publication . Preprint . 2016

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

YoSon Park; Marco Trizzino; Marcia Holsbach-Beltrame; Katelyn M. Mika; Katherine Aracena; George H. Perry; Vincent J. Lynch; Minal Çalışkan; Christopher D. Brown;
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...
Read more
doi: 10.1101/083980
Subjects
free text keywords: Genetics, Transposable element, Exaptation, Biology, Enhancer, Regulation of gene expression, Gene expression, Promoter, Transcription factor, Gene
Related Organizations
View more
Download fromView all 2 versions
bioRxiv
Preprint . 2016
Provider: bioRxiv
https://www.biorxiv.org/conten...
Preprint
Provider: UnpayWall
https://www.biorxiv.org/conten...
Preprint
Provider: Microsoft Academic Graph
https://syndication.highwire.o...
Preprint . 2016
Provider: Crossref

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.

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.

Related research
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...
Read more
doi: 10.1101/083980
Subjects
free text keywords: Genetics, Transposable element, Exaptation, Biology, Enhancer, Regulation of gene expression, Gene expression, Promoter, Transcription factor, Gene
Related Organizations
View more
Download fromView all 2 versions
bioRxiv
Preprint . 2016
Provider: bioRxiv
https://www.biorxiv.org/conten...
Preprint
Provider: UnpayWall
https://www.biorxiv.org/conten...
Preprint
Provider: Microsoft Academic Graph
https://syndication.highwire.o...
Preprint . 2016
Provider: Crossref

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.

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.

Related research
Powered by OpenAIRE Research Graph
Any information missing or wrong?Report an Issue