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51
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Ray-Jones H, Spivakov M. Transcriptional enhancers and their communication with gene promoters. Cell Mol Life Sci 2021; 78:6453-6485. [PMID: 34414474 PMCID: PMC8558291 DOI: 10.1007/s00018-021-03903-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Revised: 07/08/2021] [Accepted: 07/19/2021] [Indexed: 12/13/2022]
Abstract
Transcriptional enhancers play a key role in the initiation and maintenance of gene expression programmes, particularly in metazoa. How these elements control their target genes in the right place and time is one of the most pertinent questions in functional genomics, with wide implications for most areas of biology. Here, we synthesise classic and recent evidence on the regulatory logic of enhancers, including the principles of enhancer organisation, factors that facilitate and delimit enhancer-promoter communication, and the joint effects of multiple enhancers. We show how modern approaches building on classic insights have begun to unravel the complexity of enhancer-promoter relationships, paving the way towards a quantitative understanding of gene control.
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Affiliation(s)
- Helen Ray-Jones
- MRC London Institute of Medical Sciences, London, W12 0NN, UK
- Institute of Clinical Sciences, Faculty of Medicine, Imperial College, London, W12 0NN, UK
| | - Mikhail Spivakov
- MRC London Institute of Medical Sciences, London, W12 0NN, UK.
- Institute of Clinical Sciences, Faculty of Medicine, Imperial College, London, W12 0NN, UK.
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52
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Pierce SE, Granja JM, Corces MR, Brady JJ, Tsai MK, Pierce AB, Tang R, Chu P, Feldser DM, Chang HY, Bassik MC, Greenleaf WJ, Winslow MM. LKB1 inactivation modulates chromatin accessibility to drive metastatic progression. Nat Cell Biol 2021; 23:915-924. [PMID: 34341533 PMCID: PMC8355205 DOI: 10.1038/s41556-021-00728-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Accepted: 07/05/2021] [Indexed: 12/11/2022]
Abstract
Metastasis is the leading cause of cancer-related deaths and enables cancer cells to compromise organ function by expanding in secondary sites. Since primary tumours and metastases often share the same constellation of driver mutations, the mechanisms that drive their distinct phenotypes are unclear. Here we show that inactivation of the frequently mutated tumour suppressor gene LKB1 (encoding liver kinase B1) has evolving effects throughout the progression of lung cancer, which leads to the differential epigenetic re-programming of early-stage primary tumours compared with late-stage metastases. By integrating genome-scale CRISPR-Cas9 screening with bulk and single-cell multi-omic analyses, we unexpectedly identify LKB1 as a master regulator of chromatin accessibility in lung adenocarcinoma primary tumours. Using an in vivo model of metastatic progression, we further show that loss of LKB1 activates the early endoderm transcription factor SOX17 in metastases and a metastatic-like sub-population of cancer cells within primary tumours. The expression of SOX17 is necessary and sufficient to drive a second wave of epigenetic changes in LKB1-deficient cells that enhances metastatic ability. Overall, our study demonstrates how the downstream effects of an individual driver mutation can change throughout cancer development, with implications for stage-specific therapeutic resistance mechanisms and the gene regulatory underpinnings of metastatic evolution.
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Affiliation(s)
- Sarah E Pierce
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA.
| | - Jeffrey M Granja
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
- Center for Personal and Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA, USA
| | - M Ryan Corces
- Center for Personal and Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA, USA
| | - Jennifer J Brady
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Min K Tsai
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Aubrey B Pierce
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Rui Tang
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Pauline Chu
- Department of Comparative Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - David M Feldser
- Department of Cancer Biology and Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Howard Y Chang
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
- Center for Personal and Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA, USA
- HHMI, Stanford University School of Medicine, Stanford, CA, USA
| | - Michael C Bassik
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
- Chemistry, Engineering, and Medicine for Human Health (ChEM-H), Stanford University, Stanford, CA, USA
| | - William J Greenleaf
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA.
- Center for Personal and Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA, USA.
| | - Monte M Winslow
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA.
- Chemistry, Engineering, and Medicine for Human Health (ChEM-H), Stanford University, Stanford, CA, USA.
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA.
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53
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Granja JM, Corces MR, Pierce SE, Bagdatli ST, Choudhry H, Chang HY, Greenleaf WJ. ArchR is a scalable software package for integrative single-cell chromatin accessibility analysis. Nat Genet 2021; 53:403-411. [PMID: 33633365 PMCID: PMC8012210 DOI: 10.1038/s41588-021-00790-6] [Citation(s) in RCA: 494] [Impact Index Per Article: 164.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Accepted: 01/19/2021] [Indexed: 12/26/2022]
Abstract
The advent of single-cell chromatin accessibility profiling has accelerated the ability to map gene regulatory landscapes but has outpaced the development of scalable software to rapidly extract biological meaning from these data. Here we present a software suite for single-cell analysis of regulatory chromatin in R (ArchR; https://www.archrproject.com/) that enables fast and comprehensive analysis of single-cell chromatin accessibility data. ArchR provides an intuitive, user-focused interface for complex single-cell analyses, including doublet removal, single-cell clustering and cell type identification, unified peak set generation, cellular trajectory identification, DNA element-to-gene linkage, transcription factor footprinting, mRNA expression level prediction from chromatin accessibility and multi-omic integration with single-cell RNA sequencing (scRNA-seq). Enabling the analysis of over 1.2 million single cells within 8 h on a standard Unix laptop, ArchR is a comprehensive software suite for end-to-end analysis of single-cell chromatin accessibility that will accelerate the understanding of gene regulation at the resolution of individual cells. ArchR is a software suite that enables efficient and end-to-end analysis of single-cell chromatin accessibility data (scATAC-seq).
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Affiliation(s)
- Jeffrey M Granja
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA. .,Program in Biophysics, Stanford University, Stanford, CA, USA. .,Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA, USA.
| | - M Ryan Corces
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA, USA.,Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA.,Gladstone Institute of Neurological Disease, Gladstone Institute of Data Science and Biotechnology, San Francisco, CA, USA.,Department of Neurology, University of California San Francisco, San Francisco, CA, USA
| | - Sarah E Pierce
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA.,Program in Cancer Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - S Tansu Bagdatli
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Hani Choudhry
- Department of Biochemistry, Faculty of Science, Cancer and Mutagenesis Unit, King Fahd Center for Medical Research, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Howard Y Chang
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA. .,Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA, USA. .,Howard Hughes Medical Institute, Stanford University, Stanford, CA, USA.
| | - William J Greenleaf
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA. .,Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA, USA. .,Department of Applied Physics, Stanford University, Stanford, CA, USA. .,Chan Zuckerberg Biohub, San Francisco, CA, USA.
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