Targeted Deletion Of Functionally Validated Enhancers Defines Their Role in Mouse Limb Development

Transcriptional enhancers are genomic DNA sequences that contain clustered transcription factor (TF) binding sites. When combinations of TFs bind to enhancer sequences they act together with basal transcriptional machinery to regulate the timing, location and quantity of gene transcription. Elucidating the genetic mechanisms responsible for differential gene expression, including the role of enhancers, during embryological and postnatal development is essential to an understanding of evolutionary processes and disease etiology. Numerous methods are in use to identify and characterize enhancers. Several high-throughput methods generate large datasets of enhancer sequences with putative roles in embryonic development. However, few enhancers have been deleted from the genome to determine their roles in the development of specific structures, such as the limb. Manipulation of enhancers at their endogenous loci, such as the deletion of such elements, leads to a better understanding of the regulatory interactions, rules and complexities that contribute to faithful and variant gene transcription – the molecular genetic substrate of evolution and disease. To understand the endogenous roles of two distinct enhancers known to be active in the mouse embryo limb bud we deleted them from the mouse genome. I hypothesized that deletion of these enhancers would lead to aberrant limb development. The enhancers were selected because of their association with p300, a protein associated with active transcription, and because the human enhancer sequences drive distinct lacZ expression patterns in limb buds of embryonic day (E) 11.5 transgenic mice. To confirm that the orthologous mouse enhancers, mouse 280 and 1442 (M280 and M1442, respectively), regulate expression in the developing limb we generated stable transgenic lines, and examined lacZ expression. In M280-lacZ mice, expression was detected in E11.5 fore- and hindlimbs in a region that corresponds to digits II-IV. M1442-lacZ mice exhibited lacZ expression in posterior and anterior margins of the fore- and hindlimbs that overlapped with digits I and V and several wrist bones. We generated mice lacking the M280 and M1442 enhancers by gene targeting. Intercrosses between M280 -/+ and M1442 -/+, respectively, generated M280 and M1442 null mice, which are born at expected Mendelian ratios and manifest no gross limb malformations. Quantitative real-time PCR of mutant E11.5 limb buds indicated that significant changes in transcriptional output of enhancer-proximal genes accompanied the deletion of both M280 and M1442. In neonatal null mice we observed that all limb bones are present in their expected positions, an observation also confirmed by histology of E18.5 distal limbs. Fine-scale measurement of E18.5 digit bone lengths found no differences between mutant and control embryos. Furthermore, when the developmental progression of cartilaginous elements was analyzed in M280 and M1442 embryos from E13.5-E15.5, transient development defects were not detected. These results demonstrate that M280 and M1442 are not required for mouse limb development. Though M280 is not required for embryonic limb development it is required for the development and/or maintenance of body size – adult M280 mice are significantly smaller than control littermates. These studies highlight the importance of experiments that manipulate enhancers in situ to understand their contribution to development.

{\it cis\/} -acting elements and {\it trans\/} -acting factors that control serum amyloid A gene expression during inflammation

To understand how the serum amyloid A (SAA) genes are regulated, the cis-acting elements and trans-acting factors involved in the regulation of mouse SAA3 and rat SAA1 genes expression during inflammation were analyzed.^ To identify DNA sequences involved in the liver-specific expression of the mouse SAA3 gene, the 5$\sp\prime$ flanking region of this gene was analyzed by transient transfection studies. Results suggest that C/EBP, a liver-enriched transcription factor, plays an important role for the enhanced expression of the mouse SAA3 gene in hepatocytes.^ Transfection studies of the regulation of the expression of rat SAA1 gene indicated that a 322 bp fragment ($-$304 to +18) of the gene contains sufficient information for cytokine-induced expression of the reporter gene in a liver cell-specific manner. Further functional analysis of the 5$\sp\prime$ flanking region of the rat SAA1 gene demonstrated that a 65 bp DNA fragment ($-$138/$-$73) can confer cytokine-inducibility onto a heterologous promoter both in liver and nonliver cells. DNase I footprint and gel retardation assays identified five putative cis-regulatory elements within the 5$\sp\prime$ flanking region of the gene: one inducible element, a NF$\kappa$B binding site and four constitutive elements. Two constitutive elements, footprint regions I and III, were identified as C/EBP binding sites with region III having over a 10-fold higher affinity for C/EBP binding than region I. Functional analysis of the cis-elements indicated that C/EBP(I) and C/EBP(III) confer liver cell-specific activation onto a heterologous promoter, while sequences corresponding to the NF$\kappa$B element and C/EBP(I) impart cytokine responsiveness onto the heterologous promoter. These results suggest that C/EBP(I) possesses two functions: liver-specific activation and cytokine responsiveness. The identification of two cytokine responsive elements (NF$\kappa$B and C/EBP(I)), and two liver-specific elements (C/EBP(I) and C/EBP(III)) implies that multiple cis-acting elements are involved in the regulation of the expression of the rat SAA1 gene. The tissue-specific and cytokine-induced expression of rat SAA1 gene is likely the result of the interactions of these cis-acting elements with their cognate trans-acting factors as well as the interplay between the different cis-acting elements and their binding factors. (Abstract shortened with permission of author.) ^

