Imperial College London

ProfessorBorisLenhard

Faculty of MedicineInstitute of Clinical Sciences

Professor of Computational Biology
 
 
 
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Contact

 

+44 (0)20 3313 8353b.lenhard Website

 
 
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Assistant

 

Mr Alastair Douglas Ivor Williams +44 (0)20 3313 4318

 
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Location

 

230ICTEM buildingHammersmith Campus

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Summary

 

Publications

Citation

BibTex format

@article{Danks:2018:10.1186/s12864-018-4504-5,
author = {Danks, GB and Navratilova, P and Lenhard, B and Thompson, EM},
doi = {10.1186/s12864-018-4504-5},
journal = {BMC Genomics},
title = {Distinct core promoter codes drive transcription initiation at key developmental transitions in a marine chordate},
url = {http://dx.doi.org/10.1186/s12864-018-4504-5},
volume = {19},
year = {2018}
}

RIS format (EndNote, RefMan)

TY  - JOUR
AB - BACKGROUND: Development is largely driven by transitions between transcriptional programs. The initiation of transcription at appropriate sites in the genome is a key component of this and yet few rules governing selection are known. Here, we used cap analysis of gene expression (CAGE) to generate bp-resolution maps of transcription start sites (TSSs) across the genome of Oikopleura dioica, a member of the closest living relatives to vertebrates. RESULTS: Our TSS maps revealed promoter features in common with vertebrates, as well as striking differences, and uncovered key roles for core promoter elements in the regulation of development. During spermatogenesis there is a genome-wide shift in mode of transcription initiation characterized by a novel core promoter element. This element was associated with > 70% of male-specific transcription, including the use of cryptic internal promoters within operons. In many cases this led to the exclusion of trans-splice sites, revealing a novel mechanism for regulating which mRNAs receive the spliced leader. Binding of the cell cycle regulator, E2F1, is enriched at the TSS of maternal genes in endocycling nurse nuclei. In addition, maternal promoters lack the TATA-like element found in zebrafish and have broad, rather than sharp, architectures with ordered nucleosomes. Promoters of ribosomal protein genes lack the highly conserved TCT initiator. We also report an association between DNA methylation on transcribed gene bodies and the TATA-box. CONCLUSIONS: Our results reveal that distinct functional promoter classes and overlapping promoter codes are present in protochordates like in vertebrates, but show extraordinary lineage-specific innovations. Furthermore, we uncover a genome-wide, developmental stage-specific shift in the mode of TSS selection. Our results provide a rich resource for the study of promoter structure and evolution in Metazoa.
AU - Danks,GB
AU - Navratilova,P
AU - Lenhard,B
AU - Thompson,EM
DO - 10.1186/s12864-018-4504-5
PY - 2018///
SN - 1471-2164
TI - Distinct core promoter codes drive transcription initiation at key developmental transitions in a marine chordate
T2 - BMC Genomics
UR - http://dx.doi.org/10.1186/s12864-018-4504-5
UR - https://www.ncbi.nlm.nih.gov/pubmed/29482522
UR - http://hdl.handle.net/10044/1/57879
VL - 19
ER -