Mouse Genome Sequence Research Articles

Parathyroid Hormone Controls Receptor Activator of NF-κB Ligand Gene Expression via a Distant Transcriptional Enhancer

RANKL, a protein essential for osteoclast development and survival, is stimulated by parathyroid hormone (PTH) via a PTH receptor 1/cyclic AMP (cAMP)/protein kinase A (PKA)/CREB cascade, exclusively in osteoblastic cells. We report that a bacterial artificial chromosome-based transcriptional reporter construct containing 120 kb of RANKL 5'-flanking region was stimulated by dibutyryl-cAMP in stromal/osteoblastic cells, but not other cell types. Full cAMP responsiveness was dependent upon a conserved 715-bp region located 76 kb upstream from the transcription start site, which we identified by sequential deletion analysis and by comparison of human and mouse genomic sequences in silico. This region contained conserved consensus sequences which bound CREB and the osteoblast-specific transcription factor Runx2, and when mutated blunted cAMP responsiveness. Overexpression of Runx2 potentiated cAMP responsiveness of the endogenous RANKL gene in a cell-type-specific manner. Lastly, PTH responsiveness of the endogenous RANKL gene was abrogated in mice from which we deleted this conserved upstream region. Thus, PTH responsiveness of the RANKL gene is determined by a distant regulatory region that responds to cAMP in a cell-type-specific manner and Runx2 may contribute to such cell-type specificity.

Chromatin immunoprecipitation‐mediated target identification proved aquaporin 5 is regulated directly by estrogen in the uterus

Estrogens play a central role in the reproduction of vertebrates and affect a variety of biological processes. The major target molecules of estrogens are nuclear estrogen receptors (ERs), which have been studied extensively at the molecular level. In contrast, our knowledge of the genes that are regulated directly by ERs remains limited, especially at the level of the whole organism rather than cultured cells. In order to identify genes that are regulated directly by ERs in vivo, we used estrogen treated mouse uterus and performed chromatin immunoprecipitation. Sequence analysis of a precipitated DNA fragment enabled alignment with the mouse genomic sequence and revealed that the promoter region of the gene encoding aquaporin 5 (AQP5) was precipitated with antibody against ER alpha. Quantitative PCR and DNA microarray analyses confirmed that AQP5 is activated soon after administration of estrogen. In addition, the promoter region of AQP5 contained a functional estrogen response element that was activated directly by estrogen. Although several AQP genes are expressed in the uterus, only direct activation of AQP5 could be detected following treatment with estrogen. This chromatin immunoprecipitation-mediated target identification may be applicable to the study of other transcription factor networks.

Cloning and expression of mouse cytosolic α-mannosidase (Man2c1)

It is known that the neutral/cytosolic α-mannosidase (Man2c1) which can cleave α 1,2-, α 1,3-, and α 1,6-linked mannose residues, is stimulated by cobalt and is inhibited by furanose analogues swainsonine (SW) and 1,4-dideoxy-1,4-imino- d-mannitol (DIM). The enzyme is involved in the degradation of oligomannosides derived from dolichol intermediates and the degradation of newly synthesized glycoproteins. An immunological relationship has been demonstrated between the rat endoplasmic reticulum α-mannosidase and the cytosolic α-mannosidase. In fact antibodies raised against the soluble α-mannosidase recognized the membrane form of the ER α-mannosidase. A cDNA encoding the mouse cytosolic α-mannosidase was obtained by RZPD (Deutsches Ressourcenzentrum fur Genomforschung GmbH), Berlin, Germany. Comparison of the mouse genomic sequence with the cDNA sequence revealed the presence of 25 introns within the cytosolic α-mannosidase gene. The gene spans 11.5 kb from the major transcription initiation site to the RNA cleavage site. The transcription initiation site of mouse cytosolic α-mannosidase was mapped to 170 bases upstream of the ATG codon using 5′ RACE. Northern blotting analysis revealed expression of a major transcript of 3.8 kb in all tissues examined. COS cells transfected with the cDNA showed a 20-fold increase in cytosolic α-mannosidase activity. This enzyme activity was stimulated by cobalt and inhibited by DIM and EDTA. Furthermore we demonstrated that the expressed enzyme was active towards the radiolabeled substrate Man9GlcNAc1 giving the final product Man5GlcNAc1 through the formation of Man8GlcNAc1 isomer C as intermediate.