A novel DNA damage inducible inhibitor of p53

p53 is required for the maintenance of the genomic stability of cells. Mutations in the p53 tumor-suppressor gene occur in more than 50% of human cancers of diverse types. In addition, 70% of families with Li-Fraumeni syndrome have a germline mutation in p53, predisposing these individuals to multiple forms of cancer. In response to DNA damage, p53 becomes stabilized and activated. However the exact mechanism by which DNA damage signals the stabilization and activation of p53 still remains elusive. The biochemical activity of p53 that is required for tumor suppression, and presumably the cellular response to DNA damage, involves the ability of the protein to bind to specific DNA sequences and to function as a transcription factor. For the downstream targets, p53 transactivates many genes involved in growth arrest, apoptosis and DNA repair such as p21, Bax and GADD45, respectively. An open question in the field is how cells can determine the downstream effects of p53. ^ We hypothesize that, through its associated proteins, p53 can differentially transactivate its target genes, which determine its downstream effect. Additionally, p53 interacting proteins may be involved in signaling for the stabilization and activation of p53. Therefore, a key aspect to understanding p53 function is the identification and analysis of proteins that interact with it. We have employed the Sos recruitment system (SRS), a cytoplasmic yeast two-hybrid screen to identify p53 interacting proteins. The SRS is based on the ability of Sos to activate Ras when it becomes localized to the plasma membrane. The system takes advantage of an S. cerevisiae strain, cdc25-2 temperature sensitive mutant, harboring a mutation in Sos. In this strain, fusion proteins containing a truncated Sos will only localize to the membrane by protein-protein interaction, which allows growth at non-permissive temperature. This system allows the use of intact transcriptional activators such as p53. ^ To date, using a modified SRS library screen to identify p53 interacting proteins, I have identified p53 (known to interact with itself) and a novel p53-interacting protein (PIP). PIP is a specific p53 interacting protein in the SRS. The interaction of p53 and PIP was further confirmed by performing in vitro and in vivo binding assays. In the in vivo binding study, the interaction can only be detected in the presence of ionizing radiation suggesting that this interaction might be involved in DNA-damage induced p53-signalling pathway. After screening cDNA and genomic libraries, a full-length PIP-cDNA clone ( ∼ 3kb) was obtained which encodes a protein of 429 amino acids with calculated molecular weight of 46 kDa. The results of genebank search indicated that the PIP is an unidentified gene and contains a conserved ring-finger domain, which is present in a diverse family of regulatory proteins involved in different aspects of cellular function. Northern blot analysis revealed that the size of its messenge is approximately 3 kb preferentially expressed in brain, heart, liver and kidney. The PIP protein is mainly located in the cytoplasm as determined by the cellular localization of a green fluorescence fusion protein. Preliminary functional analysis revealed that PIP downregulated the transactivation activity of p53 on both p21 and mdm2 promoters. Thus, PIP may be a novel negative regulator of p53 subsequent to DNA damage. ^

A distinct element involved in the lipopolysaccharide activation of the tumor necrosis factor -alpha promoter in a promonocytic cell line, THP-1

TNF-α is a pleiotropic cytokine involved in normal homeostasis and plays a key role in defending the host from infection and malignancy. However when deregulated, TNF-α can lead to various disease states. Therefore, understanding the mechanisms by which TNF-α is regulated may aid in its control. In spite of the knowledge gained regarding the transcriptional regulation of TNF-α further characterization of specific TNF-α promoter elements remains to be elucidated. In particular, the T&barbelow;NF-α A&barbelow;P-1/C&barbelow;RE-like (TAC) element of the TNF-α promoter has been shown to be important in the regulation of TNF-α in lymphocytes. Activating transcription factor-2 (ATF-2) and c-Jun were shown to bind to and transactivate the TAC element However, the role of TAC and transcription factors ATF-2 and c-Jun in the regulation of TNF-α in monocytes is not as well characterized. Lipopolysaccharide (LPS), a potent activator of TNF-α in monocytes, provides a good model to study the involvement of TAC in TNF-α regulation. On the other hand, all-tram retinoic acid (ATRA), a physiological monocyte-differentiation agent, is unable to induce TNF-α protein release. ^ To delineate the functional role of TAC, we transfected the wildtype or the TAC deleted TNF-α promoter-CAT construct into THP-1 promonocytic cells before stimulating them with LPS. CAT activity was induced 17-fold with the wildtype TNF-α promoter, whereas the CAT activity was uninducible when the TAC deletion mutant was used. This daft suggests that TAC is vital for LPS to activate the TNF-α promoter. Electrophoretic mobility shift assays using the TAC element as a probe showed a unique pattern for LPS-activated cells: the disappearance of the upper band of a doublet seen in untreated and ATRA treated cells. Supershift analysis identified c-Jun and ATF-2 as components of the LPS-stimulated binding complex. Transient transfection studies using dominant negative mutants of JNK, c-Jun, or ATF-2 suggest that these proteins we important for LPS to activate the TNF-α promoter. Furthermore, an increase in phosphorylated or activated c-Jun was bound to the TAC element in LPS-stimulated cells. Increased c-Jun activation was correlated with increased activity of Jun N-terminal kinase (JNK), a known upstream stimulator of c-Jun and ATF-2, in LPS-stimulated monocytes. On the other hand, ATRA did not induce TNF-α protein release nor changes in the phosphorylation of c-Jun or JNK activity, suggesting that pathways leading to ATRA differentiation of monocytic cells are independent of TNF-α activation. Together, the induction of TNF-α gene expression seems to require JNK activation, and activated c-Jun binding to the TAC element of the TNF-α promoter in THP-1 promonocytic cells. ^

