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Human Molecular Genetics Advance Access originally published online on September 9, 2005
Human Molecular Genetics 2005 14(20):3057-3063; doi:10.1093/hmg/ddi338
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© The Author 2005. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

Mapping cis-regulatory domains in the human genome using multi-species conservation of synteny

Nadav Ahituv1,2,{dagger}, Shyam Prabhakar1,2,{dagger}, Francis Poulin1,{ddagger}, Edward M. Rubin1,2 and Olivier Couronne1,2,*

1Genomics Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA and 2US DOE Joint Genome Institute, Walnut Creek, CA, USA

* To whom correspondence should be addressed at: Genomics Division, Lawrence Berkeley National Laboratory, One Cyclotron Road, MS 84-171, Berkeley, CA 94720, USA. Tel: +1 5104865468; Fax: +1 5104864229; Email: ocouronne{at}mac.com

Received July 1, 2005; Revised August 31, 2005; Accepted September 6, 2005

Our inability to associate distant regulatory elements with the genes they regulate has largely precluded their examination for sequence alterations contributing to human disease. One major obstacle is the large genomic space surrounding targeted genes in which such elements could potentially reside. In order to delineate gene regulatory boundaries, we used whole-genome human–mouse–chicken (HMC) and human–mouse–frog (HMF) multiple alignments to compile conserved blocks of synteny (CBSs), under the hypothesis that these blocks have been kept intact throughout evolution at least in part by the requirement of regulatory elements to stay linked to the genes they regulate. A total of 2116 and 1942 CBSs >200 kb were assembled for HMC and HMF, respectively, encompassing 1.53 and 0.86 Gb of human sequence. To support the existence of complex long-range regulatory domains within these CBSs, we analyzed the prevalence and distribution of chromosomal aberrations leading to position effects (disruption of a gene's regulatory environment), observing a clear bias not only for mapping onto CBS but also for longer CBS size. Our results provide an extensive data set characterizing the regulatory domains of genes and the conserved regulatory elements within them.

{dagger} The authors wish it to be known that, in their opinion, the first two authors should be regarded as joint First Authors.

{ddagger} Present address: Department of Integrative Biology, University of California, Berkeley, CA, USA.


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