bluuebunny/crossref_metadata_2025 huggingface dataset:
Direct recognition of initiator elements by a component of the transcription factor IID complex.
Authors: Kaufmann J , Smale S T
Published: June 2007

A core promoter element called an initiator (Inr) overlaps the transcription start site of numerous mammalian protein-coding genes. In promoters that lack a TATA box, the Inr is functionally analogous to TATA, in that it is capable of directing basal transcription by RNA polymerase II and of determining the precise site of transcription initiation. In promoters that contain a TATA box, the Inr can greatly enhance promoter strength. Mammalian Inr consensus sequences have been defined through functional studies and sequence comparisons of the start site regions of protein-coding genes. Here, we show that, in a DNase I footprinting assay with synthetic promoters, the purified TATA-binding protein complex TFIID specifically contacted the Inr. The TFIID-Inr interaction relies on the precise nucleotides needed for Inr function. Detection of the interaction was dependent either on a TATA box or on Sp1 bound to upstream sites. Furthermore, recombinant TFIIB appeared to influence the TFIID-Inr interaction, whereas TFIIA stabilized the TFIID-TATA interaction. These results demonstrate that distinct components of TFIID interact with the TATA boxes and Inr elements of core promoters for RNA polymerase II.
TFIID sequence recognition of the initiator and sequences farther downstream in Drosophila class II genes.
Authors: Purnell B A , Emanuel P A , Gilmour D S
Published: June 2007

Immunopurified TFIID produces a large DNase I footprint over the hsp70, hsp26, and histone H3 promoters of Drosophila. These footprints span from the TATA element to a position approximately 35 nucleotides downstream from the transcription start site. Using a "missing nucleoside" analysis, four regions within the three promoters have been found to be important for TFIID binding: the TATA element, the initiator, and two regions located approximately 18 and 28 nucleotides downstream of the transcription start site. On the basis of the missing nucleoside data, the initiator appears to contribute as much to the affinity as the TATA element. However, there is weak conservation of the sequence in this region. To determine whether a preferred binding sequence exists in the vicinity of the initiator, the nucleotide composition of this region within the hsp70 promoter was randomized and then subjected to selection by TFIID. After five rounds of selection, the preferred sequence motif--G/A/T C/TAT/GTG--emerged. This motif is a close match to consensus sequences that have been derived by comparing the initiator region of numerous insect promoters. Selection of this sequence demonstrates that sequence-specific interactions downstream of the TATA element contribute to the interaction of TFIID on a wide spectrum of promoters.
Molecular cloning and functional analysis of the adenovirus E1A-associated 300-kD protein (p300) reveals a protein with properties of a transcriptional adaptor.
Authors: Eckner R , Ewen M E , Newsome D , Gerdes M , DeCaprio J A , Lawrence J B , Livingston D M
Published: June 2007

The growth-controlling functions of the adenovirus E1A oncoprotein depend on its ability ot interact with a set of cellular proteins. Among these are the retinoblastoma protein, p107, p130, and p300. We have isolated a cDNA encoding full-length human p300 and mapped the chromosomal location of the gene to chromosome 22q13. p300 contains three cysteine- and histidine-rich regions of which the most carboxy-terminal region interacts specifically with E1A. In its center, p300 contains a bromodomain, a hallmark of certain transcriptional coactivators. We have examined the ability of p300 to overcome the repressive effect of E1A on the SV40 enhancer. We show that p300 molecules lacking an intact E1A-binding site can bypass E1A repression and restore to a significant extent the activity of the SV40 enhancer, even in the presence of high levels of E1A protein. These results imply that p300 may function as a transcriptional adaptor protein for certain complex transcriptional regulatory elements.
The Drosophila sex determination gene snf encodes a nuclear protein with sequence and functional similarity to the mammalian U1A snRNP protein.
Authors: Flickinger T W , Salz H K
Published: June 2007

Alternative splicing controls the expression of many genes, including the Drosophila sex determination gene Sex-lethal. Previous studies have suggested that snf plays a role in regulating Sex-lethal splicing. Here, we demonstrate that snf is an integral component of the machinery required for splice site recognition. We have cloned snf and found that it has sequence homology to the mammalian U1A and U2B" snRNP proteins. Moreover, we establish that snf encodes a Drosophila protein shown previously to have functional similarity to U1A. Finally, with the isolation and analysis of a null mutation, we demonstrate that snf is an essential gene. These studies provide the first demonstration, in a multicellular organism, that mutations in a U1 snRNP protein alter splicing in vivo.
repo encodes a glial-specific homeo domain protein required in the Drosophila nervous system.
Authors: Xiong W C , Okano H , Patel N H , Blendy J A , Montell C
Published: June 2007

We report the identification of a Drosophila locus, reversed polarity (repo). Weak repo alleles were viable but affected glia in the optic lobe, resulting in a reversal in polarity of the electrophysiological to light in the adult. Strong repo alleles caused defects in embryonic glia and resulted in embryonic lethality. Expression of repo appeared to be specific to glia throughout development. In the adult visual system, repo was expressed in laminal glia, medullar glia, and subretinal cells; in the embryo, repo was expressed in nearly all of the identified glia in the central and peripheral nervous systems except midline glia. The repo gene encoded a homeo domain protein suggesting that it might be a transcriptional regulator of genes required for glial development.
Influence of immunoglobulin heavy- and light-chain expression on B-cell differentiation.
Authors: Young F , Ardman B , Shinkai Y , Lansford R , Blackwell T K , Mendelsohn M , Rolink A , Melchers F , Alt F W
Published: June 2007

