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Science China Life Sciences

, Volume 62, Issue 4, pp 526–534 | Cite as

Gain of transcription factor binding sites is associated to changes in the expression signature of human brain and testis and is correlated to genes with higher expression breadth

  • Vandeclécio Lira da Silva
  • André Mauricio Ribeiro dos Santos
  • Wilfredo Blanco
  • Sandro José de SouzaEmail author
Research Paper
  • 8 Downloads

Abstract

The gain of transcription factor binding sites (TFBS) is believed to represent one of the major causes of biological innovation. Here we used strategies based on comparative genomics to identify 21,822 TFBS specific to the human lineage (TFBS-HS), when compared to chimpanzee and gorilla genomes. More than 40% (9,206) of these TFBS-HS are in the vicinity of 1,283 genes. A comparison of the expression pattern of these genes and the corresponding orthologs in chimpanzee and gorilla identified genes differentially expressed in human tissues. These genes show a more divergent expression pattern in the human testis and brain, suggesting a role for positive selection in the fixation of TFBS gains. Genes associated with TFBS-HS were enriched in gene ontology categories related to transcriptional regulation, signaling, differentiation/development and nervous system. Furthermore, genes associated with TFBS-HS present a higher expression breadth when compared to genes in general. This biased distribution is due to a preferential gain of TFBS in genes with higher expression breadth rather than a shift in the expression pattern after the gain of TFBS.

Keywords

TFBS transcript factor human evolution expression breadth 

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Notes

Acknowledgements

The authors are indebted to Jorge E.S. de Souza for discussions on the gene expression analysis. VLS and AMRS were supported by CAPES Ph.D. fellowships. This work was supported by the Ludwig Institute for Cancer Research and by CAPES (23038.004629/2014-19).

Supplementary material

11427_2018_9454_MOESM1_ESM.xlsx (10 kb)
Supplementary Table 1: Enrichment analysis of transcritpion factors within the set of TFBS-HS
11427_2018_9454_MOESM2_ESM.xlsx (166 kb)
Supplementary Table 2: Differential expression of genes associated to TFBS-HS.

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Copyright information

© Science China Press and Springer-Verlag GmbH Germany, part of Springer Nature 2019

Authors and Affiliations

  • Vandeclécio Lira da Silva
    • 1
  • André Mauricio Ribeiro dos Santos
    • 1
    • 2
  • Wilfredo Blanco
    • 3
  • Sandro José de Souza
    • 4
    Email author
  1. 1.Bioinformatics Multidisciplinary Environment (BioME)Universidade Federal do Rio Grande do Norte (UFRN)NatalBrazil
  2. 2.Programa de Pós-Graduação em Genética e Biologia Molecular (PPGBM)Universidade Federal do Pará (UFPA)BelemBrazil
  3. 3.Department of Computer ScienceUniversidade Estadual do Rio Grande do Norte (UERN)NatalBrazil
  4. 4.Brain InstituteUniversidade Federal do Rio Grande do Norte (UFRN)NatalBrazil

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