Alan Packer

Splicing and evolutionary change

LEONARD I. ZON CHILDREN’S HOSPITAL, BOSTON, USA With the estimated number of genes in the human genome hovering at a modest 30,000, alternative splicing has received much attention as a potential amplifier of genomic complexity, albeit without direct evidence across an entire genome. In a new study in Nature Genetics, Modrek and Lee outline a bioinformatic approach that, for the first time, makes the case that alternative splicing is indeed associated with increased evolutionary change. The authors used databases of expressed sequence tags (ESTs) to compare exon–intron structure and exon sequence conservation in pairs of orthologues from the human and mouse. As expected, ~90% of the exons had identical boundaries in the two genomes, and there was a high degree of sequence similarity between matching exons. Also, for each exon, they estimated the fraction of total transcripts of a gene that include this particular exon. An alternatively spliced exon was said to be the ‘major form’ if it was included in the mature mRNA more than 50% of the time. By relating the frequency of inclusion of a particular exon to the likelihood that it would be conserved between the two genomes, the authors hit on a notable finding. Constitutive exons are almost always conserved, as are alternatively spliced exons that are classified as the major form. ‘Minor form’ exons, however, were conserved only ~25% of the time. Strikingly, the frequency of inclusion of an exon in human ESTs can predict whether it will be conserved in the mouse. Modrek and Lee note that the presence of an exon in the orthologue from one genome but not the other, could be explained by exon creation or exon loss, both occurring after the divergence of each lineage from their most recent common ancestor. Constitutive and majorform exons changed little after the divergence of the human and mouse genomes, and most minor-form alternatively spliced exons appeared since then, which indicates that alternative splicing might accompany evolutionary change. The authors propose a scenario in which a new exon with weak splice signals is added to a gene, and as a result is included in only a small fraction of the mature transcripts. As the major form is still produced in near-to-normal quantities, initially deleterious effects of adding a new exon would be neutral, leaving the minor-form free to evolve rapidly, possibly serving as an ‘internal paralogue’ and ultimately acquiring a useful function. The search is now on for alternatively spliced exons that are linked definitively to a specific instance of evolutionary novelty. Alan Packer, Acting Editor, Nature Genetics

Epigenetics: Family feud

The NHGRI Policy and Legislation Database • http://www.genome.gov/ LegislativeDatabase A new web-based searchable database for US genetics-related policy and legislative documents promises to be a valuable resource for anyone interested in this ever-expanding and important area. Francis Collins, director of the US National Human Genome Research Institute (NHGRI), said this tool will be useful for everybody “...from academic researchers seeking to patent genetic technologies to average citizens trying to determine what protections exist in their states against genetic discrimination.” Database users can find legislation and laws from specific states through an interactive US map, as well as doing more specific searches for particular combinations of content type (for example, federal legislative materials), topic (such as genetic testing and counselling) and source (for example, the Department of Health and Human Services). Keyword searching is also possible, but only for words in document titles, not those in their content. Perhaps the most useful ‘value-added’ feature that the database incorporates is a summary, in layman’s terms, of each document: this enables quick identification of relevant documents without the need to trawl through pages of legal jargon. Of course, one of the biggest limitations of this extremely useful tool is that it only encompasses US policy and legislation. However, this focus is understandable given that the US National Institutes of Health fund this resource. Moreover, the addition of further content categories this autumn, such as foreign statutes and laws and policy material from international organizations, will, at least partially, address this limitation. Nick Campbell Although relatively few in number, imprinted loci have been of intense interest. The Gnas locus on distal mouse chromosome 2 is one of the more complex imprinted regions yet discovered, having an antisense transcript and alternatively spliced isoforms that show biallelic as well as maternaland paternal-specific expression. The parent-of-origin-specific expression of these and other imprinted genes has yielded insights into the mechanisms of gene regulation, whereas the functional role of imprinting has been one of biology’s most intriguing mysteries. Two new studies on the Gnas cluster published in Nature Genetics advance our understanding on both fronts. The Gnas locus encodes alternative transcripts that arise from 4 different promoters, with different first exons spliced to a common exon 2. Among these, Gnas encodes G s α, the α-subunit of the ubiquitous heterotrimeric G protein G s , which couples receptors to adenylyl cyclase. Although Gnas is biallelically expressed in most tissues, it is preferentially maternally expressed in the proximal tubules of the kidney and in brown and white adipose tissue. Williamson et al. have now identified a cis-acting element that regulates this tissue-specific aspect of Gnas imprinting — the first such control region to be identified. Deletion of a 2.3-Kb differentially methylated region (DMR) that encompasses exon 1A resulted in increased expression of the paternal allele in the kidney and in adipose tissue. The loss of tissue-specific silencing was confirmed by a clever functional assay, in which mice with parathyroid hormone (PTH) resistance were found to have increased G s α-mediated PTH signalling, thanks to increased GNAS production from the paternal allele. The mechanism by which the exon 1A DMR contributes to tissue-specific silencing of the paternal allele remains to be determined. Plagge et al. used a similar gene-targeting approach to examine the function of a paternally expressed Gnas transcript, Gnasxl, which encodes XLαs. Clues to the function of the various proteins encoded by the Gnas locus have come from studies of mice with targeted mutations. Mice that lack G s α die shortly after birth, with maternal and paternal transmission showing opposing effects on adipose tissue and metabolic rate. As there is no evidence for exclusive paternal expression of G s α in any tissue, attention turned to the paternally expressed GNASXL as having a distinct functional role. Plagge and colleagues found that mice in which the XLαs-specific XL domain was deleted also died soon after birth. The pups’ growth was retarded, they did not suckle and their lipid stores in adipose tissue were depleted. XLαs sites of expression — nuclei that innervate orofacial and tongue muscles, and the pituitary, pancreas and hypothalamus — are consistent with its role in the postnatal adaptation to feeding and in energy homeostasis. Notably, the XLαs-deficient phenotype provides compelling support for the parental conflict theory of imprinting, which proposes that paternal genes would increase resource uptake from the mother by offspring, and that maternal genes would restrict nutritional demands. Although this theory has received support from mice with mutations in other imprinted genes, the authors note that this is the first example in which an imprinted locus encodes two proteins that act antagonistically in postnatal physiology — regulating cyclic AMP (cAMP) production in this instance. The Gnas locus will no doubt continue to provide a unique window into the role of imprinting in negotiating the competing demands of mothers and fathers.