To study the influence of immunoglobulin heavy-chain (HC) and light-chain (LC) expression in promoting B-cell differentiation, we have introduced functional immunoglobulin HC and/or LC transgenes into the recombinase activating gene-2-deficient background (RAG-2-/-). RAG-2-/- mice do not undergo endogenous V(D)J rearrangement events and, therefore, are blocked in B- and T-cell development at the early pro-B- and pro-T-cell stages. Introduction of immunoglobulin HC transgenes into the RAG-2-/- background promotes the development of a B-lineage cell population that phenotypically has the characteristics of pre-B cells. We have shown further that this population has altered growth characteristics as measured by interleukin-7 responsiveness in culture. Bone marrow cells from immunoglobulin HC transgenic RAG-2-/- mice have up-regulated expression of germ-line kappa LC gene transcripts and down-regulated expression of lambda 5 surrogate LCs (SLCs). Although mu HC/SLC complexes are detectable intracellularly in HC/RAG-2-/- pre-B-cell populations, HC expression is not readily detectable on the surface of these cells. lambda LC RAG-2-/- mice had a bone marrow B-lineage cell phenotype indistinguishable from that of RAG-2-/- littermates, indicating that LC expression by itself has no influence on pro-B cell differentiation. Strikingly, simultaneous introduction of mu HC and lambda LC transgenes into RAG-2-/- mice led to the generation of a substantial population of "monoclonal" peripheral B-cells that were functional with regard to immunoglobulin secretion, indicating that T cells or diverse immunoglobulin repertoires are not necessary for peripheral B-cell development.
G1 cyclins CLN1 and CLN2 repress the mating factor response pathway at Start in the yeast cell cycle.
Authors: Oehlen L J , Cross F R
Published: June 2007

Transcriptional induction by the mating pheromone alpha-factor was monitored at different stages of the yeast cell cycle. G2/M-phase and pre-Start cells showed strong FUS1 mRNA induction, whereas in post-Start cells the signaling was reduced significantly. This reduction in signaling activity in post-Start cells was correlated with the presence of CLN1 or CLN2 transcripts and was not observed in synchronized cells lacking functional CLN1 and CLN2 genes. Activation of the Cln-Cdc28p kinase by overexpression of CLN2 from the GAL1 promoter strongly reduced FUS1 mRNA induction. CLN1 overexpression had a similar effect when the FAR1 gene, encoding a negative regulator of CLN1/2 function, was deleted. This reduction of pheromone signaling was specific for CLN1 and CLN2, as it was not observed when CLN3 was overexpressed. Inactivation of the Cln-Cdc28p kinase complex by thermal inactivation of temperature-sensitive Cdc28p prevented repression of FUS1 signaling. CLN2 overexpression suppressed the constitutive signaling and division-arrest phenotypes of cells with a disrupted gpa1 gene, indicating that the site of action for repression is downstream of the alpha-subunit (Gpa1p) of the heterotrimeric G protein. The repression at Start of pheromone signaling by Cln1-Cdc28p or Cln2-Cdc28p kinase complexes may contribute to the acquisition of pheromone resistance as cells execute Start.
Randomization-selection analysis of snRNAs in vivo: evidence for a tertiary interaction in the spliceosome.
Authors: Madhani H D , Guthrie C
Published: June 2007

Putative components of the spliceosomal active site include a bulged helix between U2 and U6 snRNAs (U2-U6 helix I) and the adjacent ACAGAG hexanucleotide in U6. We have developed an in vivo, bimolecular randomization-selection method to functionally dissect these elements. Although a portion of U2-U6 helix I resembles the G-binding site of group I introns, the data are inconsistent with an analogous functional role for this structure in the spliceosome. Instead, analysis of several novel covariants supports the existence of a structure in which the helix I bulge engages in a tertiary interaction with the terminal residue of the U6 hexanucleotide (ACAGAG). Such a higher order structure, together with other known interactions, would juxtapose the two clusters of residues of the U2-U6 complex that are specifically required for the second chemical step of pre-mRNA splicing with the 3' splice site. Indeed, mutations in the residues that participate in the tertiary interaction affect both the efficiency and fidelity of 3' splice site usage.
Intron creation and polyadenylation in maize are directed by AU-rich RNA.
Authors: Luehrsen K R , Walbot V
Published: June 2007

Intron recognition in Angiosperms is hypothesized to require AU-rich motifs within introns. In this report we examined the role of AU-rich motifs in pre-mRNA processing. AU-rich segments of maize introns inserted near the single intron of the maize Bronze-2(Bz2) gene result in alternative splicing. Other insertions of AU-rich sequence in the Bz2 cDNA resulted in de novo intron creation using splice junctions at the edges of the AU-rich region. Surprisingly, the five AU-rich inserts that we tested also caused polyadenylation, even though none had been selected for that function in plants. Insertions of GC-rich sequence into Bz2 did not cause either splicing or polyadenylation. We propose that AU-rich motifs are a general signal for RNA processing in maize and that in the absence of a 5' splice site, polyadenylation is the default pathway.
Targeted disruption of the murine VCAM1 gene: essential role of VCAM-1 in chorioallantoic fusion and placentation.
Authors: Gurtner G C , Davis V , Li H , McCoy M J , Sharpe A , Cybulsky M I
Published: June 2007