Widely Divergent Biochemical Properties of the Complete Set of Mouse DC-SIGN-related Proteins

The mouse genome sequence has been examined to identify the complete set of proteins related to the human glycanbinding receptor, DC-SIGN. In addition to five SIGNR proteins previously described, a pseudogene, encoding a hypothetical SIGNR6, and a further two expressed proteins, SIGNR7 and SIGNR8, have been identified. The ligand-binding properties of these novel proteins and of the previously described mouse SIGNs have been systematically investigated in order to define the mouse proteins that most resemble human DC-SIGN and DC-SIGNR. Results from screening of a glycan array demonstrate that only mouse SIGNR3 shares with human DC-SIGN the ability to bind both high mannose and fucose-terminated glycans in this format and to mediate endocytosis. The finding that neither SIGNR1 nor SIGNR5 binds with high affinity to specific ligands in a large panel of mammalian glycans is consistent with the suggestion that these receptors bind surface polysaccharides on bacterial and fungal pathogens in a manner analogous to serum mannose-binding protein. The data also reveal that two of the mouse SIGNs have unusual binding specificities that have not been previously described for members of the C-type lectin family; the newly identified SIGNR7 binds preferentially to the 6-sulfo-sialyl Lewis(x) oligosaccharide, whereas SIGNR2 binds almost exclusively to glycans that bear terminal GlcNAc residues. The results presented demonstrate that the mouse homologs of DC-SIGN have a diverse set of ligand-binding and intracellular trafficking properties, some of which are distinct from the properties of any of the human receptors.

Essential Role of 3′-Untranslated Region-mediated mRNA Decay in Circadian Oscillations of Mouse Period3 mRNA

Daily oscillations in mRNA levels are a general feature of most clock genes. Although mRNA oscillations largely depend on transcriptional regulation, it has been suggested that post-transcriptional controls also contribute to mRNA oscillations in Drosophila. Currently, however, there is no direct evidence for post-transcriptional regulation of mammalian clock genes. To investigate the roles of post-transcriptional regulations, we focused on the 3'-untranslated region (3'-UTR) of mouse Period3 (mPer3) mRNA, one of the clock genes. Insertion of the entire mPer3 3'-UTR downstream of a reporter gene resulted in a dramatic decrease in mRNA stability. Deletion and point mutation analyses led to the identification of critical sequences responsible for mRNA decay. To explore the effects of the mPer3 3'-UTR-mediated mRNA decay on circadian oscillations, we established NIH3T3 stable cell lines that express luciferase mRNA with wild-type or mutant mPer3 3'-UTR. Interestingly, a stabilizing mutation of 3'-UTR induced a significant alteration in the oscillation profile of luciferase mRNA. Above all, the peak time, during which the mRNAs reached their highest levels, was significantly delayed (for 12 h). In addition, the luciferase mRNA level with mutant 3'-UTR began to increase earlier than that in the presence of wild-type 3'-UTR. Consequently, luciferase mRNA with mutant 3'-UTR displayed oscillation patterns with a prolonged rising phase. Our results indicate that mPer3 3'-UTR-mediated mRNA decay plays an essential role in mRNA cycling and provide direct evidence for post-transcriptional control of circadian mRNA oscillations.

