We have catalogued the protein kinase complement of the human genome (the "kinome") using public and proprietary genomic, complementary DNA, and expressed sequence tag (EST) sequences. This provides a starting point for comprehensive analysis of protein phosphorylation in normal and disease states, as well as a detailed view of the current state of human genome analysis through a focus on one large gene family. We identify 518 putative protein kinase genes, of which 71 have not previously been reported or described as kinases, and we extend or correct the protein sequences of 56 more kinases. New genes include members of well-studied families as well as previously unidentified families, some of which are conserved in model organisms. Classification and comparison with model organism kinomes identified orthologous groups and highlighted expansions specific to human and other lineages. We also identified 106 protein kinase pseudogenes. Chromosomal mapping revealed several small clusters of kinase genes and revealed that 244 kinases map to disease loci or cancer amplicons.

http://science.sciencemag.org/content/sci/298/5600/1912.full.pdf

The Protein Kinase Complement of the Human Genome

The small (40S) subunit of eukaryotic ribosomes is believed to bind initially at the capped 5'-end of messenger RNA and then migrate, stopping at the first AUG codon in a favorable context for initiating translation. The first-AUG rule is not absolute, but there are rules for breaking the rule. Some anomalous observations that seemed to contradict the scanning mechanism now appear to be artifacts. A few genuine anomalies remain unexplained.

/pdf/the-scanning-model-for-translation-an-update-52r2in8l71.pdf

The scanning model for translation: an update.

Cell-fate transitions involve the integration of genomic information encoded by regulatory elements, such as enhancers, with the cellular environment. However, identification of genomic sequences that control human embryonic development represents a formidable challenge. Here we show that in human embryonic stem cells (hESCs), unique chromatin signatures identify two distinct classes of genomic elements, both of which are marked by the presence of chromatin regulators p300 and BRG1, monomethylation of histone H3 at lysine 4 (H3K4me1), and low nucleosomal density. In addition, elements of the first class are distinguished by the acetylation of histone H3 at lysine 27 (H3K27ac), overlap with previously characterized hESC enhancers, and are located proximally to genes expressed in hESCs and the epiblast. In contrast, elements of the second class, which we term 'poised enhancers', are distinguished by the absence of H3K27ac, enrichment of histone H3 lysine 27 trimethylation (H3K27me3), and are linked to genes inactive in hESCs and instead are involved in orchestrating early steps in embryogenesis, such as gastrulation, mesoderm formation and neurulation. Consistent with the poised identity, during differentiation of hESCs to neuroepithelium, a neuroectoderm-specific subset of poised enhancers acquires a chromatin signature associated with active enhancers. When assayed in zebrafish embryos, poised enhancers are able to direct cell-type and stage-specific expression characteristic of their proximal developmental gene, even in the absence of sequence conservation in the fish genome. Our data demonstrate that early developmental enhancers are epigenetically pre-marked in hESCs and indicate an unappreciated role of H3K27me3 at distal regulatory elements. Moreover, the wealth of new regulatory sequences identified here provides an invaluable resource for studies and isolation of transient, rare cell populations representing early stages of human embryogenesis.

