In Vivo Characterization of Linc-p21 Reveals Functional cis-Regulatory DNA Elements

Abigail F Groff; Diana B Sanchez-Gomez; Marcela M L Soruco; Chiara Gerhardinger; A Rasim Barutcu; Eric Li; Lara Elcavage; Olivia Plana; Lluvia V Sanchez; James C Lee; Martin Sauvageau; John L Rinn

doi:10.1016/j.celrep.2016.07.050

In Vivo Characterization of Linc-p21 Reveals Functional cis-Regulatory DNA Elements

Cell Rep. 2016 Aug 23;16(8):2178-2186. doi: 10.1016/j.celrep.2016.07.050. Epub 2016 Aug 11.

Authors

Affiliations

¹ Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA; Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA; The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
² Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA.
³ Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA; Department of Pathology, Beth Israel Deaconess Medical Center, Boston, MA 02215, USA.
⁴ Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA; The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
⁵ Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA; Department of Medicine, University of Cambridge School of Clinical Medicine, Addenbrooke's Hospital, Cambridge CB2 0QQ, UK.
⁶ Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA; The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Pathology, Beth Israel Deaconess Medical Center, Boston, MA 02215, USA.
⁷ Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA; The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Pathology, Beth Israel Deaconess Medical Center, Boston, MA 02215, USA. Electronic address: john_rinn@harvard.edu.

Abstract

The Linc-p21 locus, encoding a long non-coding RNA, plays an important role in p53 signaling, cell-cycle regulation, and tumor suppression. However, despite extensive study, confusion exists regarding its mechanism of action: is activity driven by the transcript acting in trans, in cis, or by an underlying functional enhancer? Here, using a knockout mouse model and a massively parallel enhancer assay, we delineate the functional elements at this locus. We observe that, even in tissues with no detectable Linc-p21 transcript, deletion of the locus significantly affects local gene expression, including of the cell-cycle regulator Cdkn1a. To characterize this RNA-independent regulatory effect, we systematically interrogated the underlying DNA sequence for enhancer activity at nucleotide resolution and confirmed the existence of multiple enhancer elements. Together, these data suggest that, in vivo, the cis-regulatory effects mediated by Linc-p21, in the presence or absence of transcription, are due to DNA enhancer elements.

Publication types

Research Support, N.I.H., Extramural

MeSH terms

Animals
Base Sequence*
Cell Line
Cyclin-Dependent Kinase Inhibitor p21 / genetics*
Cyclin-Dependent Kinase Inhibitor p21 / metabolism
Enhancer Elements, Genetic*
Gene Expression Regulation
Genetic Loci
High-Throughput Nucleotide Sequencing
High-Throughput Screening Assays
Mice
Mice, Knockout
Myoblasts / cytology
Myoblasts / metabolism
Promoter Regions, Genetic
RNA, Long Noncoding / genetics*
RNA, Long Noncoding / metabolism
Sequence Deletion*
Signal Transduction
Tumor Suppressor Protein p53 / genetics*
Tumor Suppressor Protein p53 / metabolism

Substances

Cdkn1a protein, mouse
Cyclin-Dependent Kinase Inhibitor p21
RNA, Long Noncoding
Tumor Suppressor Protein p53

Abstract

Publication types

MeSH terms

Substances

Grants and funding