TY - JOUR AB - The superior colliculus (SC) in the mammalian midbrain is essential for multisensory integration and is composed of a rich diversity of excitatory and inhibitory neurons and glia. However, the developmental principles directing the generation of SC cell-type diversity are not understood. Here, we pursued systematic cell lineage tracing in silico and in vivo, preserving full spatial information, using genetic mosaic analysis with double markers (MADM)-based clonal analysis with single-cell sequencing (MADM-CloneSeq). The analysis of clonally related cell lineages revealed that radial glial progenitors (RGPs) in SC are exceptionally multipotent. Individual resident RGPs have the capacity to produce all excitatory and inhibitory SC neuron types, even at the stage of terminal division. While individual clonal units show no pre-defined cellular composition, the establishment of appropriate relative proportions of distinct neuronal types occurs in a PTEN-dependent manner. Collectively, our findings provide an inaugural framework at the single-RGP/-cell level of the mammalian SC ontogeny. AU - Cheung, Giselle T AU - Pauler, Florian AU - Koppensteiner, Peter AU - Krausgruber, Thomas AU - Streicher, Carmen AU - Schrammel, Martin AU - Özgen, Natalie Y AU - Ivec, Alexis AU - Bock, Christoph AU - Shigemoto, Ryuichi AU - Hippenmeyer, Simon ID - 12875 IS - 2 JF - Neuron SN - 0896-6273 TI - Multipotent progenitors instruct ontogeny of the superior colliculus VL - 112 ER - TY - JOUR AB - Little is known about the critical metabolic changes that neural cells have to undergo during development and how temporary shifts in this program can influence brain circuitries and behavior. Inspired by the discovery that mutations in SLC7A5, a transporter of metabolically essential large neutral amino acids (LNAAs), lead to autism, we employed metabolomic profiling to study the metabolic states of the cerebral cortex across different developmental stages. We found that the forebrain undergoes significant metabolic remodeling throughout development, with certain groups of metabolites showing stage-specific changes, but what are the consequences of perturbing this metabolic program? By manipulating Slc7a5 expression in neural cells, we found that the metabolism of LNAAs and lipids are interconnected in the cortex. Deletion of Slc7a5 in neurons affects the postnatal metabolic state, leading to a shift in lipid metabolism. Additionally, it causes stage- and cell-type-specific alterations in neuronal activity patterns, resulting in a long-term circuit dysfunction. AU - Knaus, Lisa AU - Basilico, Bernadette AU - Malzl, Daniel AU - Gerykova Bujalkova, Maria AU - Smogavec, Mateja AU - Schwarz, Lena A. AU - Gorkiewicz, Sarah AU - Amberg, Nicole AU - Pauler, Florian AU - Knittl-Frank, Christian AU - Tassinari, Marianna AU - Maulide, Nuno AU - Rülicke, Thomas AU - Menche, Jörg AU - Hippenmeyer, Simon AU - Novarino, Gaia ID - 12802 IS - 9 JF - Cell KW - General Biochemistry KW - Genetics and Molecular Biology SN - 0092-8674 TI - Large neutral amino acid levels tune perinatal neuronal excitability and survival VL - 186 ER - TY - JOUR AB - The generation of a correctly-sized cerebral cortex with all-embracing neuronal and glial cell-type diversity critically depends on faithful radial glial progenitor (RGP) cell proliferation/differentiation programs. Temporal RGP lineage progression is regulated by Polycomb Repressive Complex 2 (PRC2) and loss of PRC2 activity results in severe neurogenesis defects and microcephaly. How PRC2-dependent gene expression instructs RGP lineage progression is unknown. Here we utilize Mosaic Analysis with Double Markers (MADM)-based single cell technology and demonstrate that PRC2 is not cell-autonomously required in neurogenic RGPs but rather acts at the global tissue-wide level. Conversely, cortical astrocyte production and maturation is cell-autonomously controlled by PRC2-dependent transcriptional regulation. We thus reveal highly distinct and sequential PRC2 functions in RGP lineage progression that are dependent on complex interplays between intrinsic and tissue-wide properties. In a broader context our results imply a critical role for the genetic and cellular niche environment in neural stem cell behavior. AU - Amberg, Nicole AU - Pauler, Florian AU - Streicher, Carmen AU - Hippenmeyer, Simon ID - 11336 IS - 44 JF - Science Advances SN - 2375-2548 TI - Tissue-wide genetic and cellular landscape shapes the execution of sequential PRC2 functions in neural stem