title: Systematic dissection of coding exons at single nucleotide resolution supports an additional role in cell-specific transcriptional regulation.
abstract: In addition to their protein coding function, exons can also serve as transcriptional enhancers. Mutations in these exonic-enhancers (eExons) could alter both protein function and transcription. However, the functional consequence of eExon mutations is not well known. Here, using massively parallel reporter assays, we dissect the enhancer activity of three liver eExons (SORL1 exon 17, TRAF3IP2 exon 2, PPARG exon 6) at single nucleotide resolution in the mouse liver. We find that both synonymous and non-synonymous mutations have similar effects on enhancer activity and many of the deleterious mutation clusters overlap known liver-associated transcription factor binding sites. Carrying a similar massively parallel reporter assay in HeLa cells with these three eExons found differences in their mutation profiles compared to the liver, suggesting that enhancers could have distinct operating profiles in different tissues. Our results demonstrate that eExon mutations could lead to multiple phenotypes by disrupting both the protein sequence and enhancer activity and that enhancers can have distinct mutation profiles in different cell types.
authors.affiliation: Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, California, United States of America; Institute for Human Genetics, University of California San Francisco, San Francisco, California, United States of America; Department of Life Sciences, Ben-Gurion University at the Negev, Beer-Sheva, Israel.
authors.forename: Ramon Y
authors.initials: RY
authors.lastname: Birnbaum
authors.affiliation: Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America.
authors.forename: Rupali P
authors.initials: RP
authors.lastname: Patwardhan
authors.affiliation: Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, California, United States of America; Institute for Human Genetics, University of California San Francisco, San Francisco, California, United States of America.
authors.forename: Mee J
authors.initials: MJ
authors.lastname: Kim
authors.affiliation: Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America.
authors.forename: Gregory M
authors.initials: GM
authors.lastname: Findlay
authors.affiliation: Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America.
authors.forename: Beth
authors.initials: B
authors.lastname: Martin
authors.affiliation: Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, California, United States of America; Institute for Human Genetics, University of California San Francisco, San Francisco, California, United States of America; Key Laboratory of Advanced Control and Optimization for Chemical Processes of the Ministry of Education, East China University of Science and Technology, Shanghai, China.
authors.forename: Jingjing
authors.initials: J
authors.lastname: Zhao
authors.affiliation: Institute for Human Genetics, University of California San Francisco, San Francisco, California, United States of America; Department of Neurological Surgery, University of California San Francisco, San Francisco, California, United States of America; Biomedical Sciences (BMS) Graduate Program, University of California San Francisco, San Francisco, California, United States of America.
authors.forename: Robert J A
authors.initials: RJ
authors.lastname: Bell
authors.affiliation: Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, California, United States of America; Institute for Human Genetics, University of California San Francisco, San Francisco, California, United States of America.
authors.forename: Robin P
authors.initials: RP
authors.lastname: Smith
authors.affiliation: Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, California, United States of America; Institute for Human Genetics, University of California San Francisco, San Francisco, California, United States of America.
authors.forename: Angel A
authors.initials: AA
authors.lastname: Ku
authors.affiliation: Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America.
authors.forename: Jay
authors.initials: J
authors.lastname: Shendure
authors.affiliation: Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, California, United States of America; Institute for Human Genetics, University of California San Francisco, San Francisco, California, United States of America.
authors.forename: Nadav
authors.initials: N
authors.lastname: Ahituv
mesh_terms: D048868:Adaptor Proteins, Signal Transducing / Q000235:genetics*; D000818:Animals; D001665:Binding Sites; D004742:Enhancer Elements, Genetic; D005091:Exons / Q000235:genetics*; D005786:Gene Expression Regulation; D006367:HeLa Cells; D006801:Humans; D008099:Liver / Q000378:metabolism; D026901:Membrane Transport Proteins / Q000235:genetics*; D051379:Mice; D020125:Mutation, Missense; D047495:PPAR gamma / Q000235:genetics*; D020641:Polymorphism, Single Nucleotide; D012326:RNA Splicing / Q000235:genetics; D011973:Receptors, LDL / Q000235:genetics*; D014157:Transcription Factors / Q000096:biosynthesis
chemical_list: D048868:Adaptor Proteins, Signal Transducing; D026901:Membrane Transport Proteins; D047495:PPAR gamma; D011973:Receptors, LDL; C491168:Sorl1 protein, mouse; C515963:Traf3ip2 protein, mouse; D014157:Transcription Factors