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To link to full-text access for this article, visit this link: http://dx.doi.org/10.1016/j.ydbio.2007.12.011 Byline: Takayoshi Inoue (a)(b), Yukiko U. Inoue (a), Junko Asami (a), Hitomi Izumi (a), Shun Nakamura (a), Robb Krumlauf (b) Keywords: Cdh6 (cadherin-6); Mouse; Gene regulation; BAC; Transposon; Homologous recombination; Forebrain; Hindbrain; Compartment; Neural crest cells Abstract: Classic cadherins are cell adhesion molecules whose expression patterns are dynamically modulated in association with their diverse functions during morphogenesis. The large size and complexity of cadherin loci have made it a challenge to investigate the organization of cis-regulatory modules that control their spatiotemporal patterns of expression. Towards this end, we utilized bacterial artificial chromosomes (BACs) containing the Cdh6 gene, a mouse type II classic cadherin, to systematically identify cis-regulatory modules that govern its expression. By inserting a lacZ reporter gene into the Cdh6 BAC and generating a series of modified variants via homologous recombination or transposon insertions that have been examined in transgenic mice, we identified an array of genomic regions that contribute to specific regulation of the gene. These regions span [approximately equal to]350 kb of the locus between 161-kb upstream and 186-kb downstream of the Cdh6 transcription start site. Distinct modules independently regulate compartmental expression (i.e. forebrain, hindbrain rhombomeres, and spinal cord) and/or cell lineage-specific expression patterns (i.e. neural crest subpopulations such as Schwann cells) of Cdh6 at the early developmental stages. With respect to regulation of expression in neural crest cells, we have found that distinct regions contribute to different aspects of expression and have identified a short 79-bp region that is implicated in regulating expression in cells once they have emigrated from the neural tube. These results build a picture of the complex organization of Cdh6 cis-regulatory modules and highlight the diverse inputs that contribute to its dynamic expression during early mouse embryonic development. Author Affiliation: (a) Department of Biochemistry and Cellular Biology, National Institute of Neuroscience, National Center of Neurology and Psychiatry, Ogawahigashi 4-1-1, Kodaira, Tokyo 187-8502, Japan (b) Stowers Institute for Medical Research, 1000 East, 50th Street, Kansas City, MO 64110, USA Article History: Received 29 June 2007; Revised 5 November 2007; Accepted 9 December 2007

To link to full-text access for this article, visit this link: http://dx.doi.org/10.1016/j.ydbio.2007.03.020 Byline: Federico Gonzalez, Denis Duboule, Francois Spitz Keywords: Hox genes; Global and shared enhancers; Regulatory landscapes; Limb morphogenesis; Evolution of gene regulation Abstract: In tetrapods, posterior Hoxd genes (from groups 10 to 13) are necessary to properly pattern the developing autopods, including the number and identities of digits. Their coordinated expression is achieved by sharing a global control region (GCR), which was isolated and localized 200 kb 5' (centromeric) of the gene cluster. However, in transgenic assays, the GCR was unable to fully recapitulate all aspects of the endogenous Hoxd expression patterns during distal limb development. In this paper, we further analyze the regulatory potential of this locus and report the characterization of Prox, a second enhancer element that contributes to the transcriptional activity of posterior Hoxd genes in developing distal limb buds. We show that the GCR and Prox elements complement each other and work in combination to correctly establish the late phase of Hoxd genes expression. Based on DNA sequence conservation and transgenic assays, we discuss the functions of these regulatory regions as well as a potential evolutionary scheme accounting for their emergence along with the evolution of tetrapod limbs. Author Affiliation: National Center for Competence in Research 'Frontiers in Genetics', Department of Zoology and Animal Biology, University of Geneva, Sciences III, Quai Ernest Ansermet 30, 1211 Geneva 4, Switzerland Article History: Received 11 January 2007; Revised 27 February 2007; Accepted 19 March 2007

The human [beta]-globin locus has been extensively studied as a model of tissue and developmental stage-specific gene expression. Structural mapping of naturally occurring mutations, including transfection and transgenic studies, and the recent finding of intergenic transcripts have suggested that there are cis-acting sequence elements in the [sup.A.[gamma]]-[delta] intergenic region involved in regulating [gamma]- and [beta]-globin gene expression. To determine whether previously identified sequences in the [sup.A.[gamma]]-[delta] intergenic region are required for appropriate developmental expression of the human [beta]-globin gene cluster, transgenic mice were generated by transfer of yeast artificial chromosomes containing the entire human [beta]-globin locus. Three different deletions of the [sup.A.[gamma]]-[delta]] intergenic region were introduced, including (i) deletion of the 750-bp [sup.A.[gamma]] 3' regulatory element ([sup.A.[gamma]]e), (ii) deletion of 3.2 kb upstream of the [delta]-globin gene encompassing pyrimidine-rich sequences and the recently described intergenic transcript initiation site, and (iii) deletion of a 12.5-kb fragment encompassing most of the [sup.A.[gamma]-[delta] globin intergenic region. Analysis of multiple transgenic lines carrying these deletion constructs demonstrated that the normal stage-specific sequential expression of the [epsilon]-, [gamma]-, and [beta]-globin genes was preserved, despite deletion of these putative regulatory sequences. These studies suggest that regulatory sequences required for activation and silencing of the human [beta]-globin gene family during ontogeny reside proximally to the genes and immediately 5' to the human [gamma]- and [beta]-globin genes.

