publication . Preprint . 2016

Transposable element exaptation is the primary source of novelty in the primate gene regulatory landscape

YoSon null;
Open Access English
  • Published: 27 Oct 2016
  • Publisher: Cold Spring Harbor Laboratory
Abstract
<jats:title>Abstract</jats:title><jats:p>Gene regulation plays a critical role in the evolution of phenotypic diversity. We investigated the evolution of liver promoters and enhancers in six primate species. We performed ChlP-seq for two histone modifications and RNA-seq to profile cis-regulatory element (CRE) activity and gene expression. The primate regulatory landscape is largely conserved across the lineage. Conserved CRE function is associated with sequence conservation, proximity to coding genes, cell type specificity of CRE function, and transcription factor binding. Newly evolved CREs are enriched in immune response and neurodevelopmental functions, whil...

Hinrichs, A.S., Karolchik, D., Baertsch, R., Barber, G.P., Bejerano, G., Clawson, H., Diekhans, M., Furey, T.S., Harte, R.A., Hsu, F., et al. (2006). The UCSC Genome Browser Database: update 2006. Nucleic Acids Research 34, D590-D598.

Hubley, R., Finn, R.D., Clements, J., Eddy, S.R., Jones, T.A., Bao, W., Smit, A.F.A., and Wheeler, T.J. (2016). The Dfam database of repetitive DNA families. Nucleid Acids Research 44, D81-D89. [OpenAIRE]

Gupta, S, Stamatoyannopoulos, J.A., Bailey, T.L., and Noble, W.S. (2007). Quantifying similarity between motifs. Genome Biology 8, R24. [OpenAIRE]

Innocenti, F., Cooper, G.M., Stanaway, I.B., Gamazon, E.R., Smith, J.D., Mirkov, S., Ramirez, J., Liu, W., Lin, Y.S., Moloney, C., et al. (2011). Identification, Replication, and Functional Fine-Mapping of Expression Quantitative Trait Loci in Primary Human Liver Tissue. PLoS Genet 7, e1002078.

Abstract
<jats:title>Abstract</jats:title><jats:p>Gene regulation plays a critical role in the evolution of phenotypic diversity. We investigated the evolution of liver promoters and enhancers in six primate species. We performed ChlP-seq for two histone modifications and RNA-seq to profile cis-regulatory element (CRE) activity and gene expression. The primate regulatory landscape is largely conserved across the lineage. Conserved CRE function is associated with sequence conservation, proximity to coding genes, cell type specificity of CRE function, and transcription factor binding. Newly evolved CREs are enriched in immune response and neurodevelopmental functions, whil...

Hinrichs, A.S., Karolchik, D., Baertsch, R., Barber, G.P., Bejerano, G., Clawson, H., Diekhans, M., Furey, T.S., Harte, R.A., Hsu, F., et al. (2006). The UCSC Genome Browser Database: update 2006. Nucleic Acids Research 34, D590-D598.

Hubley, R., Finn, R.D., Clements, J., Eddy, S.R., Jones, T.A., Bao, W., Smit, A.F.A., and Wheeler, T.J. (2016). The Dfam database of repetitive DNA families. Nucleid Acids Research 44, D81-D89. [OpenAIRE]

Gupta, S, Stamatoyannopoulos, J.A., Bailey, T.L., and Noble, W.S. (2007). Quantifying similarity between motifs. Genome Biology 8, R24. [OpenAIRE]

Innocenti, F., Cooper, G.M., Stanaway, I.B., Gamazon, E.R., Smith, J.D., Mirkov, S., Ramirez, J., Liu, W., Lin, Y.S., Moloney, C., et al. (2011). Identification, Replication, and Functional Fine-Mapping of Expression Quantitative Trait Loci in Primary Human Liver Tissue. PLoS Genet 7, e1002078.

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