Thousands of corresponding human and mouse genomic regions unalignable in primary sequence contain common RNA structure

Human and mouse genome sequences contain roughly 100,000 regions that are unalignable in primary sequence and neighbor corresponding alignable regions between both organisms. These pairs are generally assumed to be nonconserved, although the level of structural conservation between these has never been investigated. Owing to the limitations in computational methods, comparative genomics has been lacking the ability to compare such nonconserved sequence regions for conserved structural RNA elements. We have investigated the presence of structural RNA elements by conducting a local structural alignment, using FOLDALIGN, on a subset of these 100,000 corresponding regions and estimate that 1800 contain common RNA structures. Comparing our results with the recent mapping of transcribed fragments (transfrags) in human, we find that high-scoring candidates are twice as likely to be found in regions overlapped by transfrags than regions that are not overlapped by transfrags. To verify the coexpression between predicted candidates in human and mouse, we conducted expression studies by RT-PCR and Northern blotting on mouse candidates, which overlap with transfrags on human chromosome 20. RT-PCR results confirmed expression of 32 out of 36 candidates, whereas Northern blots confirmed four out of 12 candidates. Furthermore, many RT-PCR results indicate differential expression in different tissues. Hence, our findings suggest that there are corresponding regions between human and mouse, which contain expressed non-coding RNA sequences not alignable in primary sequence.

Competition may determine the diversity of transposable elements

Transposable elements are genomic parasites that replicate independently from their hosts. They harm their hosts by causing mutations or genomic rearrangements, and most organisms have evolved various mechanisms to suppress their activity. The evolutionary dynamics of transposons in insects, fish, birds and mammals are dramatically different. Mammalian genomes contain few, very abundant but relatively inactive transposon strains, while Drosophila and fish species harbour diverse strains, which typically have low abundance but are much more virulent. We hypothesise that the variation in the diversity and activity of transposable elements between various animal genomes is caused by the differences in the host defence mechanisms against transposon activity. In recent years RNAi, a mechanism capable of gene, virus and transposon silencing has been discovered. We model RNAi as a density dependant mechanism of defence, which can cause competition among transposons depending on its specificity, and test its predictions using the complete Caenorhabditis elegans, Drosophila melanogaster, Fugu rubripes, chicken, mouse, rat and human genome sequences.

Energetics of small hearts

Little is known about the energetics of the failing heart. In man it is well known that energy metabolism is affected in chronic heart failure (Ingwall & Weiss, 2004). Genetically modified mice are useful in the study of heart disease. A persistent headache has been the lack of basic energetic data. In this issue of The Journal of PhysiologyWiden & Barclay (2006) give us both a method and the first data. For the first time, the basic energetic characteristics of mouse heart muscle activation and contraction have been measured in papillary muscle. Mice can be obtained relatively easily and the mouse genome has been sequenced. The proportion of mouse genes without a human homologue is probably less than 1% (Mouse Genome Sequencing Consortium, 2002). Numerous mouse models for studying heart disease exist already and the number is increasing (Wang et al. 2004). Gene products are processed in cells resulting in many more proteins than genes and a staggering number of possible interactions between the different proteins exist. One important question is then: How does one relate gene function to the final contractile characteristics of cardiomyocytes? Muscles produce mechanical work and heat in different amounts and proportions, depending on the type of muscle and the load (Hill, 1965; Woledge et al. 1985). ATP required for ion pumps and cardiomyocyte shortening is buffered by the Lohmann reaction in the myoplasm. This keeps the ATP concentration constant while the phosphocreatine concentration decreases when the muscle is activated. Net splitting of phosphocreatine releases 34 kJ mol−1 (Woledge et al. 1985). This energy is partly converted into mechanical work during systole when the phosphocreatine concentration decreases and the rest is liberated as heat. A metabolic steady state can only be maintained when creatine is rephosphorylated during one heart cycle. The energy for this is produced by oxidation of fat or carbohydrate, 439 or 473 kJ (mol O2)−1, respectively. Depending on the efficiency of the oxidation (the ∼P/O2 ratio), part of the energy is used to rephosphorylate creatine, and the remainder is liberated as heat. Heat production increases the temperature of the heart muscle preparation, which can be measured using a thermopile. The myothermic technique has a higher time resolution than oxygen consumption or 31P-NMR which are too slow to determine energy fluxes during a single contraction. The interpretation of heat production data requires that the biochemical reaction producing it is known. This is complicated in heart muscle because contraction-related processes, i.e. heat production due to ion pumps and cross-bridge cycling, and oxidative phosphorylation, usually occur simultaneously. Another challenge is that mouse hearts are small (about 0.1–0.2 g) and operate at high metabolic rates (Gibbs & Loiselle, 2001). The risk that the preparation becomes anoxic is considerable. This is a problem because heat production by partly anoxic preparations cannot be interpreted reliably, and because reoxygenation can damage anoxic cardiomyocytes. The maximum rate of oxygen consumption of mouse heart muscle is not known, but can be estimated on the basis of volume density of mitochondria and the rate of oxygen consumption of rat myocardial trabeculae, 0.58 nmol mm−3 s−1 at the maximum heart rate (van der Laarse et al. 2005), 600 beats min−1, which is the resting rate in mice. Mouse cardiomyocytes contain 38% (v/v) mitochondria and rat cardiomyocytes contain 32% (Barth et al. 1992). Assuming the maximum rate of oxygen consumption is proportional to volume density of mitochondria, the maximum rate of oxygen consumption of mouse trabeculae is about 0.7 nmol mm−3 s−1. At this rate of oxygen consumption, the mouse heart becomes anoxic a few seconds after perfusion stops and superfused preparations, e.g. papillary muscles or trabeculae at experimental PO2 of 500 mmHg, must have diameters of less than 160 µm to prevent an anoxic core. Widen & Barclay (2006) solved these problems and determined heat produced by calcium cycling and heat produced by cross-bridge cycling in papillary muscles of Swiss mice. Contraction-related heat was determined during the first three contractions of a series, making use of the relatively slow onset of recovery metabolism at 27°C. Hypoxia was prevented using stimulus periods of 20 s, sufficiently short not to deplete oxygen stored in the muscle, and contraction and activation-related heat were separated by partial inhibition of cross-bridges using butanedione monoxime (Alpert et al. 1989). The results indicate that about one Ca2+ cycles per three cross-bridge cycles, and that the number of cross-bridge cycles per cardiac twitch is half the number of available cross-bridges. How these numbers vary with genotype and intervention remains to be determined.