Constitutive expression of interleukin-6 in renal cell carcinoma is modulated by p53

Several studies indicate that interleukin-6 (IL-6) production is elevated in renal cell carcinoma (RCC) cells, and that IL-6 can serve as an autocrine growth factor in this malignancy. Wild type (wt) p53 represses transcription from the IL-6 promoter in an inducible system. The objective of this study was to determine the role of p53 in regulating constitutive IL-6 production in RCC cells. RCC cell lines containing mutant (mut) p53 produced significantly higher levels of IL-6 than those containing wt p53 (p < 0.05). Transfection of wt p53 into RCC cell lines resulted in significant repression of IL-6 promoter CAT activity p < 0.05). Mutant p53 was less effective at repressing IL-6 promoter activity in ACHN cells, and actually enhanced IL-6 promoter activity in the A498 cell line. A498 cells stably transfected with mutant p53 produced significantly higher levels of IL-6 than A498 cells transfected with an empty expression vector (p < 0.05). Electrophoretic mobility shift assay showed a significant decrease in binding of C/EBP, CREB, and NF-kB transcription factors to the IL-6 promoter in A498 cells transfected with wt p53. Mut p53 was unable to inhibit transcription factor binding to the IL-6 promoter in these cells. Mutant p53-expressing UOK 121LN cells showed decreased binding of C/EBP and CREB, but not NF-kB, following wt p53 transfection. These data suggest that (i) mutation of p53 contributes to the over-expression of IL-6 in RCC; and (ii) wt p53 represses IL-6 expression at least in part by interfering with the binding of C/EBP, CREB, and in some cases, NF-kB transcription factors to the IL-6 promoter. ^

Identification and characterization of cellular genes differentially expressed in a subset of tumors with non -functional WT1

Wilms tumor (WT) or nephroblastoma is a genetically heterogeneous pediatric renal tumor that accounts for 6–7% of all childhood cancers in the U.S. WT1, located at 11p13, is the sole WT gene cloned to date. Additional genomic regions containing genes that play a role in the development of Wilms tumor include 11p15, 7p, 16q, 1p, 17q and 19q. This heterogeneity has made it extremely difficult to develop an understanding of the pathways involved in the development of WT, even in the 5–20% of tumors that show mutations at the WT1 locus. My research addresses this gap in our current comprehension of the development of WT. ^ I have used two complementary approaches to extend the current understanding of molecular changes involved in the development of WT. In order to minimize complexities due to genetic heterogeneity, I confined my analysis to the WT1 pathway by assessing those genetically defined tumors that carry WT1 mutations. WT1 encodes a zinc finger transcription factor, and in vitro studies have identified many genes that are potentially regulated in vivo by WT1. However, there is very little in vivo data that suggests that they are transcriptionally regulated endogenously by WT1. In one approach I assessed the role of WT1 in the in vivo regulation of PDGFA and IGF2, two genes that are strong contenders for endogenous regulation by WT1. Using primary tissue samples, I found no correlation between the level of RNA expression of WT1 with either PDGFA or IGF2, suggesting that WT1 does not play a critical role in their expression in either normal kidney or WT. ^ In a parallel strategy, using differential display analysis I compared global gene expression in a subset of tumors with known homozygous inactivating WT1 mutations (WT1-tumors) to the gene expression in a panel of appropriate control tissues (fetal kidney, normal kidney, rhabdoid tumor and pediatric renal cell carcinoma). Transcripts that are aberrantly expressed in this subset of Wilms tumors are candidates for endogenous transcriptional regulation by WT1 as well as for potentially functioning in the development of WT. By this approach I identified several differentially expressed transcripts. I further characterized two of these transcripts, identifying a candidate WT gene in the process. I then performed a detailed analysis of this WT candidate gene, which maps to 7p. Future studies will shed more light on the role of these differentially expressed genes in WT. ^