/pdf/a-unique-chromatin-signature-uncovers-early-developmental-i7uokufaxi.pdf

A unique chromatin signature uncovers early developmental enhancers in humans

The aim of this review is to consider the potential benefits that females may gain from mating more than once in a single reproductive cycle. The relationship between non-genetic and genetic benefits is briefly explored. We suggest that multiple mating for purely non-genetic benefits is unlikely as it invariably leads to the possibility of genetic benefits as well. We begin by briefly reviewing the main models for genetic benefits to mate choice, and the supporting evidence that choice can increase offspring performance and the sexual attractiveness of sons. We then explain how multiple mating can elevate offspring fitness by increasing the number of potential sires that compete, when this occurs in conjunction with mechanisms of paternity biasing that function in copula or post-copulation. We begin by identifying cases where females use pre-copulatory cues to identify mates prior to remating. In the simplest case, females remate because they identify a superior mate and 'trade up' genetically. The main evidence for this process comes from extra-pair copulation in birds. Second, we note other cases where pre-copulatory cues may be less reliable and females mate with several males to promote post-copulatory mechanisms that bias paternity. Although a distinction is drawn between sperm competition and cryptic female choice, we point out that the genetic benefits to polyandry in terms of producing more viable or sexually attractive offspring do not depend on the exact mechanism that leads to biased paternity. Post-copulatory mechanisms of paternity biasing may: (1) reduce genetic incompatibility between male and female genetic contributions to offspring; (2) increase offspring viability if there is a positive correlation between traits favoured post-copulation and those that improve performance under natural selection; (3) increase the ability of sons to gain paternity when they mate with polyandrous females. A third possibility is that genetic diversity among offspring is directly favoured. This can be due to bet-hedging (due to mate assessment errors or temporal fluctuations in the environment), beneficial interactions between less related siblings or the opportunity to preferentially fertilise eggs with sperm of a specific genotype drawn from a range of stored sperm depending on prevailing environmental conditions. We use case studies from the social insects to provide some concrete examples of the role of genetic diversity among progeny in elevating fitness. We conclude that post-copulatory mechanisms provide a more reliable way of selecting a genetically compatible mate than pre-copulatory mate choice. Some of the best evidence for cryptic female choice by sperm selection is due to selection of more compatible sperm. Two future areas of research seem likely to be profitable. First, more experimental evidence is needed demonstrating that multiple mating increases offspring fitness via genetic gains. Second, the role of multiple mating in promoting assortative fertilization and increasing reproductive isolation between populations may help us to understand sympatric speciation.

Why do females mate multiply? A review of the genetic benefits.

The transcriptional profiles of mouse embryonic, neural, and hematopoietic stem cells were compared to define a genetic program for stem cells. A total of 216 genes are enriched in all three types of stem cells, and several of these genes are clustered in the genome. When compared to differentiated cell types, stem cells express a significantly higher number of genes (represented by expressed sequence tags) whose functions are unknown. Embryonic and neural stem cells have many similarities at the transcriptional level. These results provide a foundation for a more detailed understanding of stem cell biology.

https://science.sciencemag.org/content/sci/298/5593/597.full.pdf

"Stemness": Transcriptional Profiling of Embryonic and Adult Stem Cells

1. An introduction to mice 2. Town mouse, country mouse 3. Laboratory mice 4. Reproduction and breeding 5. The mouse genome 6. Mutagenesis and transgenesis 7. Mapping in the mouse: An overview 8. Genetic markers 9. Classical linkage analysis and mapping panels 10. Non-breeding mapping strategies Appendices A. Suppliers of mice B. Computational tools and electronic databases C. Source materials for further reading D. Statistics E. Glossary

Mouse Genetics: Concepts and Applications

A novel family of genes, charac- terized by the presence of a region of homology to the DNA-binding domain of the Brachyury (2') lo- cus product, has recently been identified. The re- gion of homology has been named the T-box, and the new mouse genes that contain the T-box do- main have been named T-box 1-6 (Tbxl through TbxG). As the basis for further study of the func- tion and evolution of these genes, we have exam- ined the expression of 5 of these genes, Tbxl- Tbx5, across a wide range of embryonic stages from blastocyst through gastrulation and early or- ganogenesis by in situ hybridization of whole- mounts and tissue sections. Tbx3 is expressed ear- liest, in the inner cell mass of the blastocyst. Four of the genes are expressed in different compo- nents of the mesoderm or mesodedendoderm during gastrulation (Tbxl and Tbx3-5). All of these genes have highly specific patterns of ex- pression during later embryogenesis, notably in areas undergoing inductive tissue interactions. In several cases there is complementary expression of different genes in 2 interacting tissues, as in the lung epithelium (Tbxl) and lung mesenchyme (Tbx2-5), and in mammary buds (Tbx3) and mam- mary stroma (Tbx2). Tbxl shows very little over- lap in the sites of expression with the other 4 genes, in contrast to a striking similarity in ex- pression between members of the 2 cognate gene sets, Tbx21Tbx3 and Tbx4lTbx5. This is a clear re- flection of the evolutionary relationship between the 5 genes since the divergence of Tbxl occurred long before the relatively recent divergence of Tbx2 and 3 and Tbx4 and 5 from common ances- tral genes. These studies are a good indication that the T-box family of genes has important roles in inductive interactions in many stages of mam- malian embryogenesis.