Vascular cell adhesion molecule-1 (VCAM-1) is expressed on vascular endothelium in a variety of inflammatory conditions and mediates leukocyte recruitment from blood into tissues. In this study we report a novel role for VCAM-1 in the formation of the umbilical cord and placenta during development. The murine VCAM1 gene was disrupted by targeted homologous recombination, and a distinct phenotype was found in VCAM-1-deficient embryos. At 8.5 days of gestation, the allantois failed to fuse to the chorion, resulting in abnormal placental development and embryonic death within 1-3 days. In addition, a role for VCAM-1 in early placental formation after chorioallantoic fusion was observed. In a minority of VCAM-1-deficient embryos, the allantois was able to fuse with the chorion, but the allantoic mesoderm was abnormally distributed over the chorionic surface. A small number of VCAM-1-deficient embryos survived, presumably by circumventing the placentation defects. They became viable and fertile adult mice with lack of VCAM-1 expression, normal organs, and an elevated number of circulating blood mononuclear leukocytes.
Genetic interaction between hoxb-5 and hoxb-6 is revealed by nonallelic noncomplementation.
Authors: Rancourt D E , Tsuzuki T , Capecchi M R
Published: June 2007

hoxb-5 and hoxb-6 are adjacent genes in the mouse HoxB locus and are members of the homeotic transcription factor complex that governs establishment of the mammalian body plan. To determine the roles of these genes during development, we generated mice with a targeted disruption in each gene. Three phenotypes affecting brachiocervicothoracic structures were found in the mutant mice. First, hoxb-5- homozygotes have a rostral shift of the shoulder girdle, analogous to what is seen in the human Sprengel anomaly. This suggests a role for hoxb-5 in specifying the position of limbs along the anteroposterior axis of the vertebrate body. Second, hoxb-6- homozygotes frequently have a missing first rib and a bifid second rib. The third phenotype, an anteriorizing homeotic transformation of the cervicothoracic vertebrae from C6 through T1, is common to both hoxb-5- and hoxb-6- homozygotes. Quite unexpectedly, hoxb-5, hoxb-6 transheterozygotes (hoxb-5-hoxb-6+/hoxb-5+ hoxb-6-) also show the third phenotype. By this classical genetic complementation test, these two mutations appear as alleles of the same gene. This phenomenon is termed nonallelic noncomplementation and suggests that these two genes function together to specify this region of the mammalian vertebral column.
Identification of a novel serine/threonine kinase and a novel 15-kD protein as potential mediators of the gamma interferon-induced cell death.
Authors: Deiss L P , Feinstein E , Berissi H , Cohen O , Kimchi A
Published: June 2007

Programmed cell death is often triggered by the interaction of some cytokines with their cell surface receptors. Here, we report that gamma interferon (IFN-gamma) induced in HeLa cells a type of cell death that had cytological characteristics of programmed cell death. In this system we have identified two novel genes whose expression was indispensable for the execution of this type of cell death. The rescue was based on positive growth selection of cells after transfection with antisense cDNA expression libraries. The antisense RNA-mediated inactivation of the two novel genes protected the cells from the IFN-gamma-induced cell death but not from the cytostatic effects of the cytokine or from a necrotic type of cell death. One of those genes (DAP-1) is expressed as a single 2.4-kb mRNA that codes for a basic, proline-rich, 15-kD protein. The second is transcribed into a single 6.3-kb mRNA and codes for a unique 160-kD calmodulin-dependent serine/threonine kinase (DAP kinase) that carries eight ankyrin repeats. The expression levels of the two DAP proteins were selectively reduced by the corresponding antisense RNAs. Altogether, it is suggested that these two novel genes are candidates for positive mediators of programmed cell death that is induced by IFN-gamma.
The DIMINUTO gene of Arabidopsis is involved in regulating cell elongation.
Authors: Takahashi T , Gasch A , Nishizawa N , Chua N H
Published: June 2007

We have isolated a recessive mutation named diminuto (dim) from T-DNA transformed lines of Arabidopsis thaliana. Under normal growth conditions, the dim mutant has very short hypocotyls, petioles, stems, and roots because of the reduced size of cells along the longitudinal axes of these organs. In addition, dim results in the development of open cotyledons and primary leaves in dark-grown seedlings. The gene for DIM was cloned by T-DNA tagging. DIM encodes a novel protein of 561 amino acids that possesses bipartite sequence domains characteristic of nuclear localization signals. Molecular and physiological studies indicate that the loss-of-function mutant allele does not abolish the response of seedlings to light or phytohormones, although the inhibitory effect of light on hypocotyl elongation is greater in the mutant than in wild type. Moreover, the dim mutation affects the expression of a beta-tubulin gene, TUB1, which is thought to be important for plant cell growth. Our results suggest that the DIM gene product plays a critical role in the general process of plant cell elongation.
Trophinin and tastin, a novel cell adhesion molecule complex with potential involvement in embryo implantation.
Authors: Fukuda M N , Sato T , Nakayama J , Klier G , Mikami M , Aoki D , Nozawa S
Published: June 2007