*Ras proteins and human tumor cell radiosensitivity

Ras proteins (H-, N-, K4A-, and K4B) are associated with cellular resistance to ionizing radiation (IR) and, consequently, may provide a potential target for radiosensitization strategies in cancer treatment. Several approaches have been used to compromise Ras activity and enhance IR-induced cell killing; however, these techniques either target proteins in addition to Ras or only target one member of the Ras family. In this study, I have used an adenovirus (AV1Y28) that expresses a single-chain antibody fragment directed against Ras proteins to investigate the mechanism(s) responsible for Ras-mediated radiation resistance. AV1Y28 enhanced the radiosensitivity of a number of human tumor cell lines without affecting the radiosensitivity of normal human fibroblasts. Whereas AV1Y28-mediated sensitization was independent of ras gene mutational status, it was dependent on active Ras proteins suggesting that AV1Y28 may be useful against a broad range of tumors. AV1Y28-mediated cell killing was not the result of redistributing cells into a more radiosensitive phase of the cell cycle and did not enhance IR-induced apoptosis. Given that Ras proteins transduce environmental signals to the nucleus, the effect of AV1Y28 on the IR-inducible transcription factor NF-κB were determined. Although AV1Y28 inhibited IR-induced NF-κB through the suppression of IKK, additional work established that NF-κB did not play a role in AV1Y28-mediated radiosensitization. However, a novel component of the signaling pathway responsible for IR-induced NF-κB was identified. Previous studies had suggested a relationship between mutant ras genes and IR-induced G2 delay; therefore the effects of AV1Y28 on the progression of cells from G2 to M after IR were determined. Pretreatment of cells with AV1Y28 prevented the IR-induced G2 arrest. AV1Y28-mediated abrogation of IR-induced G2 arrest correlated with those cell line lines that were sensitized by AV1Y28. Moreover, a significant increase in cells undergoing mitotic catastrophe was found after IR in AV1Y28 treated cells. The abrogation of G2 arrest by AV1Y28 was the result of maintaining the active form of cdc2, an inducer of mitosis, after exposure to IR. This study identified the mechanism of AV1Y28-mediated radiosensitization and has provided insight into the signal transduction pathways responsible for Ras-mediated radiation resistance. ^

Arabidopsis thaliana DOF6 negatively affects germination in non-after ripened seeds and interacts with TCP14

Seed dormancy prevents seeds from germinating under environmental conditions unfavourable for plant growth and development and constitutes an evolutionary advantage. Dry storage, also known as after-ripening, gradually decreases seed dormancy by mechanisms not well understood. An Arabidopsis thaliana DOF transcription factor gene (DOF6) affecting seed germination has been characterized. The transcript levels of this gene accumulate in dry seeds and decay gradually during after-ripening and also upon seed imbibition. While constitutive over-expression of DOF6 produced aberrant growth and sterility in the plant, its over-expression induced upon seed imbibition triggered delayed germination, abscisic acid (ABA)-hypersensitive phenotypes and increased expression of the ABA biosynthetic gene ABA1 and ABA-related stress genes. Wild-type germination and gene expression were gradually restored during seed after-ripening, despite of DOF6-induced over-expression. DOF6 was found to interact in a yeast two-hybrid system andin planta with TCP14, a previously described positive regulator of seed germination. The expression of ABA1 and ABA-related stress genes was also enhanced in tcp14 knock-out mutants. Taken together, these results indicate that DOF6 negatively affects seed germination and opposes TCP14 function in the regulation of a specific set of ABA-related genes

Genes implicados en la respuesta molecular al estrés hídrico en Pinus pinaster Ait

