples of NPM1/HIF-1α-dependent cellular functions (ALDOC: metabolism, BIRC3: apoptosis, TGFBI: angiogenesis and ECM organization, FA2H: oxidation-reduction), for validation of the RNAsequencing results with RT-PCR. Indeed, expression of ALDOC, BIRC3, TGFBI and FA2H was decreased when either HIF-1α or NPM1 were silenced under hypoxia (Fig. 4C). These data support the notion that NPM1, by stabilizing the interaction between HIF-1 and HRE-containing chromatin, supports the general transcriptional response to hy...

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Hypoxia and the DNA Damage Response

Pires

and

Hammond

2010

Tumor Microenvironment

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Genome-wide Association of Hypoxia-inducible Factor (HIF)-1α and HIF-2α DNA Binding with Expression Profiling of Hypoxia-inducible Transcripts

Cited by 496 publications

References 61 publications

Genome-wide identification and annotation of HIF-1α binding sites in two cell lines using massively parallel sequencing

Genome-wide identification and annotation of HIF-1α binding sites in two cell lines using massively parallel sequencing

ERK signaling controls productive HIF‐1 binding to chromatin and cancer cell adaptation to hypoxia through HIF‐1α interaction with NPM1

Hypoxia and the DNA Damage Response

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