Two human epithelial cell lines, trophoblastic teratocarcinoma HT-H and endometrial adenocarcinoma SNG-M cells, adhere to each other at their respective apical cell surfaces in a divalent cation-independent manner. Two novel molecules responsible for the adhesion between these two cell types were identified by expression cDNA cloning. One, named trophinin, is an intrinsic membrane protein and mediates homophilic self-binding. Another, named tastin, is a cytoplasmic protein and is necessary for trophinin to function as a cell adhesion molecule. Trophinin and tastin appear to be associated with the cytoskeleton in HT-H and SNG-M cells. These molecules are normally not expressed in various types of human cells in tissues, with the exception of macrophages. Strong expression of these molecules was detected in the trophectoderm surface of monkey blastocyst. These molecules are also expressed in human endometrial surface epithelium on day 16/17 at the early secretory phase of human endometrium, the time consistent with that expected for the "implantation window."
Gene trap capture of a novel mouse gene, jumonji, required for neural tube formation.
Authors: Takeuchi T , Yamazaki Y , Katoh-Fukui Y , Tsuchiya R , Kondo S , Motoyama J , Higashinakagawa T
Published: June 2007

A mouse mutation, termed jumonji (jmj), was generated by a gene trap strategy. Expression of the trapped gene (jmj gene), as monitored by X-gal staining, was detected predominantly at the midbrain-hindbrain boundary and in the cerebellum, depending on the stage of development. All embryos homozygous for the jmj mutation died before embryonic day 15.5. Some, but not all, of the homozygotes developed an abnormal groove in a region just anterior to the midbrain-hindbrain boundary on the neural plate at embryonic day 8-8.5 and showed a defect in neural tube closure in the midbrain region. Analyses of jmj cDNA revealed that the jmj gene is novel, conserved among vertebrates, and disrupted by vector insertion in the jmj homozygotes. The amino acid sequence deduced from the cDNA shared a portion of significant homology with human retinoblastoma-binding protein RBP-2 and with a putative protein encoded by human gene XE169 that escapes X-chromosome inactivation. These results suggest that jmj gene is essential for normal morphogenesis of the neural tube.
On the functional overlap between two Drosophila POU homeo domain genes and the cell fate specification of a CNS neural precursor.
Authors: Yeo S L , Lloyd A , Kozak K , Dinh A , Dick T , Yang X , Sakonju S , Chia W
Published: June 2007

The approximately 200 distinct neurons comprising each hemisegment of the Drosophila embryonic CNS are derived from a stereotypic array of approximately 30 progenitor stem cells, called neuroblasts (NBs). Each NB undergoes repeated asymmetric divisions to produce several smaller ganglion mother cells (GMCs), each of which, in turn, divides to produce two neurons and/or glia cells. To understand the process by which cell type diversity is generated in the CNS, we are focusing on identifying genes that affect cell identity in the NB4-2 lineage from which the RP2 motoneuron is derived. We show here that within the early part of the NB4-2 lineage, two closely linked and structurally related POU homeo domain genes, pdm-2 (dPOU28) and pdm-1 (dPOU19), both encode proteins that accumulate to high levels only in the first GMC (GMC4-2a) and not in its progeny, the RP2 motoneuron. Our results from the genetic and developmental analysis of pdm-1 and pdm-2 demonstrate that these genes are not required for the birth of GMC4-2a; however, they are both involved in specifying the identity of GMC4-2a and, ultimately, in the genesis of RP2 neurons, with pdm-2 being the more dominant player in this process. In mutant animals where both pdm-1 and pdm-2 functions are removed, GMC4-2a fails to express markers consistent with a GMC4-2a identity and no mature (Eve protein expressing) RP2 neurons are produced. We demonstrate that in some mutant combinations in which no mature RP2 neurons are produced, some GMC4-2a cells can nevertheless divide. Hence, the failure of the POU mutants to produce mature RP2 neurons is not attributable to a block in GMC4-2a cell division per se but, rather, because the GMC4-2a cells fail to acquire their correct cellular identity.
Position effect variegation in Drosophila is associated with an altered chromatin structure.
Authors: Wallrath L L , Elgin S C
Published: June 2007

A euchromatic gene placed in the vicinity of heterochromatin by a chromosomal rearrangement generally exhibits position effect variegation (PEV), a clonally inherited pattern showing gene expression in some somatic cells but not in others. The mechanism responsible for this loss of gene expression is investigated here using fly lines carrying a P element containing the Drosophila melanogaster white and hsp26 genes. Following mobilization of the P element, a screen for variegation of white expression recovered inserts at pericentric, telomeric, and fourth chromosome regions. Previously identified suppressors of PEV suppressed white variegation of pericentric and fourth chromosome inserts but not telomeric inserts on the second and third chromosomes. This implies a difference in the mechanism for gene repression at telomeres. Heat shock-induced hsp26 expression was reduced from pericentric and fourth chromosome inserts but not from telomeric inserts. Chromatin structure analysis revealed that the variegating inserts showed a reduction in accessibility to restriction enzyme digestion in the hsp26 regulatory region in isolated nuclei. Micrococcal nuclease digests showed that pericentric inserts were packaged in a more regular nucleosome array than that observed for euchromatic inserts. These data suggest that altered chromatin packaging plays a role in PEV.
Inactivation of the myogenic bHLH gene MRF4 results in up-regulation of myogenin and rib anomalies.
Authors: Zhang W , Behringer R R , Olson E N
Published: June 2007