La presente tesis doctoral se centra en el estudio de la respuesta molecular de las coníferas mediterráneas al estrés hídrico. Para ello se ha escogido como especie modelo Pinus pinaster Ait., la conífera más abundante en España, y que habita un amplio rango de situaciones ecológicas, especialmente en lo relativo a la disponibilidad de agua. En primer lugar, se ha aplicado un estrés hídrico controlado en cultivo hidropónico y se ha generando una genoteca sustractiva con objeto de identificar los genes inducidos por el estrés, analizando su expresión en raíces, tallos y acículas. A continuación, se ha analizado, la expresión de los genes anteriormente obtenidos así como de otros seleccionados de las bases de datos disponibles, durante una sequía prolongada en tierra, similar a las que las plantas deben afrontar en la naturaleza. Se ha utilizado en este caso, además de P. pinaster, P. pinea, otra conífera mediterránea adaptada a las sequías recurrentes. Este trabajo ha permitido identificar genes candidato expresionales, presumiblemente comunes en la respuesta molecular de las coníferas al déficit hídrico. Se han detectado diferencias notables en la expresión de determinados genes, que podrían ser los responsables de las diferencias exhibidas por ambas especies en el comportamiento frente a la sequía. Entre los genes identificados como inducidos por el estrés hídrico se encuentran varios miembros de la familia de las deshidrinas. Trabajos previos han utilizado deshidrinas como genes candidato; no obstante, la falta de especificidad de ciertos fragmentos y marcadores utilizados, debido a la complejidad estructural de esta familia, resta fiabilidad a algunos de los resultados publicados. Por este motivo, se ha estudiado en detalle esta familia en P. pinaster, se han identificado y caracterizado 8 miembros y se ha analizado su patrón de expresión frente a sequía. Este estudio ha permitido describir por primera vez unos segmentos conservados en la secuencia de aminoácidos de las deshidrinas de pináceas, cuya presencia y número de repeticiones parece estar relacionado con su especificidad. Por último, se han escogido tres genes implicados en distintas fases de la respuesta al estrés hídrico para su análisis exhaustivo: una deshidrina, una nodulina y un factor de transcripción tipo AP2. Se ha caracterizado su estructura exón/intrón y secuenciado su región promotora. Además, se han obtenido líneas transformadas que sobreexpresan estos genes tanto de forma heteróloga, en la especie modelo Arabidopsis thaliana, como en el propio P. pinaster. Este material facilitará la realización de futuros estudios sobre la función y el mecanismo de actuación de estos genes en la respuesta al estrés hídrico. ABSTRACT This thesis focuses in the study of the molecular response to water stress in Mediterranean conifers. For this purpose, P. pinaster was selected as model species. It’s the most abundant conifer in Spain, living in a wide range of ecological conditions, especially regarding water availability. First, we have applied a controlled polyethylene glycol-induced water stress in hydroponic culture and obtained a suppression subtractive hybridization (SSH) library, with the aim of identifying genes induced by water stress, analysing their expression in roots, stems and needles. We have then analysed the expression patterns of the identified genes, together with other genes selected from public databases. This study was conducted throughout a prolonged drought stress in soil, similar to the ones plants have to face in nature. In this case not only P. pinaster was analysed but also P. pinea, another Mediterranean conifer well adapted to recurrent droughts. This work has enabled us to identify of reliable candidate genes, presumably shared with other conifers in the response to water stress. We observed remarkable differences in the expression of some genes, which could be involved in the differential behaviour that these species show in the water stress response. Within the genes induced by water stress, several members of the dehydrin gene family were identified. Due to the structural complexity of the family, certain ambiguities and inconsistencies have been detected in previous works that have used dehydrins as candidate genes. For this reason, we have analysed thoroughly this gene family in P. pinaster, and have identified and characterized eight different members, whose expression patterns during drought have also been assessed. This study has allowed us to identify for the first time novel conserved segments in the amino acids sequences of Pinaceae. The presence and number of repetitions of these segments could be associated with the functional specificity of these proteins. Finally, three genes involved in different steps of the water stress response were selected for an exhaustive analysis: a dehydrin, a nodulin and an AP2 transcription factor. For all of them, the exon/intron structure was established and their promoter region was sequenced. Also, transformed lines were obtained both in Arabidopsis thaliana and in P. pinaster for the constitutive overexpression of these genes. This material will facilitate the development of further studies to investigate the function of these genes during the water stress response

Genomic analyses of flowering transition and inflorescence development in grapevine = Análisis genómicos de la transición floral y del desarrollo de la inflorescencia en la vid

