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Poster Full Abstracts - Evolution and Quantitative Genetics
Poster board number is above title. The first author is the presenter
260
genome, 20,223 IDs were detected in nonrepetitive intergenic regions, far more than expectation under the neutrality model. 3,846 of these IDs were
identified to have stable hairpin structure (i.e., the structural IDs). Based on whole-genome transcriptome profiling data, we found 628 unannotated
expressed structural IDs, which had significantly different genomic distributions and structural properties from the unexpressed IDs. Among the expressed
structural IDs, 130 exhibited higher expression in males than in females (i.e., male-biased expression). Compared with sex-unbiased ones, these male-biased
IDs were significantly underrepresented on the X chromosome, similar to previously reported pattern of male-biased protein-coding genes. These analyses
suggest that a selection-driven process, rather than a purely neutral mutation-driven mechanism, contributes to the maintenance of IDs in the Drosophila
genome.
478A
Neo-Y chromosome divergence among populations of Drosophila albomicans.
Chia-Hao Cheng, Hwei-yu Chang. Entomology department, NTU, Taipei,
Taiwan.
Drosophila albomicans (2n = 6) has a pair of metacentric neo-sex chromosomes with a large portion (i.e., about 40% of the genome) of neo-Y chromosome
arm originally from an autosome. Due to the lack of recombination in Drosophila males, the divergence time between neo-X and neo-Y chromosomes was
estimated to be about 0.07 MY based on the synonymous substitutions rate. Our previous study of crossing D. albomicans and its sibling species D. nasuta
has shown high non-disjunction rate of sex chromosomes in hybrid males with a neo-Y chromosome. Although X,neo-Y/Y males are viable, not a single
X,neo-Y/neo-Y male has ever been found in our experiments which implies the existence of recessive deleterious alleles on the 3rd arm of the neo-Y
chromosome. The hypothesis we proposed here is that the 3rd arms of neo-Y chromosomes in different populations accumulated recessive deleterious alleles
independently. This can be investigated by complementation tests between two strains. Different fragments of recombinant 3rd arm of the neo-Y
chromosome can be obtained through a fertile 3,X,X/neo-Y female. Special cross schemes were designed to reveal differential evolution of the 3rd arms of
the neo-Y chromosomes. Molecular markers were mainly PCR fragments, genetically mapped and confirmed by in situ hybridization on salivary gland
chromosomes. Recombinant strains were established and with proper genetic markers a more detailed examination can be done by comparing different neo-
Y segments. Our contemporary result showed that the recessive deleterious effect of neo-Y can be complemented in other words we did obtain X,neo-Y/neo-
Y’ individuals if the two Y chromosomes were from different populations. As for where the deleterious alleles located, it’s roughly shown that they’re at
both the distal and the basal fragments but not the middle portion of the 3rd arm of the neo-Y chromosome. Further confirmation is needed for detailed
mapping is still ongoing.
479B
Comparative and functional analysis of CTCF binding site divergence in the Drosophila genome.
Eldon Emberly
1
, Joyce Stamm
2
, Nickodemo Pavoni
3
,
Kyrillos Awad
3
, Amy Lloyd
3
, Brittany Pasierb
3
, Carlos Ortiz
3
, Sheryl Smith
3
. 1) Physics, Simon Fraser University, Burnaby, B.C., Canada; 2) Biology,
University of Evansville, Evansville, IN; 3) Biology, Arcadia University, Glenside, PA.
Insulator sequences have defined functions in genome organization, regulation of enhancer-promoter communication and in barrier activity to prevent the
spread of repressive chromatin. We have previously conducted a genome-wide analysis of sequences that bind to the insulator-associated protein CTCF in
Drosophila melanogaster.
Our analysis has revealed that the majority of CTCF-associated sequences were not found within intergenic regions as predicted,
but were biased toward genes. CTCF-associated sites were predominantly found within 1000 base pairs of a transcription start site (TSS), suggesting a more
direct role for these sequences in regulating transcription of the nearby linked gene. We have recently conducted an analysis of the conservation of promoter-
associated CTCF binding sites across 11 species of
Drosophila
and show that genes associated with highly conserved CTCF elements function in regulating
essential metabolic processes, while genes associated with poorly conserved CTCF elements function in metamorphic/ post-embryonic developmental
processes. These findings suggest that promoter-associated CTCF sites and their linked genes are subject to similar selective evolutionary pressures. To
further investigate the role of promoter-associated CTCF binding on transcriptional regulation of linked genes we analyzed several odor receptor family loci
with closely linked CTCF-associated sequences across the 11
Drosophila
species. We found sequence divergence from homologous CTCF-bound loci in
D.
melanogaster
is associated with loss of CTCF binding and changes in linked gene expression. A comprehensive analysis of the chromatin structure at these
loci is currently in progress and will provide valuable insight into the role of CTCF binding site divergence as a potential evolutionary tool for altering gene
expression.
480C
Identification of transcriptional regulatory networks using structural equation modeling along with priori biological knowledge.
Justin M Fear
1
,
Daniel Campos
2
, Sergey V Nuzhdin
2
, Lauren McIntyre
1,3
. 1) Genetics & Genomics, Univ Florida, Gainesville, FL; 2) Section of Molecular and
Computational Biology, Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089; 3) Department of Molecular
Genetics and Microbiology, University of Florida, Gainesville, FL 32611.
Assays for transcriptome profiling, such as microarrays or RNA-seq, generate lists of significantly differentially expressed genes (DEGs). These lists are
then the starting point for making biological inferences. One means to extract biological knowledge utilizes Go Ontology (GO) enrichment of statistically
significant genes. Combined with the investigator’s biological knowledge, enrichment analyses can lead to hypotheses about underlying mechanism.
However, genes connected in a regulatory pathway may not share GO terms given that the underlying premise of the GO is to describe function and not to
describe interactions. Transcriptional pathways can be reconstructed algorithmically, but these computational exercises often lack incorporation of
biochemical knowledge and ignore genetic variation. By integrating gene expression data with published interactomes, sub-networks responsible for
transcriptional regulation can be identified. Inclusion of protein-encoding genes regulated by means other than transcription into the sub-networks grounds
the work in biochemical knowledge and allows for the identification of transcripts connected by biological processes. These specific sub-networks can then
be tested for directionality in transcript regulation using structural equations. We demonstrate the utility of this approach using RNA-seq data from female
heads.
481A
Genomic evidence that heightened gene duplicate accumulation gave a boost to the energy metabolism of the higher Diptera.
Markus H. Friedrich,