cell lineage progression VL - 8 ER - TY - JOUR AB - Mutations are acquired frequently, such that each cell's genome inscribes its history of cell divisions. Common genomic alterations involve loss of heterozygosity (LOH). LOH accumulates throughout the genome, offering large encoding capacity for inferring cell lineage. Using only single-cell RNA sequencing (scRNA-seq) of mouse brain cells, we found that LOH events spanning multiple genes are revealed as tracts of monoallelically expressed, constitutionally heterozygous single-nucleotide variants (SNVs). We simultaneously inferred cell lineage and marked developmental time points based on X chromosome inactivation and the total number of LOH events while identifying cell types from gene expression patterns. Our results are consistent with progenitor cells giving rise to multiple cortical cell types through stereotyped expansion and distinct waves of neurogenesis. This type of retrospective analysis could be incorporated into scRNA-seq pipelines and, compared with experimental approaches for determining lineage in model organisms, is applicable where genetic engineering is prohibited, such as humans. AU - Anderson, Donovan J. AU - Pauler, Florian AU - Mckenna, Aaron AU - Shendure, Jay AU - Hippenmeyer, Simon AU - Horwitz, Marshall S. ID - 11449 IS - 6 JF - Cell Systems SN - 2405-4712 TI - Simultaneous brain cell type and lineage determined by scRNA-seq reveals stereotyped cortical development VL - 13 ER - TY - JOUR AB - The mammalian neocortex is composed of diverse neuronal and glial cell classes that broadly arrange in six distinct laminae. Cortical layers emerge during development and defects in the developmental programs that orchestrate cortical lamination are associated with neurodevelopmental diseases. The developmental principle of cortical layer formation depends on concerted radial projection neuron migration, from their birthplace to their final target position. Radial migration occurs in defined sequential steps, regulated by a large array of signaling pathways. However, based on genetic loss-of-function experiments, most studies have thus far focused on the role of cell-autonomous gene function. Yet, cortical neuron migration in situ is a complex process and migrating neurons traverse along diverse cellular compartments and environments. The role of tissue-wide properties and genetic state in radial neuron migration is however not clear. Here we utilized mosaic analysis with double markers (MADM) technology to either sparsely or globally delete gene function, followed by quantitative single-cell phenotyping. The MADM-based gene ablation paradigms in combination with computational modeling demonstrated that global tissue-wide effects predominate cell-autonomous gene function albeit in a gene-specific manner. Our results thus suggest that the genetic landscape in a tissue critically affects the overall migration phenotype of individual cortical projection neurons. In a broader context, our findings imply that global tissue-wide effects represent an essential component of the underlying etiology associated with focal malformations of cortical development in particular, and neurological diseases in general. AU - Hansen, Andi H AU - Pauler, Florian AU - Riedl, Michael AU - Streicher, Carmen AU - Heger, Anna-Magdalena AU - Laukoter, Susanne AU - Sommer, Christoph M AU - Nicolas, Armel AU - Hof, Björn AU - Tsai, Li Huei AU - Rülicke, Thomas AU - Hippenmeyer, Simon ID - 10791 IS - 1 JF - Oxford Open Neuroscience TI - Tissue-wide effects override cell-intrinsic gene function in radial neuron migration VL - 1 ER - TY - GEN AB - Acquired mutations are sufficiently frequent such that the genome of a single cell offers a record of its history of cell divisions. Among more common somatic genomic alterations are loss of heterozygosity (LOH). Large LOH events are potentially detectable in single cell RNA sequencing (scRNA-seq) datasets as tracts of monoallelic expression for constitutionally heterozygous single nucleotide variants (SNVs) located among contiguous genes. We identified runs of monoallelic expression, consistent with LOH, uniquely distributed throughout the genome in single cell brain cortex transcriptomes of F1 hybrids involving different inbred mouse strains. We then phylogenetically reconstructed single cell lineages and simultaneously identified cell types by corresponding gene expression patterns. Our results are consistent with progenitor cells giving rise to multiple cortical cell types through