The general objective of this work is to analyze the regulatory processes underlying flowering transition and inflorescence and flower development in grapevine. Most of these crucial developmental events take place within buds growing during two seasons in two consecutive years. During the first season, the shoot apical meristem within the bud differentiates all the basic elements of the shoot including flowering transition in lateral primordia and development of inflorescence primordia. These events practically end with bud dormancy. The second season, buds resume shoot growth associated to flower formation and development. In grapevine, the lateral meristems can give rise either to tendril or inflorescence primordia that are homologous organs. With this purpose, we performed global transcriptome analyses along the bud annual cycle and during inflorescence and tendril development. In addition, we approach the genomic analysis of the MIKC type MADS-box gene family in grapevine to identify all its members and assign them putative biological functions. Regarding buds developmental cycle, the results indicate that the main factors explaining the global gene expression differences were the processes of bud dormancy and active growth as well as stress responses. Non dormant buds exhibited up-regulation in functional categories typical of actively proliferating and growing cells (photosynthesis, cell cycle regulation, chromatin assembly) whereas in dormant ones the main functional categories up-regulated were associated to stress response pathways together with transcripts related to starch catabolism. Major transcriptional changes during the dormancy period were associated to the para/endodormancy, endo/ecodormancy and ecodormancy/bud break transitions. Global transcriptional analyses along tendril and inflorescence development suggested that these two homologous organs share a common transcriptional program related to cell proliferation functions. Both structures showed a progressive decrease in the expression of categories such as cell-cycle, auxin metabolism/signaling, DNA metabolism, chromatin assembly and a cluster of five transcripts belonging to the GROWTH-REGULATING FACTOR (GRF) transcription factor family, that are known to control cell proliferation in other species and determine the size of lateral organs. However, they also showed organ specific transcriptional programs that can be related to their differential organ structure and function. Tendrils showed higher transcription of genes related to photosynthesis, hormone signaling and secondary metabolism than inflorescences, while inflorescences have higher transcriptional activity for genes encoding transcription factors (especially those belonging to the MADS-box gene family). Further analysis along inflorescence development evidenced the relevance of additional functions likely related to processes of flower development such as fatty acid and lipid metabolism, jasmonate signaling and oxylipin biosynthesis. The transcriptional analyses performed highlighted the relevance of several groups of transcriptional regulators in the developmental processes studied. The expression profiles along bud development revealed significant differences for some MADS-box subfamilies in relation to other plant species, like the members of the FLC and SVP subfamilies suggesting new roles for these groups in grapevine. In this way, it was found that VvFLC2 and VvAGL15.1 could participate, together with some members of the SPL-L family, in dormancy regulation, as was shown for some of them in other woody plants. Similarly, the expression patterns of the VvFLC1, VvFUL, VvSOC1.1 (together with VvFT, VvMFT1 and VFL) genes could indicate that they play a role in flowering transition in grapevine, in parallel to their roles in other plant systems. The expression levels of VFL, the grapevine LEAFY homolog, could be crucial to specify the development of inflorescence and flower meristems instead of tendril meristems. MADS-box genes VvAP3.1 and 2, VvPI, VvAG1 and 3, VvSEP1-4, as well as VvBS1 and 2 are likely associated with the events of flower meristems and flower organs differentiation, while VvAP1 and VvFUL-L (together with VvSOC1.1, VvAGL6.2) could be involved on tendril development given their expression patterns. In addition, the biological function ofVvAP1 and VvTFL1A was analyzed using a gene silencing approach in transgenic grapevine plants. Our preliminary results suggested a possible role for both genes in the initiation and differentiation of tendrils. Finally, the genomic analysis of the MADS-box gene family in grapevine revealed differential features regarding number and expression pattern of genes putatively involved in the flowering transition process as compared to those involved in the specification of flower and fruit organ identity. Altogether, the results obtained allow identifying putative candidate genes and pathways regulating grapevine reproductive developmental processes paving the way to future experiments demonstrating specific gene biological functions. RESUMEN El objetivo general de este trabajo es analizar los procesos regulatorios subyacentes a la inducción floral así como al desarrollo de la inflorescencia y la flor en la vid. La mayor parte de estos eventos cruciales tienen lugar en las yemas a lo largo de dos estaciones de crecimiento consecutivas. Durante la primera estación, el meristemo apical contenido en la yema diferencia los elementos básicos del pámpano, lo cual incluye la inducción de la floración en los meristemos laterales y el subsiguiente desarrollo de primordios de inflorescencia. Estos procesos prácticamente cesan con la entrada en dormición de la yema. En la segunda estación, se reanuda el crecimiento del pámpano acompañado por la formación y desarrollo de las flores. En la vid, los meristemos laterales pueden dar lugar a primordios de inflorescencia o de zarcillo que son considerados órganos homólogos. Con este objetivo llevamos a cabo un estudio a nivel del transcriptoma de la yema a lo largo de su ciclo anual, así como a lo largo del desarrollo de la inflorescencia y del zarcillo. Además realizamos un análisis genómico de la familia MADS de factores transcripcionales (concretamente aquellos del tipo MIKC) para identificar todos sus miembros y tratar de asignarles posibles funciones biológicas. En cuanto al ciclo de desarrollo de la yema, los resultados indican que los principales factores que explican las diferencias globales en la expresión génica fueron los procesos de dormición de la yema y el crecimiento activo junto con las respuestas a diversos tipos de estrés. Las yemas no durmientes mostraron un incremento en la expresión de genes contenidos en categorías funcionales típicas de células en proliferación y crecimiento activo (como fotosíntesis, regulación del ciclo celular, ensamblaje de cromatina), mientras que en las yemas durmientes, las principales categorías funcionales activadas estaban asociadas a respuestas a estrés, así como con el catabolismo de almidón. Los mayores cambios observados a nivel de transcriptoma en la yema coincidieron con las transiciones de para/endodormición, endo/ecodormición y ecodormición/brotación. Los análisis transcripcionales globales a lo largo del desarrollo del zarcillo y de la inflorescencia sugirieron que estos dos órganos homólogos comparten un programa transcripcional común, relacionado con funciones de proliferación celular. Ambas estructuras mostraron un descenso progresivo en la expresión de genes pertenecientes a categorías funcionales como regulación del ciclo celular, metabolismo/señalización por auxinas, metabolismo de ADN, ensamblaje de cromatina y un grupo de cinco tránscritos pertenecientes a la familia de factores transcripcionales GROWTH-REGULATING FACTOR (GRF), que han sido asociados con el control de la proliferación celular y en determinar el tamaño de los órganos laterales en otras especies. Sin embargo, también pusieron de manifiesto programas transcripcionales que podrían estar relacionados con la diferente estructura y función de dichos órganos. Los zarcillos mostraron mayor actividad transcripcional de genes relacionados con fotosíntesis, señalización hormonal y metabolismo secundario que las inflorescencias, mientras que éstas presentaron mayor actividad transcripcional de genes codificantes de factores de transcripción (especialmente los pertenecientes a la familia MADS-box). Análisis adicionales a lo largo del desarrollo de la inflorescencia evidenciaron la relevancia de otras funciones posiblemente relacionadas con el desarrollo floral, como el metabolismo de lípidos y ácidos grasos, la señalización mediada por jasmonato y la biosíntesis de oxilipinas. Los análisis transcripcionales llevados a cabo pusieron de manifiesto la relevancia de varios grupos de factores transcripcionales en los procesos estudiados. Los perfiles de expresión estudiados a lo largo del desarrollo de la yema mostraron diferencias significativas en algunas de las subfamilias de genes MADS con respecto a otras especies vegetales, como las observadas en los miembros de las subfamilias FLC y SVP, lo cual sugiere que podrían desempeñar nuevas funciones en la vid. En este sentido, se encontró que los genes VvFLC2 y VvAGL15.1 podrían participar, junto con algunos miembros de la familia SPL-L, en la regulación de la dormición. De un modo similar, los patrones de expresión de los genes VvFLC1, VvFUL, VvSOC1.1 (junto con VvFT, VvMFT1 y VFL) podría indicar que desempeñan un papel en la regulación de la inducción de la floración en la vid, como se ha observado en otros sistemas vegetales. Los niveles de expresión de VFL, el homólogo en vid del gen LEAFY de A. thaliana podrían ser cruciales para la especificación del desarrollo de meristemos de inflorescencia y flor en lugar de meristemos de zarcillo. Los genes VvAP3.1 y 2, VvPI, VvAG1 y 3, VvSEP1-4, así como VvBS1 y 2 parecen estar asociados con los eventos de diferenciación de meristemos y órganos florales, mientras que VvAP1 y VvFUL-L (junto con VvSOC1.1 y VvAGL6.2) podrían estar implicados en el desarrollo del zarcillo dados sus patrones de expresión. Adicionalmente, se analizó la función biológica de los genes VvAP1 y VvTFL1A por medio de una estrategia de silenciamiento génico. Los datos preliminares sugieren un posible papel para ambos genes en la iniciación y diferenciación de los zarcillos. Finalmente, el análisis genómico de la familia MADS en vid evidenció diferencias con respecto a otras especies vegetales en cuanto a número de miembros y patrón de expresión en genes supuestamente implicados en la inducción de la floración, en comparación con aquellos relacionados con la especificación de identidad de órganos florales y desarrollo del fruto. En conjunto, los resultados obtenidos han permitido identificar posibles rutas y genes candidatos a participar en la regulación de los procesos de desarrollo reproductivo de la vid, sentando las bases de futuros experimentos encaminados a conocer la funciones biológicas de genes específicos.