The transcription factor absent, small, or homeotic discs 2 (ash2) gene is a member of the trithorax group of positive regulators of homeotic genes. Mutant alleles for ash2 are larval/pupal lethals and display imaginal disc and brain abnormalities. The allele used in this study is a true mutant for the trithorax function and lacks the longest transcript present in wild-type flies. In an attempt to identify gene targets of ash2, we have performed an expression analysis by using cDNA microarrays. Genes involved in cell cycle, cell proliferation, and cell adhesion are among these targets, and some of them are validated by functional and expression studies. Even though trithorax proteins act by modulating chromatin structure at particular chromosomal locations, evidence of physical aggregation of ash2-regulated genes has not been found. This work represents the first microarray analysis, to our knowledge, of a trithorax-group gene.

Regulation of physiological functions with approximate daily periodicity, or circadian rhythms, is a characteristic feature of eukaryotes. Until recently, cyanobacteria were the only prokaryotes reported to possess circadian rhythmicity. It is controlled by a cluster of three genes: kaiA, kaiB, and kaiC. Using sequence data of [approximately equal to] 70 complete prokaryotic genomes from the various public depositories, we show here that the kai genes and their homologs have quite a different evolutionary history and occur in Archaea and Proteobacteria as well. Among the three genes, kaiC is evolutionarily the oldest, and kaiA is the youngest and likely evolved only in cyanobacteria. Our data suggest that the prokaryotic circadian pacemakers have evolved in parallel with the geological history of the earth, and that natural selection, multiple lateral transfers, and gene duplications and losses have been the major factors shaping their evolution.

Research has been conducted on srr1, an Arabidopsis mutant altered in circadian clock outputs. The cloning of SRR1 gene demonstrates that it codes for proteins with homologs in different eukaryotes and that it may encode a circadian clock regulator conserved between plants and animals.

Mutations at the mouse microphthalmia locus (Mitf) affect the development of different cell types, including melanocytes, retinal pigment epithelial cells of the eye, and osteoclasts. The MITF protein is a member of the MYC supergene family of basic-helix-loop-helix-leucine-zipper (bHLHZip) transcription factors and is known to regulate the expression of cell-specific target genes by binding DNA as homodimer or as heterodimer with related proteins. The many mutations isolated at the locus have different effects on the phenotype and can be arranged in an allelic series in which the phenotypes range from near normal to white microphthalmic animals with osteopetrosis. Previous investigations have shown that certain combinations of Mitf alleles complement each other, resulting in a phenotype more normal than that of each homozygote alone. Here we analyze this interallelic complementation in detail and show that it is limited to one particular allele, [Mitf.sup.Mi-white] ([Mitf.sup.Mi-wh]), a mutation affecting the DNA-binding domain. Both loss- and gain-of-function mutations are complemented, as are other Mitf mutations affecting the DNA-binding domain. Furthermore, this behavior is not restricted to particular cell types: Both eye development and coat color phenotypes are complemented. Our analysis suggests that [Mitf.sup.Mi-wh]-associated interallelic complementation is due to the unique biochemical nature of this mutation.

The transcription factors WHITE COLLAR-1 (WC-1) and WHITE COLLAR-2 (WC-2) interact to form a heterodimeric complex (WCC) that is essential for most of the light-mediated processes in Neurospora crassa. WCC also plays a distinct non-light-related role as the transcriptional activator in the FREQUENCY (FRQ)/WCC feedback loop that is central to the N. crassa circadian system. Although an activator role was expected for WC-1, unanticipated phenotypes resulting from some wc-1 alleles prompted a closer examination of an allelic series for WC-1 that has uncovered roles for this central regulator in constant darkness and in response to light. We analyzed the phenotypes of five different wc-1 mutants for expression of FRQ and WC-1 in constant darkness and following light induction. While confirming the absolute requirement of WC-1 for light responses, the data suggest multiple levels of control for light-regulated genes.