Gene functional similarity search tool (GFSST)

BackgroundWith the completion of the genome sequences of human, mouse, and other species and the advent of high throughput functional genomic research technologies such as biomicroarray chips, more and more genes and their products have been discovered and their functions have begun to be understood. Increasing amounts of data about genes, gene products and their functions have been stored in databases. To facilitate selection of candidate genes for gene-disease research, genetic association studies, biomarker and drug target selection, and animal models of human diseases, it is essential to have search engines that can retrieve genes by their functions from proteome databases. In recent years, the development of Gene Ontology (GO) has established structured, controlled vocabularies describing gene functions, which makes it possible to develop novel tools to search genes by functional similarity.ResultsBy using a statistical model to measure the functional similarity of genes based on the Gene Ontology directed acyclic graph, we developed a novel Gene Functional Similarity Search Tool (GFSST) to identify genes with related functions from annotated proteome databases. This search engine lets users design their search targets by gene functions.ConclusionAn implementation of GFSST which works on the UniProt (Universal Protein Resource) for the human and mouse proteomes is available at GFSST Web Server. GFSST provides functions not only for similar gene retrieval but also for gene search by one or more GO terms. This represents a powerful new approach for selecting similar genes and gene products from proteome databases according to their functions.

Are molecular cytogenetics and bioinformatics suggesting diverging models of ancestral mammalian genomes?

