Alterations in Ptch1 Cis-Regulation Underlie Loss of Antero-Posterior

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Alterations in Ptch1 Cis-Regulation Underlie Loss of Antero-Posterior Alterations in Ptch1 Cis-Regulation underlie loss of antero-posterior identity and digit reductions in bovine limbs Rolf Zeller, Amandine Duchesne, Sepziale Dario, Guillaume Andrey, Erkan Uenal, Christian Basel, Benoit Robert, Carol Wicking, Denis Duboule, Javier Lopez-Rios To cite this version: Rolf Zeller, Amandine Duchesne, Sepziale Dario, Guillaume Andrey, Erkan Uenal, et al.. Alterations in Ptch1 Cis-Regulation underlie loss of antero-posterior identity and digit reductions in bovine limbs. 16. International Society of Developmental Biologists Congress, Jun 2013, Cancun, Mexico. hal- 01193898 HAL Id: hal-01193898 https://hal.archives-ouvertes.fr/hal-01193898 Submitted on 3 Jun 2020 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. International Society of Developmental Biologists 17th International Congress of Developmental Biology Cancun, Mexico June 16 - 20, 2013 72nd Annual Meeting of the Society for Developmental Biology VII Latin American Society of Developmental Biology Meeting XI Congreso de la Sociedad Mexicana de Biologia del Desarrollo ABSTRACTS 1 Program/Abstract # 1 Mechanical force controls chemical signals in creating plant pattern Elliot Meyerowitz (Caltech, USA) One pattern generated by the stem cells at the tip of each plant shoot – the shoot apical meristem – of flowering plants has held a fascination for generations of biologists and mathematicians. This is the phyllotactic pattern, the pattern of leaves and flowers around the stem. The most common such pattern is the spiral phyllotactic pattern, which creates the highly recognizable organization of compound fruits such as pineapples, of flowers like roses, and of inflorescences such as sunflowers. The model plant Arabidopsis thaliana also has a spiral phyllotaxis, and we have used genetic, genomic, and cell biological approaches to learn in detail how the cells of the meristem collaborate to generate this pattern. The major chemical signal is auxin, which has a specific transport system, in which a family of plasma membrane proteins directs the efflux of the hormone from cells. The efflux proteins are not uniformly distributed, thereby causing efflux directionally, leading to a net flow of auxin in complex patterns across the surface of the meristem. Auxin not only induces new primordia of leaves and flowers, but also changes the physical properties of the cell wall. These physical changes alter the stress pattern in the meristem surface, which in turn regulates the position of the auxin efflux carrier in anisotropically stressed cells. The feedback between auxin concentration and physical stress creates the dynamic auxin patterns that cause successive auxin peaks at positions approximately 130-140 degrees around the stem, creating the spiral (and other patterns of) phyllotaxis. The stress pattern in the meristem also regulates the microtubule cytoskeleton of meristematic cells, and consequently it may also dictate the plane of cell division. The stress pattern may also determine directions of cellulose synthesis in the cell wall, and thus the subsequent direction of cellular growth, and the anisotropy of cells – leading to changes in auxin flow, and, consequently, feedbacks on the stress pattern. Program/Abstract # 2 Unusual patterns of Hox cluster evolution Peter Holland, Ferdinand Marletaz, Laura Ferguson, Jordi Papas, (Oxford, UK), Fei Xu (Chinese Academy of Science, China), Willie Taylor (NIMR, UK), Pete Olson (Nat Hist Museum London, UK) In the 1980s, the discovery of Hox gene clusters in very different animals paved the way for an integrated science in which principles and processes of embryonic development could be compared between widely divergent evolutionary lineages. A picture has emerged of a conserved Hox gene cluster pattering the ancient head-to-tail axis across all bilaterian animals. Yet there are modifications, and these differences between species may be very helpful in our attempts to link genotype evolution to phenotype evolution. Using examples from on-going research, I will discuss intriguing examples of Hox cluster breakage, Hox cluster expansion and Hox cluster shrinkage. Program/Abstract # 3 Regulation of gene expression by RNA polymerase II promoter pausing during mouse embryonic development Megan Jane Wilson (Univ. of Otago, New Zealand) Proximal-promoter pausing by RNA polymerase II (RNA-polII) is a key rate-limiting step in transcription initiation. Recent genome- wide studies using