Members of the R/B basic helix-loop-helix (bHLH) family of plant transcription factors are involved in a variety of growth and differentiation processes. We isolated a dominant mutation in an R/B-related bHLH transcription factor in the course of studying Arabidopsis tryptophan pathway regulation. This mutant, atr2D, displayed increased expression of several tryptophan genes as well as a subset of other stress-responsive genes. The atr2D mutation creates an aspartate to asparagine change at a position that is highly conserved in R/B factors. Substitutions of other residues with uncharged side chains at this position also conferred dominant phenotypes. Moreover, overexpression of mutant atr2D, but not wild-type ATR2, conferred pleiotropic Effects, including reduced size, dark pigmentation, and sterility. Therefore, atr2D is likely to be an altered-function allele that identifies a key regulatory site in the R/B factor coding sequence. Double-mutant analysis with atr1D, an overexpression allele of the ATR1 Myb factor previously isolated in tryptophan regulation screens, showed that atr2D and atr1D have additive effects on tryptophan regulation and are likely to act through distinct mechanisms to activate tryptophan genes. The dominant atr mutations thus provide tools for altering tryptophan metabolism in plants.

Oligomerization of the 47-amino-acid beta(sub)ps is enough to begin a signaling pathway that regulates gene expression. Research with Drosophila embryos has shown integrin-mediated cell adhesion is not necessary between endodermal cells and the surrounding mesoderm to permit integrin target gene expression.

Research has been conducted on Spen proteins which regulate transcriptional effector expression in diverse signaling pathway. Results demonstrate that these proteins play important role in the transcriptional repression complex in both nuclear receptor and Notch signaling pathways.

Research has been conducted on heterochromodomain protein 1 which is required for stable epigenetic gene silencing. The authors report that the recruitment of mammalian heterochromodomain protein 1 to the euchromatic promoter establishes the epigenetically heritable silenced state.

Research has been conducted on serine/threonine kinase Pim-2. The authors reveal that Pim-2 is a direct link between growth factor-induced transcription and kinase-dependent pathway which promotes cell-autonomous survival.

The authors analyzes the study on cell survival regulation. The topics of interest include the role of serine/threonine kinase Pim-2 in growth factor-mediated apoptotic resistance in hematopoeitic cells.

Research has been conducted on B-lymphocyte development which involves DNA rearrangements of immunoglobulin heavy and light chain loci. The authors report that B-cell development is arrested at the cycling pre-B-cell stage, and they propose that interferon regulatory factors-4,8 function as genetic switch to down-regulate surrogate light-chain gene expression and induce conventional light-chain gene transcription.

The author reviews the publications on RNA polymerase I transcription regulation in the nucleolus. The topics of interest include the initiation complex formation mechanism at the rDNA promoter, and the regulatory pathways adapting cellular rRNA synthesis to cell growth and metabolism.

Research has been conducted on protein kinase C involved in Wnt signaling pathway. The authors report the identification of the genes encoding sigma-type protein kinase C in the Xenopus EST databases, and that this protein kinase C sigma regulates the activity and localization of Dishevelled.

Research has been conducted on RAD23. The authors report that RAD23 participates in DNA repair, and describe the DNA-damage-dependent regulation mechanism of DNA repair in eukaryotes.

Research has been conducted on chromatin structure which is important for the transcription regulation. The authors report that Drosophila FACT (facilitates chromatin transcription) is associated with GAGA factor via its subunit, binds to nucleotide and facilitates GAGA factor-directed chromatin remodeing.

Research has been conducted on Schizosaccharomyces pombe spindle pole component Cut12 which suppresses conditional lethal commitment defect. Results demonstrate that Cut12 associates with Plo1 in hybrid and immunoprescipitation assays.

Research has been conducted on Polycomb-group protein MEDEA which regulates Arabidopsis seed development via embryo and endosperm proliferation. Results demonstrate that seed abortion in the medea mutant is caused by deregulated expression of the type I MADS-box gene PHE1.

Research has been conducted on cyclin-dependent kinase Cdc28. The role of this kinase has been investigated via inhibition of its activity using conditional mutants which are sensitive to chemical inhibitors, and the results are reported.

Research has been conducted on mRNA-binding protein CPEB which stimulates translation of maternal mRNA. The authors demonstrate that CPEB undergoes phosphorylation at E16.5 and dephosphorylation at E18.5 when oocytes enter diplotene.

Research has been conducted on homologous yeast protein Epl1, found in NuA4 histone acetyltransferase complex and a smaller complex picNuA4 which contains Esa1, Epl1 and Yng2 as subunits. The authors suggest that essential aspect of Esa1 and Epl1 is in picNuA4 function, and that picNuA4 is a nontargeted histone acetyltransferase activity responsible for global acetylation.

Research has been conducted on DSIF and NELF which collaborate to inhibit elongation by RNA polymerase in human cell extracts. The roles of DSIF and NELF in promoter proximal pausing regulation at hsp70 promoter in Drosophila has been investigated, and the results are reported.

Research has been conducted on chromatin-remodeling activities in transcription. The role of these activities has been investigated in order to understand their interactions with transcriptional activators and their regulation of different transcription steps, and the results are reported.