The myogenic basic helix-loop-helix (bHLH) proteins MyoD, myf5, myogenin, and MRF4 can initiate myogenesis when expressed in nonmuscle cells. During embryogenesis, each of the myogenic bHLH genes is expressed in a unique temporospatial pattern within the skeletal muscle lineage, suggesting that they play distinct roles in muscle development. Gene targeting has shown that MyoD and myf5 play partially redundant roles in the genesis of myoblasts, whereas myogenin is required for terminal differentiation. MRF4 is expressed transiently in the somite myotome during embryogenesis and then becomes up-regulated during late fetal development to eventually become the predominant myogenic bHLH factor expressed in adult skeletal muscle. On the basis of its expression pattern, it has been proposed that MRF4 may regulate skeletal muscle maturation and aspects of adult myogenesis. To determine the function of MRF4, we generated mice carrying a homozygous germ-line mutation in the MRF4 gene. These mice showed only a subtle reduction in expression of a subset of muscle-specific genes but showed a dramatic increase in expression of myogenin, suggesting that it may compensate for the absence of MRF4 and demonstrating that MRF4 is required for the down-regulation of myogenin expression that normally occurs in postnatal skeletal muscle. Paradoxically, MRF4-null mice exhibited multiple rib anomalies, including extensive bifurcations, fusions, and supernumerary processes. These results demonstrate an unanticipated regulatory relationship between myogenin and MRF4 and suggest that MRF4 influences rib outgrowth through an indirect mechanism.
Overexpression of the arginine-rich carboxy-terminal region of U1 snRNP 70K inhibits both splicing and nucleocytoplasmic transport of mRNA.
Authors: Romac J M , Keene J D
Published: June 2007

Transient transfection of the U1 snRNP 70K protein into COS cells induced nuclear reorganization and redistribution of the splicing factor SC-35, whereas hnRNP proteins were not affected. Correspondingly, splicing and nucleocytoplasmic transport of a coexpressed mRNA substrate was reduced by overexpression of U1-70K. The carboxy-terminal portion of U1-70K-encompassing repeats of Arg/Ser, Arg/Glu, and Arg/Asp localizes to the nucleus independently of U1 RNA and was responsible for these inhibitory effects. This region of U1-70K contains amino acid residues similar to those found in splicing factors SC-35, U2AF, su(wa), and in other SR proteins suggesting that U1-70K protein may serve as a focus of assembly for functional components of the splicing/transport machinery. These findings are compatible with models that propose that direct interaction between U1-70K and SR proteins play a regulatory role in early events of spliceosome assembly.
Mutations in gld-1, a female germ cell-specific tumor suppressor gene in Caenorhabditis elegans, affect a conserved domain also found in Src-associated protein Sam68.
Authors: Jones A R , Schedl T
Published: June 2007

The gld-1 gene of Caenorhabditis elegans is a germ-line-specific tumor suppressor gene that is essential for oogenesis. We have cloned the gld-1 gene and find that it encodes two proteins that differ by 3 amino acids. The predicted proteins contain a approximately 170-amino-acid region that we term the GSG domain (GRP33/Sam68/GLD-1), on the basis of significant similarity between GLD-1, GRP33 from shrimp, and the Src-associated protein Sam68 from mouse (also described as GAPap62 from humans). A conserved structural motif called the KH domain is found within the larger GSG domain, suggesting a biochemical function for GLD-1 protein in binding RNA. The importance of the GSG domain to the function of gld-1 in vivo is revealed by mutations that affect 5 different conserved GSG domain residues. These include missense mutations in an absolutely conserved residue of the KH domain that eliminate the tumor suppressor function of gld-1.
c-Src enhances the spreading of src-/- fibroblasts on fibronectin by a kinase-independent mechanism.
Authors: Kaplan K B , Swedlow J R , Morgan D O , Varmus H E
Published: June 2007

We have explored the role of the tyrosine kinase c-Src in cellular adhesion. Fibroblasts derived from src-/- mice (src-/- fibroblasts) exhibit a reduced rate of spreading on fibronectin. These defect is rescued by expression of wild-type chicken c-Src. Analyses of mutants suggest that c-Src increases the rate of cell spreading in src-/- fibroblasts through a kinase-independent mechanism requiring both the SH3 and SH2 domains. To further address the role of c-Src in adhesion, we examined the activity and subcellular distribution of c-Src during the adhesion of fibroblasts on fibronectin. We observed a transient increase in the specific kinase activity of c-Src accompanied by the partial dephosphorylation of the negative regulatory site Y527. Activation of c-Src is followed by its redistribution to newly formed focal adhesions. These results suggest that the enzymatic activity and subcellular distribution of c-Src are coordinately regulated during cellular adhesion and that c-Src can affect adhesion by a kinase-independent mechanism.
Targeted disruption of the glucocorticoid receptor gene blocks adrenergic chromaffin cell development and severely retards lung maturation.
Authors: Cole T J , Blendy J A , Monaghan A P , Krieglstein K , Schmid W , Aguzzi A , Fantuzzi G , Hummler E , Unsicker K , Schütz G
Published: June 2007

The role of the glucocorticoid receptor (GR) in glucocorticoid physiology and during development was investigated by generation of GR-deficient mice by gene targeting. GR -/- mice die within a few hours after birth because of respiratory failure. The lungs at birth are severely atelectatic, and development is impaired from day 15.5 p.c. Newborn livers have a reduced capacity to activate genes for key gluconeogenic enzymes. Feedback regulation via the hypothalamic-pituitary-adrenal axis is severely impaired resulting in elevated levels of plasma adrenocorticotrophic hormone (15-fold) and plasma corticosterone (2.5-fold). Accordingly, adrenal glands are enlarged because of hypertrophy of the cortex, resulting in increased expression of key cortical steroid biosynthetic enzymes, such as side-chain cleavage enzyme, steroid 11 beta-hydroxylase, and aldosterone synthase. Adrenal glands lack a central medulla and synthesize no adrenaline. They contain no adrenergic chromaffin cells and only scattered noradrenergic chromaffin cells even when analyzed from the earliest stages of medulla development. These results suggest that the adrenal medulla may be formed from two different cell populations: adrenergic-specific cells that require glucocorticoids for proliferation and/or survival, and a smaller noradrenergic population that differentiates normally in the absence of glucocorticoid signaling.
Myogenic and morphogenetic defects in the heart tubes of murine embryos lacking the homeo box gene Nkx2-5.
Authors: Lyons I , Parsons L M , Hartley L , Li R , Andrews J E , Robb L , Harvey R P
Published: June 2007

