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Chromatin run-on and sequencing maps the transcriptional regulatory landscape of glioblastoma multiforme


The human genome encodes a variety of poorly understood RNA species that remain challenging to identify using existing genomic tools. We developed chromatin run-on and sequencing (ChRO-seq) to map the location of RNA polymerase for almost any input sample, including samples with degraded RNA that are intractable to RNA sequencing. We used ChRO-seq to map nascent transcription in primary human glioblastoma (GBM) brain tumors. Enhancers identified in primary GBMs resemble open chromatin in the normal human brain. Rare enhancers that are activated in malignant tissue drive regulatory programs similar to the developing nervous system. We identified enhancers that regulate groups of genes that are characteristic of each known GBM subtype and transcription factors that drive them. Finally we discovered a core group of transcription factors that control the expression of genes associated with clinical outcomes. This study characterizes the transcriptional landscape of GBM and introduces ChRO-seq as a method to map regulatory programs that contribute to complex diseases.

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Data availability

All ChRO-seq and leChRO-seq data can be downloaded from the database of Genotypes and Phenotypes (dbGaP) under accession phs001646.v1.p1. Data collected from Jurkat T cells are available in the Gene Expression Omnibus under accession GSE117832.

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We thank M. Viapiano and P. Sethupathy for valuable comments on the manuscript and other members of the Danko, Kwak and Lis laboratories for valuable discussions. This research was supported in part by US National Institutes of Health (NIH) grants HG009309 (to C.G.D. and H.K.) and GM25232 (to J.T.L.), and by the Walbridge Foundation for Brain Cancer Research. T.C. thanks the Croucher Foundation for the Croucher Scholarships for Doctoral Study (2013). The content is solely the responsibility of the authors and does not necessarily represent the official views of the NIH or the Walbridge Foundation.

Author information

T.C., Z.W. and C.G.D. analyzed the data. E.J.R., G.B. and H.K. performed molecular experiments. H.K. conceived the chromatin run-on technique, with input from L.J.C. and J.T.L. H.H.S. selected tumors for analysis from the GBM tissue bank. R.J.C. and H.H.S. completed the pathologic analysis. L.S.C. and H.H.S. dissected GBM-15-90 brain tissue. S.L.L. runs the GBM tissue bank and performed the murine xenograft experiments. Data collection and analysis was supervised by C.G.D. The manuscript was written by C.G.D. and T.C., with input from the other authors.

Competing interests

The authors declare no competing interests.

Correspondence to Hojoong Kwak or Charles G. Danko.

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Further reading

Fig. 1: ChRO-seq and leChRO-seq measure primary transcription in isolated chromatin.
Fig. 2: ChRO-seq detects transcription in primary human glioblastomas.
Fig. 3: Comparison of TREs in primary GBM or PDXs and reference DHSs.
Fig. 4: Tumor-associated TREs activate three regulatory programs.
Fig. 5: Transcription factors influencing transcriptional heterogeneity in GBM.
Fig. 6: Regulatory activities of transcription factors are controlled by transcription and post-transcriptional mechanisms in GBM.
Fig. 7: Transcription factors control survival-associated pathways in GBM.