Systematics and the Origin of Species On Ernst Mayr's 100th Anniversary (2005) / Chapter Skim
Currently Skimming:
15 Prospects for Identifying Functional Variation Across the Genome--STUART J. MACDONALD AND ANTHONY D. LONG
15 Prospects for Identifying Functional Variation Across the Genome--STUART J. MACDONALD AND ANTHONY D. LONG
Pages 286-306
The Chapter Skim interface presents what we've algorithmically identified as the most significant single chunk of text within every page in the chapter.
Select key terms on the right to highlight them within pages of the chapter.
From page 286... ...
Here we de scribe additional approaches that can be used to identify putative regulatory elements via signatures of nonneutral evolution. An ex amination of the pattern of polymorphism both within and between populations of Drosophila melanogaster, as well as divergence with its sibling species Drosophila simulans, across 24.2 kb of noncoding DNA identifies several nonneutrally evolving regions not identified by conservation.
|
From page 287... ...
melano gaster and Drosophila pseudoobscura, we tag 5.3 kb of noncoding DNA as potentially regulatory. Ninety-seven of the 408 common noncoding SNPs surveyed are within putatively regulatory regions.
|
From page 288... ...
Genotyping only those SNPs present within regulatory domains would allow for a reduction in the total genotyping effort in association studies. Such a strategy is simple in principal, but it is a major challenge to sift through the ocean of noncoding DNA to find those polymorphisms that are truly cis-regulatory in function.
|
From page 289... ...
Because nonneutrally evolving regions are likely to be enriched for fSNPs, a reduction in genotyping effort could be achieved in association studies by preferentially genotyping SNPs from nonneutrally evolving regions. We select 26 1-kb fragments of primarily noncoding DNA near known genes distributed across the D
|
From page 290... ...
Primers were developed for an 1-kb amplicon at each locus using Primer3 (http://frodo.wi.mit.edu/cgi-bin/ primer3/primer3_www.cgi; sequences are provided in Table 2, which is published as supporting information on the PNAS web site)
|
From page 291... ...
3, which is published as supporting information on the PNAS web site, details the exact positions of the amplicons relative to the structure of the loci.
|
From page 292... ...
In addition, for each amplicon, we sequenced eight strains from a single population. For the X- and third-chromosome amplicons, we sequenced eight chromosomal extraction strains, where the natural alleles were derived from Napa Valley, CA, whereas for amplicons on the second chromosome, we sequenced eight inbred lines derived from North Carolina (kindly provided by C
|
From page 293... ...
melanogaster, primarily from noncoding regions in or near genes involved in peripheral nervous system development and/or regulation of Notch signaling. For each amplicon, we also identified the homologous region from the closely re
|
From page 294... ...
4, which is published as supporting information on the PNAS web site, presents analyses for all amplicons. Below we document those sequenced noncoding regions that have patterns in the sliding window plots suggesting deviation from neutral expectation, and also note the number of SNPs present within such regions.
|
From page 295... ...
Nucleotide diversity within the lines derived from the single D melanogaster population (dashed line)
|
From page 296... ...
. Positive Selection A low level of diversity coupled with a frequency spectrum skewed toward an excess of rare variants (i.e., negative Tajima's D)
|
From page 297... ...
melanogaster has been impacted by positive selection, and these regions collectively harbor two common biallelic SNPs (0.5% of the total common SNPs discovered)
|
From page 298... ...
melanogaster that shows a pattern of nucleotide diversity consistent with balancing selection is 0.8 kb (3.4%) , and these regions harbor 38 common biallelic SNPs (9.3% of the common SNPs identified in the survey)
|
From page 299... ...
Comparative genome sequencing has proved quite useful for both gene prediction and for identifying conserved noncoding regions (Kellis et al., 2003) , which in some instances have been shown to exhibit regulatory activity (Boffelli et al., 2003; Hong et al., 2003; Johnson et al., 2004)
|
From page 300... ...
, suggests that other methods of locating noncoding regulatory domains may be helpful. Polymorphism and Divergence The neutral theory of molecular evolution states that, for neutrally evolving DNA, the expected ratio of polymorphism within a species to divergence between species should be constant throughout the genome (Kimura, 1983)
|
From page 301... ...
Prospects for in Silico Functional Annotation We surveyed 24.2 kb of noncoding DNA in D melanogaster, encompassing 408 common SNPs, and identified putative regulatory regions using deep phylogenetic conservation (8.6% of the sequence, 3.4% of common SNPs)
|
From page 302... ...
Collectively, we tag 5.3 kb (21.8%) of the surveyed noncoding DNAas potentially regulatory, and the identified regions harbor 97 of the 408 common biallelic SNPs discovered.
|
From page 303... ...
It is important to understand the ability of different methods of genome annotation to uncover functional regulatory variation to direct future genome sequencing studies. The current model for genome annotation employs a comparative approach, whereby annotation of a focal genome is aided by sequence comparisons to one or a set of diverged species genomes.
|
From page 304... ...
(1993) Molecular analysis of an allozyme cline: Alcohol dehydro genase in Drosophila melanogaster on the East Coast of North America.
|
From page 305... ...
(1999) The power of association studies to detect the contribu tion of candidate genetic loci to variation in complex traits.
|
From page 306... ...
(1996) Molecular dissection of a major gene effect on a quantita tive trait: The level of Alcohol dehydrogenase expression on Drosophila melanogaster.
|
Key Terms
This material may be derived from roughly machine-read images, and so is provided only to facilitate research.
More
information on Chapter Skim is available.