The murine homeo box gene Nkx2-5 is expressed in precardiac mesoderm and in the myocardium of embryonic and fetal hearts. Targeted interruption of Nkx2-5 resulted in abnormal heart morphogenesis, growth retardation and embryonic lethality at approximately 9-10 days postcoitum (p.c.). Heart tube formation occurred normally in mutant embryos, but looping morphogenesis, a critical determinant of heart form, was not initiated at the linear heart tube stage (8.25-8.5 days p.c.). Commitment to the cardiac muscle lineage, expression of most myofilament genes and myofibrillogenesis were not compromised. However, the myosin light-chain 2V gene (MLC2V) was not expressed in mutant hearts nor in mutant ES cell-derived cardiocytes. MLC2V expression normally occurs only in ventricular cells and is the earliest known molecular marker of ventricular differentiation. The regional expression in mutant hearts of two other ventricular markers, myosin heavy-chain beta and cyclin D2, indicated that not all ventricle-specific gene expression is dependent on Nkx2-5. The data demonstrate that Nkx2-5 is essential for normal heart morphogenesis, myogenesis, and function. Furthermore, this gene is a component of a genetic pathway required for myogenic specialization of the ventricles.
Cell proliferation and DNA replication defects in a Drosophila MCM2 mutant.
Authors: Treisman J E , Follette P J , O'Farrell P H , Rubin G M
Published: June 2007

The yeast MCM2, MCM3, and MCM5/CDC46 genes are required for DNA replication and have been proposed to act as factors that license the DNA for one and only one round of replication per cell cycle. We have identified a Drosophila gene, DmMCM2, that is highly homologous to MCM2. A P-element insertion into this gene, which prevents its transcription, inhibits proliferation of cells in the imaginal discs and central nervous system (CNS) and causes an apparent prolongation of S phase in the embryonic and larval CNS. DmMCM2 is expressed in the embryo in a pattern corresponding to that of S-phase cells. These results suggest that DmMCM2 plays a role in the regulation of DNA replication analogous to that of its yeast counterpart.
p107 uses a p21CIP1-related domain to bind cyclin/cdk2 and regulate interactions with E2F.
Authors: Zhu L , Harlow E , Dynlacht B D
Published: June 2007

The kinase activities of the cyclin/cdk complexes can be regulated in a number of ways. The most recently discovered mechanism of regulation is the association of cdk inhibitors (CKIs), such as p21, p27, and p57, with these complexes. In this report we demonstrate that the pRB-related protein p107, like the p21 family of cdk inhibitors, can inhibit the phosphorylation of target substrates by cyclin A/cdk2 and cyclin E/cdk2 complexes, and the associations of p107 and p21 with cyclin/cdk2 rely on a structurally and functionally related interaction domain. Furthermore, interactions between p107 or p21 with cyclin/cdk2 complexes are mutually exclusive. In cells treated with DNA-damaging agents elevated levels of p21 cause a dissociation of p107/cyclin/cdk2 complexes to yield p21/cyclin/cdk2 complexes. Finally, the consequences of cyclin/cdk2 interactions with p107 have been examined. The activation of the p107-bound cyclin/cdk kinases leads to dissociation of p107 from the transcription factor E2F. Together, these results suggest that cyclin/cdk complexes can be regulated by protein molecules from different families in a mutually exclusive manner in response to certain signals and that these inhibitory proteins may have a potential role in regulating macromolecular assembly.
Overexpression of HOXB4 in hematopoietic cells causes the selective expansion of more primitive populations in vitro and in vivo.
Authors: Sauvageau G , Thorsteinsdottir U , Eaves C J , Lawrence H J , Largman C , Lansdorp P M , Humphries R K
Published: June 2007

Hox genes were first recognized for their role in embryonic development and may also play important lineage-specific functions in a variety of somatic tissues including the hematopoietic system. We have recently shown that certain members of the Hox A and B clusters, such as HOXB3 and HOXB4, are preferentially expressed in subpopulations of human bone marrow that are highly enriched for the most primitive hematopoietic cell types. To assess the role these genes may play in regulating the proliferation and/or differentiation of such cells, we engineered the overexpression of HOXB4 in murine bone marrow cells by retroviral gene transfer and analyzed subsequent effects on the behavior of various hematopoietic stem and progenitor cell populations both in vitro and in vivo. Serial transplantation studies revealed a greatly enhanced ability of HOXB4-transduced bone marrow cells to regenerate the most primitive hematopoietic stem cell compartment resulting in 50-fold higher numbers of transplantable totipotent hematopoietic stem cells in primary and secondary recipients, compared with serially passaged neo-infected control cells. This heightened expansion in vivo of HOXB4-transduced hematopoietic stem cells was not accompanied by identifiable anomalies in the peripheral blood of these mice. Enhanced proliferation in vitro of day-12 CFU-S and clonogenic progenitors was also documented. These results indicate HOXB4 to be an important regulator of very early but not late hematopoietic cell proliferation and suggest a new approach to the controlled amplification of genetically modified hematopoietic stem cell populations.
HnRNP L binds a cis-acting RNA sequence element that enables intron-dependent gene expression.
Authors: Liu X , Mertz J E
Published: June 2007