Splicing and evolutionary change: Evolutionary genomics

LEONARD I. ZON CHILDREN’S HOSPITAL, BOSTON, USA With the estimated number of genes in the human genome hovering at a modest 30,000, alternative splicing has received much attention as a potential amplifier of genomic complexity, albeit without direct evidence across an entire genome. In a new study in Nature Genetics, Modrek and Lee outline a bioinformatic approach that, for the first time, makes the case that alternative splicing is indeed associated with increased evolutionary change. The authors used databases of expressed sequence tags (ESTs) to compare exon–intron structure and exon sequence conservation in pairs of orthologues from the human and mouse. As expected, ~90% of the exons had identical boundaries in the two genomes, and there was a high degree of sequence similarity between matching exons. Also, for each exon, they estimated the fraction of total transcripts of a gene that include this particular exon. An alternatively spliced exon was said to be the ‘major form’ if it was included in the mature mRNA more than 50% of the time. By relating the frequency of inclusion of a particular exon to the likelihood that it would be conserved between the two genomes, the authors hit on a notable finding. Constitutive exons are almost always conserved, as are alternatively spliced exons that are classified as the major form. ‘Minor form’ exons, however, were conserved only ~25% of the time. Strikingly, the frequency of inclusion of an exon in human ESTs can predict whether it will be conserved in the mouse. Modrek and Lee note that the presence of an exon in the orthologue from one genome but not the other, could be explained by exon creation or exon loss, both occurring after the divergence of each lineage from their most recent common ancestor. Constitutive and majorform exons changed little after the divergence of the human and mouse genomes, and most minor-form alternatively spliced exons appeared since then, which indicates that alternative splicing might accompany evolutionary change. The authors propose a scenario in which a new exon with weak splice signals is added to a gene, and as a result is included in only a small fraction of the mature transcripts. As the major form is still produced in near-to-normal quantities, initially deleterious effects of adding a new exon would be neutral, leaving the minor-form free to evolve rapidly, possibly serving as an ‘internal paralogue’ and ultimately acquiring a useful function. The search is now on for alternatively spliced exons that are linked definitively to a specific instance of evolutionary novelty. Alan Packer, Acting Editor, Nature Genetics

Evolutionary genomics: Splicing and evolutionary change

LEONARD I. ZON CHILDREN’S HOSPITAL, BOSTON, USA With the estimated number of genes in the human genome hovering at a modest 30,000, alternative splicing has received much attention as a potential amplifier of genomic complexity, albeit without direct evidence across an entire genome. In a new study in Nature Genetics, Modrek and Lee outline a bioinformatic approach that, for the first time, makes the case that alternative splicing is indeed associated with increased evolutionary change. The authors used databases of expressed sequence tags (ESTs) to compare exon–intron structure and exon sequence conservation in pairs of orthologues from the human and mouse. As expected, ~90% of the exons had identical boundaries in the two genomes, and there was a high degree of sequence similarity between matching exons. Also, for each exon, they estimated the fraction of total transcripts of a gene that include this particular exon. An alternatively spliced exon was said to be the ‘major form’ if it was included in the mature mRNA more than 50% of the time. By relating the frequency of inclusion of a particular exon to the likelihood that it would be conserved between the two genomes, the authors hit on a notable finding. Constitutive exons are almost always conserved, as are alternatively spliced exons that are classified as the major form. ‘Minor form’ exons, however, were conserved only ~25% of the time. Strikingly, the frequency of inclusion of an exon in human ESTs can predict whether it will be conserved in the mouse. Modrek and Lee note that the presence of an exon in the orthologue from one genome but not the other, could be explained by exon creation or exon loss, both occurring after the divergence of each lineage from their most recent common ancestor. Constitutive and majorform exons changed little after the divergence of the human and mouse genomes, and most minor-form alternatively spliced exons appeared since then, which indicates that alternative splicing might accompany evolutionary change. The authors propose a scenario in which a new exon with weak splice signals is added to a gene, and as a result is included in only a small fraction of the mature transcripts. As the major form is still produced in near-to-normal quantities, initially deleterious effects of adding a new exon would be neutral, leaving the minor-form free to evolve rapidly, possibly serving as an ‘internal paralogue’ and ultimately acquiring a useful function. The search is now on for alternatively spliced exons that are linked definitively to a specific instance of evolutionary novelty. Alan Packer, Acting Editor, Nature Genetics