Research has been conducted on Schwann cell development. The authors demonstrate that in a developmental profile these cells express Brn-2 similar to that of Oct-6, and that Brn-2 function overlaps with that of Oct-6 during the transition from promyelinating to myelinating Schwann cells.

Research has been conducted on Akt1 and Akt2 double-knockout mice which exhibit growth deficiency, impaired skin development and severe muscle atrophy. The authors suggest that Akt may be the most critical downstream effector of the IGF-1 receptor during development.

Research has been conducted on artery formation. The authors have utilized transgenic zebrafish with fluorescently labeled blood vessels to identify and characterize the mutant displaying specific defects in artery formation, and have described the results.

Research has been conducted on MSL proteins and noncoding roX RNAs which up-regulate genes on the Drosophila male X chromosome. The authors describe the model of MSL complex distribution, and report that when overexpressed, MSL proteins can recognize X chromosome, partially restore male viability in the absense of roX RNAs and modify histones.

Research has been conducted on DNA-binding protein TRF1 which is telomere length's negative regulator. The authors demonstrate that the loss of TRF1 from telomeres leads to degradation and ubiquitination of TRF1 by proteasome, and that the degradation is important for keeping TRF1 off telomeres.

The authors review the publications on transcription initiation. The topics of interest include the ability of tissue-specific and gene-selective core promoter complexes to regulate expressed genes responsible for such biological functions as DNA replication, germ cell maturation and organ development.

Research has been conducted on Hedgehog signaling which is critical for many developmental events. The authors demonstrate that Drosophila salinary gland cells are responsive to Hedgehog signaling and have been used to study the regulation of the intracellular movements of Smoothened protein occurring in response to Hedgehog signaling.

Research has been conducted on coiled-coil protein LIN-5 from Caenorhabditis elegans. The authors describe the related proteins G protein regulator 1 (GPR-1) and GPR-2 which depend on LIN-5 protein for localization to the spindle and cell cortex.

Research has been conducted on left-right asymmetry generation in the vertebrate body. The authors demonstrate that Notch signaling is important for the asymmetry establishment in mice carrying it out via Nodal gene expression regulation.

Research has been conducted on genetic transcription at the onset of Bacillus subtilis sporulation which is regulated by Spo0A. The authors report that Spo0A functions after the intitial sporulation phase, and that it becomes a cell-specific transcription factor when sporangium is divided onto a forespore and mother cell.

Research has been conducted on axillary meristem. The authors have investigated this meristem formation by Arabidopsis thaliana LATERAL SUPPERSSOR gene, and they present the results.

Research has been conducted on transcription factor Myc which regulates downstream cellular responses. The authors have investigated a large-scale sceen for genomic Myc-binding sites in human cells via the use of bioinformatics, and they report that there is high regulatory and biological diversity among Myc-target genes.

Research has been conducted on signalosomes which regulate cullin-dependent ubiquitin ligases. The authors demonstrate that signalosome subunits are required to regulate ribonucleoside reductase via small protein degradation.

Research has been conducted on DNA-damage response gene upregulation when LexA repressor undergoes autocatalytic cleavage. The authors demonstrate the LexA fragments are the substrates for ClpXP protease.

Research has been conducted on tobacco protein kinase NPK1 which is mitogen-activated protein kinase kinase kinase (MAPKKK) regulating cell plate formation during cytokinesis. The authors report the identification of tobacco NQK1/NtMEK1 and NPK1 as mitogen-activated protein kinase kinase (MAPKK) and mitogen-activated protein kinase (MAPK) doenstream of NPK1.

Research has been conducted on the CBF family of transcription factors triggered by cold temperatures. The authors report the identification of upstream transcription factor ICE1 (inducer of CBF expression 1) which regulates CBF gene transcription in the cold.

Research has been conducted on histone methylation which plays important role in eukaryotic gene expression regulation. Results demonstrate that histone methylation is a targeted event, and that it provides a mechanism by which histone methyltransferases could activate gene expression.

Research has been conducted on beta-globin. The authors describe their study of beta-globin gene activation molecular basis performed via the analysis of the factor recruitment and histone modification at the adult beta-globin gene.

Research has been conducted on Caenorhabditis elegans micoRNAs which may regulate protein-coding gene expression in animals and plants. The authors report the results of the computational investigation carried out in the effort to identify micoRNA genes conserved in more than one genome.

Research has been conducted on XOL-1 protein from Caenorhabditis elegans, a GHMP kinase family member. The role of GHMP kinase family members in mediating sexual differentiation, dosage compensation and other aspects of development has been investigated, and the details are reported.

Research has been conducted on SCL protein expression. The translational regulation of this expression and its role in hematopoietic lineage choice have been investigated, and the results are reported.