The family of DOF transcription factors in Brachypodium distachyon: BdDof24 in germinating seeds

The DOF (DNA binding with One Finger) transcription factor (TF) family is characterized by a binding domain of 52 amino acid residues that is structured as a Cys2/Cys2 Zn2+ finger that recognizes the common core 5?-T/AAAAG-3? in the promoter regions of their target genes. DOF TFs have been associated with biological processes exclusive to higher plants and their close ancestors (algae, mosses and ferns).

Papel de la interleuquina 23 en la diferenciación hacia Th17

The incidence of inflammatory and autoimmune diseases has increased among developed countries in the past 30 years, creating a demand for the development of effective and economic therapies for these diseases. Interleukin 23 (IL-23) is a pro-inflammatory cytokine whose increased production has been shown to play a key role in the establishment and maintenance of inflammatory and autoimmune diseases in different murine models such as inflammatory bowel disease, psoriasis and experimental autoimmune encephalomyelitis. More importantly, increased levels of IL-23 have been found in biopsies from patients with Crohn’s disease and ulcerative colitis, and psoriasis. The pathological consequences of excessive IL-23 signalling have been linked to its ability to promote the production of interleukin 17 (IL-17), particularly in the subpopulation of CD4 T cells Th17. However, the precise molecular mechanisms by which IL-23 sustains the Th17 response and induces pathogenic effector functions in these cells remain largely unknown. The global objective of the experiments carried out in this work was to determine the effect of IL-23 on the proliferation, survival and IL-17 and interferon gamma (IFN-ɣ) production in Th17 cells. These experiments have shown that IL-23 does not promote proliferation or survival of in vitro generated Th17 cells, and that there is no difference in the production of IL -17 in the absence or presence of IL -23. The IL-23 receptor, like other cytokine receptors, lacks intrinsic enzymatic activity. Instead, IL-23 receptor associates with members of the Janus tyrosine kinase family (Jaks). Cytokine binding to a Jak-associated receptor triggers the activation of the Signal Transducers and Activators of Transcription (STAT) family of transcription factors. Previous work indicated that the IL-23 receptor complex is associated with the tyrosine kinases Jak2 and Tyk2 that promote STAT3 phosphorylation. Subsequent studies showed that IL23 activation of STAT3 induces the expression of the transcription factor RORγt, which is crucial for IL-17 production. This work has explored the IL-23 signalling cascade, determining the optimal conditions for STAT3 activation and demonstrating the activation of other transcription factors such as STAT4, STAT5 and STAT1 that contribute to IL-23-mediated signalling pathways.