Most pre-mRNAs require an intron for efficient processing in higher eukaryotes. To test the hypothesis that intron-independent gene expression involves positive, cis-acting RNA sequence elements, we constructed chimeric genes in which various regions of the naturally intronless HSV-TK gene were inserted into an intronless variant of the highly intron-dependent human beta-globin gene. Using a transient transfection assay, we identified a 119-nucleotide sequence element contained within the transcribed region of the HSV-TK gene that enables efficient cytoplasmic accumulation of globin RNA in the absence of splicing. RNA UV-cross-linking assays indicated that a 68-kD protein present in nuclear extracts of HeLa and COS cells specifically binds to this HSV-TK sequence element. This 68-kD protein was found to cross-react with an antiserum specific to hnRNP L. Recombinant hnRNP L was shown to bind with high sequence specificity to this RNA sequence element. Analysis of substitution mutants in this element indicated that binding of hnRNP L correlates with accumulation of the RNA in the cytoplasm. Thus, we conclude that (1) hnRNP L binds in a sequence-specific manner to this RNA sequence element that enables intron-independent gene expression, and (2) intron-independent pre-mRNA processing and transport involves sequence-specific RNA-protein interactions between cis-acting RNA sequence elements and proteins such as hnRNP L. This sequence element may be of general use for the efficient expression of cDNA versions of intron-dependent genes.
Kip/Cip and Ink4 Cdk inhibitors cooperate to induce cell cycle arrest in response to TGF-beta.
Authors: Reynisdóttir I , Polyak K , Iavarone A , Massagué J
Published: June 2007

G1 progression in mammalian cells requires the activity of the cyclin D-dependent kinases Cdk4 and/or Cdk6 and the cyclin E-dependent kinase Cdk2. Proliferating Mv1Lu mink lung epithelial cells and human keratinocytes contain high levels of the universal Cdk inhibitor p27Kip1 distributed in complexes with Cdk2, Cdk4, and Cdk6. Addition of the antimitogenic cytokine transforming growth factor-beta (TGF-beta) elevates expression of the Cdk4/6-specific inhibitor p15Ink4B and induces the release of p27 from Cdk4 and Cdk6. In Mv1Lu cells, this release of p27 coincides with increased binding of p27 to Cdk2. Recombinant p15 inhibits p27 binding to Cdk4 in vitro, and p15 overexpression induces the transfer of p27 from Cdk4 to Cdk2 in vivo, suggesting that the release of Cdk4-bound p27 in TGF-beta-treated cells is caused by the surge in p15 levels. In keratinocytes, TGF-beta increases not only p15 but also p21Cip1, which binds to Cdk2. These events correlate with Cdk2 inhibition and cell cycle arrest and occur without a loss of G1 Cdk components. The results suggest that TGF-beta induces G1 arrest in these two epithelial cell types by inhibiting various cyclin-Cdk kinases through the cooperative action of an Ink4 Cdk inhibitor and a Cip/Kip Cdk inhibitor. Subsequent to cell cycle arrest, Cdk2 and Cdk4 levels decline as part of a second set of events that may represent a program of cell adaptation to the quiescent state.
Biallelic expression of imprinted genes in the mouse germ line: implications for erasure, establishment, and mechanisms of genomic imprinting.
Authors: Szabó P E , Mann J R
Published: June 2007

Genomic imprinting in mammals determines parental-specific (monoallelic) expression of a relatively small number of genes during development. Imprinting must logically be imparted in the germ line, where inherited maternal and paternal imprinting is erased and new imprinting established according to the individual's sex. We have assessed the allele-specific expression of four imprinted genes, two of which exhibit maternal-specific (H19 and Igf2r) and two of which exhibit paternal-specific (Igf2 and Snrpn) monoallelic somatic expression, in the germ line of F1 hybrid mice utilizing quantitative RT-PCR single-nucleotide primer extension assays. The expression of each gene was biallelic in the female and male germ line from the time that migratory mitotic PGCs entered the embryonic genital ridge and throughout gametogenesis, except that H19 RNA was not detected late in gametogenesis. These findings demonstrate that inherited imprinting is erased, or not recognized, in germ cells by the time of genital ridge colonization; also that new imprinting may not be established until late in gametogenesis, or that it is incomplete or not recognized at this stage. Regardless of imprinting status, a generalized neutralization of imprinting is evident in the germ line, associated with the totipotent state of this unique cell lineage.
Nucleosome positioning on the MMTV LTR results from the frequency-biased occupancy of multiple frames.
Authors: Fragoso G , John S , Roberts M S , Hager G L
Published: June 2007

