Page 55 - Mouse Molecular Genetics

Full Abstracts
Program number is above title. Author in bold is the presenter.
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reconstructed previously misassembled regions, and identified new palindromic amplicons. Comparing this revised sequence to
the mouse X chromosome, we found that only 30% of human X-ampliconic genes and 21% of mouse X-ampliconic genes share
orthologs. This is in striking contrast to single-copy genes, which tend to follow Ohnos law of conservation: ~95% are
orthologous between humans and mice. Ampliconic genes thus represent the majority of newly acquired genes in both lineages
and are the primary violators of Ohnos law. Furthermore, we found that newly acquired genes are expressed almost exclusively
in testicular germ cells, suggesting specific roles in the male germline. We conclude that during mammalian X chromosome
evolution two processes were at work: single-copy genes, which comprise the oldest genes, generally follow Ohnos law, but
ampliconic genes, acquired more recently, tend to violate it.
60
Expression QTL mapping in murine macrophages identifies novel genes and gene networks mediating resistance
to
Toxoplasma gondii
and responsiveness to IFNg/TNFa. Musa Hassan
,
Kirk Jensen, Jeroen Saeij. Dept. of Biology, MIT,
Cambridge, MA.
Effective response to infection with intracellular parasites is often dependent on the synergistic activation of macrophages by
interferon gamma (IFN) and tumor necrosis factor alpha (TNF). Activated murine macrophages inhibit parasite growth directly
through the production of nitric oxide (NO) and up-regulation of immunity-related GTPases (IRGs), which are involved in the
disruption of the vacuoles many intracellular parasites live in and subsequently the parasite itself. Macrophages can also
influence parasite growth indirectly by secreting cytokines, such as interleukin (IL)-10 and IL-12, which can further modulate the
immune response. Our hypothesis is that many genetic differences in disease resistance are due to variations in the macrophage
response to the pathogen and/or to IFN/TNF. Our goal therefore, was to elucidate the molecular mechanisms underlying variation
in murine macrophage response to IFN/TNF, the main mediators of resistance to many pathogens. As a proof of concept we are
using the intracellular parasite
Toxoplasma gondii
,
which is a common parasite in humans. We have used high throughput RNA-
sequencing to analyze the transcriptome of IFN/TNF stimulated or
T. gondii
infected bone marrow derived macrophages
obtained from AxB and BxA recombinant inbred mice. Next we used linkage analysis to map the genomic loci controlling
parasite growth (cQTL), mouse gene expression (eQTL),and parasite gene expression (pQTL) in these macrophages. Indeed
activated macrophages from the resistant AJ mice produce more NO and inhibit
Toxoplasma
growth better than macrophages
from the susceptible C57BL/6 mice, and were mapped to chr 4, and chr 13 and 17, respectively. Additionally,, these strains differ
significantly in the production of IL-10 and IL-12p70, two cytokines that play a major role in modulating the immune response.
Interestingly, unlike other studies, the majority of our eQTLs are trans mapping. We have identified
trans
-
acting eQTLs on chrs
10
and 11 following infection,
trans
-
acting eQTLs on chrs 12 and 15 in response to IFN/TNF, and
trans
-
acting pQTL on chr 2.
Majority of these
tran
-
acting loci are enriched in cell cycle pathways, Toll-like receptor (TLR) and interferon responsive factor
(
IRF) signaling, and lipid metabolism. Furthermore, we have identified
cis
-
acting eQTLs for long non-coding RNAs on chr 7,
and 17 following infection and on chr 3 in response to stimulation.
61
The Gene Expression Database for Mouse Development (GXD). Martin Ringwald
,
Constance Smith, Jacqueline Finger,
Terry Hayamizu, Jingxia Xu, Ingeborg McCright, Janan Eppig, James Kadin, Joel Richardson. The Jackson Laboratory, Bar
Harbor, ME.
The Gene Expression Database (GXD) is an extensive and freely available community resource of mouse developmental
expression information. It integrates data from RNA in situ hybridization, immunohistochemistry, in-situ reporter (knock-in),
Northern blot, Western blot, and RT-PCR experiments, covering all developmental stages and data from wild-type and mutant
mice. Data are collected through curation of the literature, via electronic data submissions from conventional laboratories, and by
collaborations with large-scale data generators such as GenePaint, EurExpress, the Brain Gene Expression Map (BGEM) project,
and the GenitoUrinary Developmental Anatomy Project (GUDMAP) project. Accession numbers are provided to researchers so
that electronic data submissions can be cited in publications. GXD currently holds more than 1.3 million expression results from
almost 60,000 expression assays for more than13,600 genes, including expression data from about 1,700 mouse mutants. In
addition, the database holds over 237,000 images of expression data. GXD database records associate these images with
extensive metadata such as the genes analyzed, the probes used, the strain and genotype of the specimen, the developmental
stages and anatomical structures in which expression was reported to be present or absent. Further, by being an integral part of
the larger Mouse Genome Informatics (MGI) resource, GXD combines its expression data with other genetic, functional,
phenotypic, and disease-oriented data. Therefore, users can search for expression data and images in many different ways, using a
variety of biologically and biomedically relevant parameters. Recent interface enhancements include the capability to search for
expression data of genes that are associated with specific phenotypes and/or human diseases, and improved and more interactive
data summaries, with the option to download these data and to export them to other application. In addition, we have significantly
boosted query performance so that even large sets of data can be returned quickly. GXD is freely available through the MGI web
site (www.informatics.jax.org), or directly at
GXD is supported by NIH grant
HD062499.
62
RNAseq Analysis of 32 KOMP Mutant Mouse Lines. David West
1,2
,
Andreana Cipollone
2
,
Michael Adkisson
1
,
Jared Rapp
2
,
Eric Engelhard
2
,
Pieter de Jong
1
,
Kent Lloyd
1
. 1)
Childrens Hospital of Oakland Research Institute, Oakland, CA; 2) University