chromatin-immunoprecipitation to detect stalled RNA-polII have shown that promoter-pausing occurs for a number of genes, particularly developmental control genes. This stalling is believed to be a mechanism of gene regulation, causing RNA-polII to be paused near a promoter region, ready to respond to environmental or developmental cues. Two transcription elongation factors DSIF and NELF control promoter stalling by RNA-polII. Our laboratory studies sex-specific differentiation of developing mouse embryo tissues and we have utilized this system to study RNA polII stalling and its effect on gene expression over key developmental stages. Using ChIP-seq with antibodies against RNApolII, we identified many promoters that have RNA-polII stalled in a sex-specific manor in both gonad and head tissue at 13.5 dpc. This corresponded to differences in gene expression between the sexes for the associated gene transcript (as assayed by qPCR). For some transcripts, RNA polII stalling marked them for future activation at a later time point in development. In other cases, paused RNA polII was associated with genes that were becoming down regulated. This data also reveals that promoter pausing can occur differently between sexes during development. We also have preliminary evidence that indicates that components of NELF and DSIF complexes are expressed differently between the sexes during embryogenesis. Together our data suggests that some genes are being poised to respond to a signal and then strongly upregulated, whereas transcription at other genes is stalled but not activated, perhaps in the absence of an appropriate signal. Program/Abstract # 4 Withdrawn Program/Abstract # 5 Characterization of human developmental enhancers: from whole genomes to single SNPs Alvaro Rada Iglesias (Univ. of Cologne, Germany) Distal regulatory elements, such as enhancers, play a preponderant role in the establishment of cell-type and developmental-stage specific gene expression profiles. However, these elements are difficult to identify, since they lack strong defining features and show limited sequence conservation. In the first part of my talk, I will summarize my postdoctoral work, in which epigenomic approaches were used to characterize the enhancer repertoire of pluripotent (i.e. human embryonic stem cells (hESC)) and multipotent (i.e. human 2 neural crest cells (hNCC)) human embryonic cell populations. In hESC, we uncovered a unique chromatin signature that identifies a novel class of enhancers, which are inactive but poised in hESC and that become active upon differentiation in a lineage-specific manner. Similarly, our epigenomic approach allowed us to characterize enhancers in hNCC, a hitherto largely inaccessible and biochemically intractable vertebrate-specific embryonic cell population that contributes to the formation of multiple tissues and organs, such as the peripheral nervous system and most of the facial bones and cartilages. Using the sequence information contained within hNCC enhancers, we uncovered NR2F1 and NR2F2, two orphan nuclear receptors, as novel neural crest and craniofacial regulators. Finally, I will briefly describe how the genomic characterization of human enhancers in relevant cell types might streamline the identification of functional non-coding genetic variants, which can have far-reaching implications in our understanding of the genetic basis of human complex diseases and human morphological evolution. Program/Abstract # 6 Super-resolution imaging of regulatory chromatin dynamics in developing embryos Alistair Boettiger, Xiaowei Zhuang (Harvard, USA) The differentiation of embryonic cells into their appropriate developmental fates is mediated in part by fine scale structural changes to chromatin. Developmental specific transcription factors may shape this chromatin structure through a variety of mechanisms, such as re-positioning of histones (e.g. to restrict or increase access to DNA) or the generation of higher-order looped chromatin structures (e.g. to facilitate looping of distal regulatory sequences to target sites). These fine scale structural changes are mostly too small (10s of nanometers) to be observed with conventional microscopy techniques (limited to several hundred nanometer resolution), and have so far evaded in vivo observation in intact embryonic tissue. We present super-resolution imaging techniques which allow for the detection of changes in chromatin on the scale of tens of nanometers in developing embryos at gene locations of interest. We can detect locus-specific clusters of modified histones and regulatory chromatin proteins,
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