The translational positions of nucleosomes in the promoter region of the mouse mammary tumor virus (MMTV) were defined at high resolution. Nucleosome boundaries were determined in primer extension assays using full-length single-stranded mononucleosomal DNA prepared from cells treated with formaldehyde, a reversible protein-DNA cross-linking agent. Multiple boundaries were observed in both the nucleosome A (Nuc-A) and Nuc-B region of the promoter, indicating multiple nucleosome translational frames. The different nucleosome frames in both the Nuc-A and Nuc-B regions were occupied unequally. The most frequently occupied frames were found clustered within 50-60 bases of each other, resulting in a distribution centered in the positions defined previously at low resolution for Nuc-A and Nuc-B. The most abundant 5' ends of the frames in the B region were found between -235 and -187, and the 3' ends between -86 and -36, whereas in the A region the most abundant 5' ends were between -22 and +42, and the 3' ends between +121 and +186. Although frames in the Nuc-B region of the LTR extend at a low frequency in the 5' direction toward the Nuc-C region, there is a sharp discontinuity in the 3' direction toward Nuc-A, suggesting the presence of a boundary constraint in the A-B linker. The positions and relative occupancies of nucleosome frames, in either the B or the A region, did not change when the promoter was activated with dexamethasone.
Rapid induction of heparin-binding epidermal growth factor/diphtheria toxin receptor expression by Raf and Ras oncogenes.
Authors: McCarthy S A , Samuels M L , Pritchard C A , Abraham J A , McMahon M
Published: June 2007

We have used differential display PCR to search for mRNAs induced by delta Raf-1:ER, an estradiol-dependent form of Raf-1 kinase. Through this approach the gene encoding heparin-binding epidermal growth factor (HB-EGF) was identified as an immediate-early transcriptional target of oncogenic Raf kinases. Activation of delta Raf-1:ER and a conditional oncogenic form of B-Raf, delta B-RAF:ER, resulted in rapid and sustained induction of HB-EGF mRNA expression and secretion of mature HB-EGF from cells. Neutralizing anti-HB-EGF antisera prevented the delayed activation of the c-Jun amino-terminal kinases that is observed in cells transformed by delta Raf-1:ER. These results demonstrate that distinct signaling pathways can cross talk via the secretion of polypeptide growth factors. Furthermore, cells transformed by oncogenic Ras, which also induced HB-EGF expression, demonstrated a marked increase in sensitivity to the cytotoxic action of diphtheria toxin, for which the membrane anchored HB-EGF precursor acts as a cell-surface receptor.
Bone morphogenetic protein-4 is required for mesoderm formation and patterning in the mouse.
Authors: Winnier G , Blessing M , Labosky P A , Hogan B L
Published: June 2007

Bone morphogenetic protein-4 (BMP-4) is a member of the TGF-beta superfamily of polypeptide signaling molecules, closely related to BMP-2 and to Drosophila decapentaplegic (DPP). To elucidate the role of BMP-4 in mouse development the gene has been inactivated by homologous recombination in ES cells. Homozygous mutant Bmp-4tm1blh embryos die between 6.5 and 9.5 days p.c., with a variable phenotype. Most Bmp-4tm1blh embryos do not proceed beyond the egg cylinder stage, do not express the mesodermal marker T(Brachyury), and show little or no mesodermal differentiation. Some homozygous mutants develop to the head fold or beating heart/early somite stage or beyond. However, they are developmentally retarded and have truncated or disorganized posterior structures and a reduction in extraembryonic mesoderm, including blood islands. These results provide direct genetic evidence that BMP-4 is essential for several different processes in early mouse development, beginning with gastrulation and mesoderm formation. Moreover, in the presumed absence of zygotic ligand, it appears that homozygous mutants can be rescued partially by related proteins or by maternal BMP-4.
Pyp1 and Pyp2 PTPases dephosphorylate an osmosensing MAP kinase controlling cell size at division in fission yeast.
Authors: Millar J B , Buck V , Wilkinson M G
Published: June 2007

Simultaneous inactivation of pyp1 and pyp2 PTPases in fission yeast leads to aberrant cell morphology and growth arrest. Spontaneous recessive mutations that bypass the requirement for pyp1 and pyp2 and reside in two complementation groups were isolated, sty1 and sty2. sty1- and sty2- mutant cells are substantially delayed in the timing of mitotic initiation. We have isolated the sty1 gene, which encodes a MAP kinase that is closely related to a subfamily of MAP kinases regulated by osmotic stress including Saccharomyces cervisiae HOG1 and human CSBP1. We find that sty2 is allelic to the wis1 MAP kinase kinase and that delta sty1 and delta wis1 cells are unable to grow in high osmolarity medium. Osmotic stress induces both tyrosine phosphorylation of Sty1 and a reduction in cell size at division. Pyp2 associates with and tyrosine dephosphorylates Sty1 in vitro. We find that wis1-dependent induction of pyp2 mRNA is responsible for tyrosine dephosphorylation of Sty1 in vivo on prolonged exposure to osmotic stress. We conclude that Pyp1 and Pyp2 are tyrosine-specific MAP kinase phosphatases that inactivate an osmoregulated MAP kinase, Sty1, which acts downstream of the Wis1 MAP kinase kinase to control cell size at division in fission yeast.
A pathway for lateral root formation in Arabidopsis thaliana.
Authors: Celenza J L , Grisafi P L , Fink G R
Published: June 2007

In plants, the hormone indole-3-acetic acid (IAA) can initiate the developmental program for lateral root formation. We have isolated mutants that have permitted the dissection of this program into initiation and maturation of lateral roots. The alf1-1 mutation causes hyperproliferation of lateral roots, alf4-1 prevents initiation of lateral roots, and alf3-1 is defective in the maturation of lateral roots. The alf3-1 mutant can be rescued by IAA, whereas the alf4-1 mutant is not rescued. Our data suggest a model in which IAA is required for at least two steps in lateral root development: (1) to initiate cell division in the pericycle, and (2) to promote cell division and maintain cell viability in the developing lateral root.