Author(s): Froenicke, Lutz; Caldes, Montserrat Garcia; Graphodatsky, Alexander; Muller, Stefan; Lyons, Leslie A; Robinson, Terence J; Volleth, Marianne; Yang, Fengtang; Wienberg, Johannes | Abstract: Excavating ancestral genomes The recent release of the chicken genome sequence (Hillier et al. 2004Go) provided exciting news for the comparative genomics community as it allows insights into the early evolution of the human genome. A bird species can now be used as an outgroup to model early mammalian genome organization and reshuffling. The genome sequence data have already been incorporated in a computational analysis of chicken, mouse, rat, and human genome sequences for the reconstruction of the ancestral genome organization of both a mammalian ancestor as well as a murid rodent ancestor (Hillier et al. 2004Go; Bourque et al. 2005Go). This bioinformatic effort joins a molecular cytogenetic model (Richard et al. 2003Go; Yang et al. 2003Go; Robinson et al. 2004Go; Svartman et al. 2004Go; Wienberg 2004Go; Froenicke 2005Go) as the second global approach to explore the architecture of the ancestral eutherian karyotype—a fundamental question in comparative genomics. Since both models use the human genome as reference, they are readily comparable. Surprisingly, however, they share few similarities. Only two small autosomes and the sex chromosomes of the hypothesized ancestral karyotypes are common to both. Unfortunately, given its significance, neither the extent of these differences nor their impact on comparative genomics have been discussed by Bourque and colleagues (2005Go). In an attempt to redress this, we compare the two methods of ancestral genome reconstruction, verify the resulting models, and discuss reasons for their apparent divergence.

Sodium and Epithelial Sodium Channels Participate in the Regulation of the Capacitation-associated Hyperpolarization in Mouse Sperm

In a process called capacitation, mammalian sperm gain the ability to fertilize after residing in the female tract. During capacitation the mouse sperm plasma membrane potential (E(m)) hyperpolarizes. However, the mechanisms that regulate sperm E(m) are not well understood. Here we show that sperm hyperpolarize when external Na(+) is replaced by N-methyl-glucamine. Readdition of external Na(+) restores a more depolarized E(m) by a process that is inhibited by amiloride or by its more potent derivative 5-(N-ethyl-N-isopropyl)-amiloride hydrochloride. These findings indicate that under resting conditions an electrogenic Na(+) transporter, possibly involving an amiloride sensitive Na(+) channel, may contribute to the sperm resting E(m). Consistent with this proposal, patch clamp recordings from spermatogenic cells reveal an amiloride-sensitive inward Na(+) current whose characteristics match those of the epithelial Na(+) channel (ENaC) family of epithelial Na(+) channels. Indeed, ENaC-alpha and -delta mRNAs were detected by reverse transcription-PCR in extracts of isolated elongated spermatids, and ENaC-alpha and -delta proteins were found on immunoblots of sperm membrane preparations. Immunostaining indicated localization of ENaC-alpha to the flagellar midpiece and of ENaC-delta to the acrosome. Incubations known to produce capacitation in vitro or induction of capacitation by cell-permeant cAMP analogs decreased the depolarizing response to the addition of external Na(+). These results suggest that increases in cAMP content occurring during capacitation may inhibit ENaCs to produce a required hyperpolarization of the sperm membrane.

Myospryn Is a Direct Transcriptional Target for MEF2A That Encodes a Striated Muscle, α-Actinin-interacting, Costamere-localized Protein

The full repertoire of proteins that comprise the striated muscle Z-disc and peripheral structures, such as the costamere, have yet to be discovered. Recent studies suggest that this elaborate protein network, which acts as a structural and signaling center for striated muscle, harbors factors that function as mechanosensors to ensure coordinated contractile activity. Mutations in genes whose products reside in this region often result in skeletal and cardio myopathies, demonstrating the importance of this macromolecular complex in muscle structure and function. Here, we describe the characterization of a direct, downstream target gene for the MEF2A transcription factor encoding a large, muscle-specific protein that localizes to the costamere in striated muscle. This gene, called myospryn, was identified by microarray analysis as a transcript down-regulated in MEF2A knock-out mice. MEF2A knock-out mice develop cardiac failure during the perinatal period with mutant hearts exhibiting several cardiac abnormalities including myofibrillar disarray. Myospryn is the mouse ortholog of a partial human cDNA of unknown function named cardiomyopathy-associated gene 5 (CMYA5). Myospryn is expressed as a single, large transcript of approximately 12 kilobases in adult heart and skeletal muscle with an open reading frame of 3739 amino acids. This protein, belonging to the tripartite motif superfamily of proteins, contains a B-box coiled-coil (BBC), two fibronectin type III (FN3) repeats, and SPRY domains and interacts with the sarcomeric Z-disc protein, alpha-actinin-2. Our findings demonstrate that myospryn functions directly downstream of MEF2A at the costamere in striated muscle potentially playing a role in myofibrillogenesis.

