About the Authors

Claudia Kutter

Contributed equally to this work with: Claudia Kutter, Stephen Watt

Affiliations Cancer Research UK, Cambridge Research Institute, Li Ka Shing Centre, Cambridge, United Kingdom, University of Cambridge, Cambridge, United Kingdom

Stephen Watt

Contributed equally to this work with: Claudia Kutter, Stephen Watt

Affiliation Cancer Research UK, Cambridge Research Institute, Li Ka Shing Centre, Cambridge, United Kingdom

Klara Stefflova

Affiliations Cancer Research UK, Cambridge Research Institute, Li Ka Shing Centre, Cambridge, United Kingdom, University of Cambridge, Cambridge, United Kingdom

Michael D. Wilson

Current address: SickKids Research Institute and Department of Molecular Genetics, University of Toronto, Toronto, Canada

Affiliations Cancer Research UK, Cambridge Research Institute, Li Ka Shing Centre, Cambridge, United Kingdom, University of Cambridge, Cambridge, United Kingdom

Angela Goncalves

Affiliations University of Cambridge, Cambridge, United Kingdom, European Bioinformatics Institute, European Molecular Biology Laboratory, Hinxton, United Kingdom

Chris P. Ponting

chris.ponting@dpag.ox.ac.uk (CPP); duncan.odom@cancer.org.uk (DTO); ana.marques@dpag.ox.ac.uk (ACM)

These authors also contributed equally to this work.

Affiliations Wellcome Trust Sanger Institute, Hinxton, United Kingdom, MRC Functional Genomics Unit, Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, United Kingdom, Department of Physiology, Anatomy, and Genetics, University of Oxford, Oxford, United Kingdom

Duncan T. Odom

chris.ponting@dpag.ox.ac.uk (CPP); duncan.odom@cancer.org.uk (DTO); ana.marques@dpag.ox.ac.uk (ACM)

These authors also contributed equally to this work.

Affiliations Cancer Research UK, Cambridge Research Institute, Li Ka Shing Centre, Cambridge, United Kingdom, University of Cambridge, Cambridge, United Kingdom, Wellcome Trust Sanger Institute, Hinxton, United Kingdom

Ana C. Marques

chris.ponting@dpag.ox.ac.uk (CPP); duncan.odom@cancer.org.uk (DTO); ana.marques@dpag.ox.ac.uk (ACM)

These authors also contributed equally to this work.

Affiliation Department of Physiology, Anatomy, and Genetics, University of Oxford, Oxford, United Kingdom

Competing Interests

The authors have declared that no competing interests exist.

Author Contributions

Conceived and designed the experiments: CK SW CPP DTO ACM. Performed the experiments: CK SW KS MDW AG ACM. Analyzed the data: CK SW ACM. Wrote the paper: CK SW CPP DTO ACM. Designed the experiments: CK SW DTO. Performed RNAseq and ChIPseq experiments: CK SW KS MDW. Processed and mapped the reads: SW AG ACM. Assembled and annotated transcripts: SW ACM. Performed qPCR and RT–PCR validations: CK SW. Estimated the transcriptional turnover of lncRNAs: CK SW ACM. Performed genome enrichments and sequence constraint analysis of intergenic lncRNAs: ACM. Analysed the effect of lineage specific gene expression on neighbouring genes: ACM. Supervised the study: DTO CPP.