Expression of the T-box family genes, Tbx1-Tbx5, during early mouse development.

Recombinant inbred (RI) strains are an important resource for mapping complex traits in many species. While large RI panels are available for Arabidopsis, maize, C. elegans, and Drosophila, mouse RI panels typically consist of fewer than 30 lines. This is a severe constraint on the power and precision of mapping efforts and greatly hampers analysis of epistatic interactions. In order to address these limitations and to provide the community with a more effective collaborative RI mapping panel we generated new BXD RI strains from two independent advanced intercrosses (AI) between C57BL/6J (B6) and DBA/2J (D2) progenitor strains. Progeny were intercrossed for 9 to 14 generations before initiating inbreeding, which is still ongoing for some strains. Since this AI base population is highly recombinant, the 46 advanced recombinant inbred (ARI) strains incorporate approximately twice as many recombinations as standard RI strains, a fraction of which are inevitably shared by descent. When combined with the existing BXD RI strains, the merged BXD strain set triples the number of previously available unique recombinations and quadruples the total number of recombinations in the BXD background. The combined BXD strain set is the largest mouse RI mapping panel. It is a powerful tool for collaborative analysis of quantitative traits and gene function that will be especially useful to study variation in transcriptome and proteome data sets under multiple environments. Additional strains also extend the value of the extensive phenotypic characterization of the previously available strains. A final advantage of expanding the BXD strain set is that both progenitors have been sequenced, and approximately 1.8 million SNPs have been characterized. This provides unprecedented power in screening candidate genes and can reduce the effective length of QTL intervals. It also makes it possible to reverse standard mapping strategies and to explore downstream effects of known sequence variants.

/pdf/a-new-set-of-bxd-recombinant-inbred-lines-from-advanced-387pn4qcjj.pdf

A new set of BXD recombinant inbred lines from advanced intercross populations in mice

A novel family of transcription factors that appears to play a critical role in the development of all animal species was recently uncovered on the basis of homology of the DNA binding domain of the Brachyury, or T locus, gene product. Phylogenetic studies have shown the ancient origin of this gene family, which has been named the T-box family, prior to the divergence of metazoa from a common ancestral type. T-box genes have now been identified in the genomes of C. elegans, Drosophila, sea urchin, ascidian, amphioxus, Xenopus, chick, zebrafish, mouse, and human and will probably be found in the genomes of all animals. Although functional analyses of T-box family members have just begun, the results show a wide range of roles in developmental processes that extend over time from the unfertilized egg through organogenesis. Only a few mutations in T-box genes are known, but all have drastic effects on development, including a targeted mutation in mice causing an embryonic lethal phenotype, and two human T-box gene mutations that results in developmental syndromes. This review presents a current overview of progress made in the analysis of T-box genes and their products in a variety of model systems.

The T-box gene family.

The precursors of several organs reside within the lateral plate mesoderm of vertebrate embryos. Here, we demonstrate that the zebrafish hands off locus is essential for the development of two structures derived from the lateral plate mesoderm - the heart and the pectoral fin. hands off mutant embryos have defects in myocardial development from an early stage: they produce a reduced number of myocardial precursors, and the myocardial tissue that does form is improperly patterned and fails to maintain tbx5 expression. A similar array of defects is observed in the differentiation of the pectoral fin mesenchyme: small fin buds form in a delayed fashion, anteroposterior patterning of the fin mesenchyme is absent and tbx5 expression is poorly maintained. Defects in these mesodermal structures are preceded by the aberrant morphogenesis of both the cardiogenic and forelimb-forming regions of the lateral plate mesoderm. Molecular analysis of two hands off alleles indicates that the hands off locus encodes the bHLH transcription factor Hand2, which is expressed in the lateral plate mesoderm starting at the completion of gastrulation. Thus, these studies reveal early functions for Hand2 in several cellular processes and highlight a genetic parallel between heart and forelimb development.

Lee M. Silver

Papers

Mouse Genetics: Concepts and Applications

Expression of the T-box family genes, Tbx1-Tbx5, during early mouse development.

A new set of BXD recombinant inbred lines from advanced intercross populations in mice

The T-box gene family.

The bHLH transcription factor hand2 plays parallel roles in zebrafish heart and pectoral fin development