Mouse models as a tool to unravel the genetic basis for human otitis media

The pathogenesis of otitis media (OM) is multifactorial and includes infection, anatomical factors, immunologic status, genetic predisposition, and environmental factors. OM remains the most common cause of hearing impairment in childhood. Genetic predisposition is increasingly recognized as an important factor. The completion of the mouse genome sequence has offered a powerful basket of tools for investigating gene function and can expect to generate a rich resource of mouse mutants for the elucidation of genetic factors underlying OM. We review the literature and discuss recent progresses in developing mouse models and using mouse models to uncover the genetic basis for human OM.

Recent translational research: Oncogene discovery by insertional mutagenesis gets a new boost

Knowledge of the genes and genetic pathways involved in onco-genesis is essential if we are to identify novel targets for cancer therapy. Insertional mutagenesis in mouse models is among the most efficient tools to detect novel cancer genes. Retrovirus-mediated insertional mutagenesis received a tremendous boost by the availability of the mouse genome sequence and new PCR methods. Application of such advances were limited to lympho-magenesis but are now also being applied to mammary tumourigenesis. Novel transposons that allow insertional muta-genesis studies to be conducted in tumors of any mouse tissue may give cancer gene discovery a further boost.

Using several pair-wise informant sequences for de novo prediction of alternatively spliced transcripts

BackgroundAs part of the ENCODE Genome Annotation Assessment Project (EGASP), we developed the MARS extension to the Twinscan algorithm. MARS is designed to find human alternatively spliced transcripts that are conserved in only one or a limited number of extant species. MARS is able to use an arbitrary number of informant sequences and predicts a number of alternative transcripts at each gene locus.ResultsMARS uses the mouse, rat, dog, opossum, chicken, and frog genome sequences as pairwise informant sources for Twinscan and combines the resulting transcript predictions into genes based on coding (CDS) region overlap. Based on the EGASP assessment, MARS is one of the more accurate dual-genome prediction programs. Compared to the GENCODE annotation, we find that predictive sensitivity increases, while specificity decreases, as more informant species are used. MARS correctly predicts alternatively spliced transcripts for 11 of the 236 multi-exon GENCODE genes that are alternatively spliced in the coding region of their transcripts. For these genes a total of 24 correct transcripts are predicted.ConclusionThe MARS algorithm is able to predict alternatively spliced transcripts without the use of expressed sequence information, although the number of loci in which multiple predicted transcripts match multiple alternatively spliced transcripts in the GENCODE annotation is relatively small.

ABS: a database of Annotated regulatory Binding Sites from orthologous promoters

Information about the genomic coordinates and the sequence of experimentally identified transcription factor binding sites is found scattered under a variety of diverse formats. The availability of standard collections of such high-quality data is important to design, evaluate and improve novel computational approaches to identify binding motifs on promoter sequences from related genes. ABS () is a public database of known binding sites identified in promoters of orthologous vertebrate genes that have been manually curated from bibliography. We have annotated 650 experimental binding sites from 68 transcription factors and 100 orthologous target genes in human, mouse, rat or chicken genome sequences. Computational predictions and promoter alignment information are also provided for each entry. A simple and easy-to-use web interface facilitates data retrieval allowing different views of the information. In addition, the release 1.0 of ABS includes a customizable generator of artificial datasets based on the known sites contained in the collection and an evaluation tool to aid during the training and the assessment of motif-finding programs.