NF-κB-dependent inhibition of apoptosis is essential for host cell survival during Rickettsia rickettsii infection

The possibility that bacteria may have evolved strategies to overcome host cell apoptosis was explored by using Rickettsia rickettsii, an obligate intracellular Gram-negative bacteria that is the etiologic agent of Rocky Mountain spotted fever. The vascular endothelial cell, the primary target cell during in vivo infection, exhibits no evidence of apoptosis during natural infection and is maintained for a sufficient time to allow replication and cell-to-cell spread prior to eventual death due to necrotic damage. Prior work in our laboratory demonstrated that R. rickettsii infection activates the transcription factor NF-κB and alters expression of several genes under its control. However, when R. rickettsii-induced activation of NF-κB was inhibited, apoptosis of infected but not uninfected endothelial cells rapidly ensued. In addition, human embryonic fibroblasts stably transfected with a superrepressor mutant inhibitory subunit IκB that rendered NF-κB inactivatable also underwent apoptosis when infected, whereas infected wild-type human embryonic fibroblasts survived. R. rickettsii, therefore, appeared to inhibit host cell apoptosis via a mechanism dependent on NF-κB activation. Apoptotic nuclear changes correlated with presence of intracellular organisms and thus this previously unrecognized proapoptotic signal, masked by concomitant NF-κB activation, likely required intracellular infection. Our studies demonstrate that a bacterial organism can exert an antiapoptotic effect, thus modulating the host cell’s apoptotic response to its own advantage by potentially allowing the host cell to remain as a site of infection.

Region-dependent dynamics of cAMP response element-binding protein phosphorylation in the basal ganglia

The cAMP response element-binding protein (CREB) is an activity-dependent transcription factor that is involved in neural plasticity. The kinetics of CREB phosphorylation have been suggested to be important for gene activation, with sustained phosphorylation being associated with downstream gene expression. If so, the duration of CREB phosphorylation might serve as an indicator for time-sensitive plastic changes in neurons. To screen for regions potentially involved in dopamine-mediated plasticity in the basal ganglia, we used organotypic slice cultures to study the patterns of dopamine- and calcium-mediated CREB phosphorylation in the major subdivisions of the striatum. Different durations of CREB phosphorylation were evoked in the dorsal and ventral striatum by activation of dopamine D1-class receptors. The same D1 stimulus elicited (i) transient phosphorylation (≤15 min) in the matrix of the dorsal striatum; (ii) sustained phosphorylation (≤2 hr) in limbic-related structures including striosomes, the nucleus accumbens, the fundus striati, and the bed nucleus of the stria terminalis; and (iii) prolonged phosphorylation (up to 4 hr or more) in cellular islands in the olfactory tubercle. Elevation of Ca2+ influx by stimulation of L-type Ca2+ channels, NMDA, or KCl induced strong CREB phosphorylation in the dorsal striatum but not in the olfactory tubercle. These findings differentiate the response of CREB to dopamine and calcium signals in different striatal regions and suggest that dopamine-mediated CREB phosphorylation is persistent in limbic-related regions of the neonatal basal ganglia. The downstream effects activated by persistent CREB phosphorylation may include time-sensitive neuroplasticity modulated by dopamine.

Assembly, subunit composition, and footprint of human DNA repair excision nuclease

The assembly and composition of human excision nuclease were investigated by electrophoretic mobility shift assay and DNase I footprinting. Individual repair factors or any combination of up to four repair factors failed to form DNA–protein complexes of high specificity and stability. A stable complex of high specificity can be detected only when XPA/RPA, transcription factor IIH, XPC⋅HHR23B, and XPG and ATP are present in the reaction mixture. The XPF⋅ERCC1 heterodimer changes the electrophoretic mobility of the DNA–protein complex formed with the other five repair factors, but it does not confer additional specificity. By using proteins with peptide tags or antibodies to the repair factors in electrophoretic mobility shift assays, it was found that XPA, replication protein A, transcription factor IIH, XPG, and XPF⋅excision repair cross-complementing 1 but not XPC⋅HHR23B were present in the penultimate and ultimate dual incision complexes. Thus, it appears that XPC⋅HHR23B is a molecular matchmaker that participates in the assembly of the excision nuclease but is not present in the ultimate dual incision complex. The excision nuclease makes an assymmetric DNase I footprint of ≈30 bp around the damage and increases the DNase I sensitivity of the DNA on both sides of the footprint.