Evolution of gene regulation of pluripotency - the case for wiki tracks at genome browsers

Abstract

BackgroundExperimentally validated data on gene regulation are hard to obtain. In particular, information about transcription factor binding sites in regulatory regions are scattered around in the literature. This impedes their systematic in-context analysis, e.g. the inference of their conservation in evolutionary history.ResultsWe demonstrate the power of integrative bioinformatics by including curated transcription factor binding site information into the UCSC genome browser, using wiki and custom tracks, which enable easy publication of annotation data. Data integration allows to investigate the evolution of gene regulation of the pluripotency-associated genes Oct4, Sox2 and Nanog. For the first time, experimentally validated transcription factor binding sites in the regulatory regions of all three genes were assembled together based on manual curation of data from 39 publications. Using the UCSC genome browser, these data were then visualized in the context of multi-species conservation based on genomic alignment. We confirm previous hypotheses regarding the evolutionary age of specific regulatory patterns, establishing their "deep homology". We also confirm some other principles of Carroll's "Genetic theory of Morphological Evolution", such as "mosaic pleiotropy", exemplified by the dual role of Sox2 reflected in its regulatory region.ConclusionsWe were able to elucidate some aspects of the evolution of gene regulation for three genes associated with pluripotency. Based on the expected return on investment for the community, we encourage other scientists to contribute experimental data on gene regulation (original work as well as data collected for reviews) to the UCSC system, to enable studies of the evolution of gene regulation on a large scale, and to report their findings.ReviewersThis article was reviewed by Dr. Gustavo Glusman and Dr. Juan Caballero, Institute for Systems Biology, Seattle, USA (nominated by Dr. Doron Lancet, Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel), Dr. Niels Grabe, TIGA Center (BIOQUANT) and Medical Systems Biology Group, Institute of Medical Biometry and Informatics, University Hospital Heidelberg, Germany (nominated by Dr. Mikhail Gelfand, Department of Bioinformatics, Institute of Information Transfer Problems, Russian Academy of Science, Moscow, Russian Federation) and Dr. Franz-Josef Müller, Center for Regenerative Medicine, The Scripps Research Institute, La Jolla, CA, USA and University Hospital for Psychiatry and Psychotherapy (part of ZIP gGmbH), University of Kiel, Germany (nominated by Dr. Trey Ideker, University of California, San Diego, La Jolla CA, United States).

Defining Essential Enhancers for Pluripotent Stem Cells Using a Features-Oriented CRISPR-Cas9 Screen

“…The enrichment of transcription factors' motifs was further compared between the hit CREs and non-hit CREs. Notably, specific enrichment of pluripotency-related transcription factor motifs (Brn1, Zic3, Sf1, and Arnt) was detected in the hit CREs, which reinforced the significances of multiple transcription factors co-binding on functional enhancers ( Figures 3D and S3D) (Forristal et al, 2010;Fuellen and Struckmann, 2010;Gu et al, 2005;Lim et al, 2007;Kim et al, 2018). Of note, when Zic3 or Brn1 motif was mutated, the enhancer activity of CRE132 was further depleted, indicating the importance of these identified motifs ( Figure 3E).…”

Identification of Candidate Transcription Factor Binding Sites in the Cattle Genome

“…The proliferation of genome sequencing and assembly has made possible the use of comparative genomics approaches for TFBS discovery. The reasoning behind the use of comparative genomics as a means of TFBS discovery is that conserved sequence upstream of a gene is likely to contain essential TFBSs due to selective pressures to conserve the sequence across several different species [3] . Since TFs typically bind to non-coding regions of the genome, accurate identification of their binding sites could provide important context to the recent influx of genetic variation discovery studies that often identify variants outside of coding regions.…”

Visualization and Exploration of Conserved Regulatory Modules Using ReXSpecies 2

“…Below the prediction tracks, the wiki track is shown. This track contains annotations that we have listed in [ 5 ], see also Table 1. The wiki track entries are linked with the PubMed [ 42 ] entries of the papers that published the corresponding transcription factor binding site.…”

“…To make the best of this situation, we and others proposed to integrate data from different sources [ 4 , 5 ]. Apart from computational predictions, curated data and gene expression experiments can be considered; some are available from genome browsers such as the UCSC browser [ 6 ].…”

“…However, such data is usually not available. Then again, conservation data on the sequence level is very often available, and conservation of transcriptional modules [ 5 ] can help to improve hypotheses about transcriptional regulation. Based on this premise, using the conservation of binding sites between species, we developed a tool called ReXSpecies [ 7 , 8 ] for the identification of transcriptional modules, and of their gain/loss patterns in evolution.…”