Gene prediction by multiple syntenic alignment

Summary Given the increasing number of available genomic sequences, one now faces the task of identifying their functional parts, like the protein coding regions. The gene prediction problem can be addressed in several ways. One of the most promising methods makes use of similarity information between the genomic DNA and previously annotated sequences (proteins, cDNAs and ESTs). Recently, given the huge amount of newly sequenced genomes, new similarity-based methods are being successfully applied in the task of gene prediction. The so-called comparative-based methods lie in the similarities shared by regions of two evolutionary related genomic sequences. Despite the number of different gene prediction approaches in the literature, this problem remains challenging. In this paper we present a new comparative-based approach to the gene prediction problem. It is based on a syntenic alignment of three or more genomic sequences. With syntenic alignment we mean an alignment that is constructed taking into account the fact that the involved sequences include conserved regions intervened by unconserved ones. We have implemented the proposed algorithm in a computer program and confirm the validity of the approach on a benchmark including triples of human, mouse and rat genomic sequences.

Connecting Mammalian Genome with Phenome by ENU Mouse Mutagenesis: Gene Combinations Specifying the Immune System

The human and mouse genome sequences bring closer the goal of understanding how characteristics of adult mammalian physiology and pathology are encoded by DNA. Here we review the challenge of understanding how genes specify mammalian traits, with particular focus on the cells and behavior of the immune system. Summarized is the emerging experience, advantages, and limitations of using ethylnitrosourea (ENU) to modify the mouse genome and select informative variants by phenotypic screens, yielding two main conclusions. First, ENU-induced variation provides an eminently feasible route to understanding how the genome encodes important mammalian processes without any prior assumptions about genes, their chromosomal locations, or expression patterns. Second, ENU alleles match those arising by natural variation. By changing individual protein domains or splice products, these alleles reveal separate gene functions specified through protein combinations.

Expression, regulation, and triglyceride hydrolase activity of Adiponutrin family members

Adiponutrin and a related protein, adipocyte triglyceride lipase (ATGL; also known as Desnutrin), were recently described as adipocyte-specific proteins with lipid hydrolase activity. Using bioinformatics, we identified three additional Adiponutrin family members (GS2, GS2-Like, and PNPLA1). Here, we report on the expression, regulation, and activity of GS2 and GS2-Like compared with Adiponutrin and Desnutrin/ATGL. GS2-Like is expressed and regulated in a manner similar to Adiponutrin; however, the absolute levels of mRNA are significantly lower than those of Adiponutrin or Desnutrin/ATGL. GS2 transcripts were identified only in humans and are highly expressed in adipose as well as other tissues. All four proteins show lipase activity in vitro, which is dependent on the presence of the active site serine for Adiponutrin, Desnutrin/ATGL, and GS2. Overexpression of Desnutrin/ATGL, GS2, and GS2-Like, but not Adiponutrin, decreases intracellular triglyceride levels. This is consistent with a function for Desnutrin/ATGL, GS2, and GS2-Like in lipolysis, but not for Adiponutrin. Consistent with previously reported data, Desnutrin/ATGL is upregulated by fasting in adipose tissue, whereas Adiponutrin is downregulated. Additionally, Adiponutrin and GS2-Like, but not Desnutrin/ATGL, are strongly induced in the liver of ob/ob mice. Our data support distinct functions for Adiponutrin and Desnutrin/ATGL and raise the possibility that GS2 may contribute significantly to lipolysis in human adipose tissue.

Murine segmental duplications are hot spots for chromosome and gene evolution

Mouse and rat genomic sequences permit us to obtain a global view of evolutionary rearrangements that have occurred between the two species and to define hallmarks that might underlie these events. We present a comparative study of the sequence assemblies of mouse and rat genomes and report an enrichment of rodent-specific segmental duplications in regions where synteny is not preserved. We show that segmental duplications present higher rates of molecular evolution and that genes in rearranged regions have evolved faster than those located elsewhere. Previous studies have shown that synteny breakpoints between the mouse and the human genomes are enriched in human segmental duplications, suggesting a causative connection between such structures and evolutionary rearrangements. Our work provides further evidence to support the role of segmental duplications in chromosomal rearrangements in the evolution of the architecture of mammalian chromosomes and in the speciation processes that separate the mouse and the rat.