stereotyped expansion and distinct waves of neurogenesis. Compared to engineered recording systems, LOH events accumulate throughout the genome and across the lifetime of an organism, affording tremendous capacity for encoding lineage information and increasing resolution for later cell divisions. This approach can conceivably be computationally incorporated into scRNA-seq analysis and may be useful for organisms where genetic engineering is prohibitive, such as humans. AU - Anderson, Donovan J. AU - Pauler, Florian AU - McKenna, Aaron AU - Shendure, Jay AU - Hippenmeyer, Simon AU - Horwitz, Marshall S. ID - 9082 T2 - bioRxiv TI - Simultaneous identification of brain cell type and lineage via single cell RNA sequencing ER - TY - JOUR AB - Genomic imprinting is an epigenetic mechanism that results in parental allele-specific expression of ~1% of all genes in mouse and human. Imprinted genes are key developmental regulators and play pivotal roles in many biological processes such as nutrient transfer from the mother to offspring and neuronal development. Imprinted genes are also involved in human disease, including neurodevelopmental disorders, and often occur in clusters that are regulated by a common imprint control region (ICR). In extra-embryonic tissues ICRs can act over large distances, with the largest surrounding Igf2r spanning over 10 million base-pairs. Besides classical imprinted expression that shows near exclusive maternal or paternal expression, widespread biased imprinted expression has been identified mainly in brain. In this review we discuss recent developments mapping cell type specific imprinted expression in extra-embryonic tissues and neocortex in the mouse. We highlight the advantages of using an inducible uniparental chromosome disomy (UPD) system to generate cells carrying either two maternal or two paternal copies of a specific chromosome to analyze the functional consequences of genomic imprinting. Mosaic Analysis with Double Markers (MADM) allows fluorescent labeling and concomitant induction of UPD sparsely in specific cell types, and thus to over-express or suppress all imprinted genes on that chromosome. To illustrate the utility of this technique, we explain how MADM-induced UPD revealed new insights about the function of the well-studied Cdkn1c imprinted gene, and how MADM-induced UPDs led to identification of highly cell type specific phenotypes related to perturbed imprinted expression in the mouse neocortex. Finally, we give an outlook on how MADM could be used to probe cell type specific imprinted expression in other tissues in mouse, particularly in extra-embryonic tissues. AU - Pauler, Florian AU - Hudson, Quanah AU - Laukoter, Susanne AU - Hippenmeyer, Simon ID - 9188 IS - 5 JF - Neurochemistry International KW - Cell Biology KW - Cellular and Molecular Neuroscience SN - 0197-0186 TI - Inducible uniparental chromosome disomy to probe genomic imprinting at single-cell level in brain and beyond VL - 145 ER - TY - JOUR AB - In mammalian genomes, differentially methylated regions (DMRs) and histone marks including trimethylation of histone 3 lysine 27 (H3K27me3) at imprinted genes are asymmetrically inherited to control parentally-biased gene expression. However, neither parent-of-origin-specific transcription nor imprints have been comprehensively mapped at the blastocyst stage of preimplantation development. Here, we address this by integrating transcriptomic and epigenomic approaches in mouse preimplantation embryos. We find that seventy-one genes exhibit previously unreported parent-of-origin-specific expression in blastocysts (nBiX: novel blastocyst-imprinted expressed). Uniparental expression of nBiX genes disappears soon after implantation. Micro-whole-genome bisulfite sequencing (µWGBS) of individual uniparental blastocysts detects 859 DMRs. We further find that 16% of nBiX genes are associated with a DMR, whereas most are associated with parentally-biased H3K27me3, suggesting a role for Polycomb-mediated imprinting in blastocysts. nBiX genes are clustered: five clusters contained at least one published imprinted gene, and five clusters exclusively contained nBiX genes. These data suggest that early development undergoes a complex program of stage-specific imprinting involving different tiers of regulation. AU - Santini, Laura AU - Halbritter, Florian AU - Titz-Teixeira, Fabian AU - Suzuki, Toru AU - Asami, Maki AU - Ma, Xiaoyan AU - Ramesmayer, Julia AU - Lackner, Andreas AU - Warr, Nick AU - Pauler, Florian AU - Hippenmeyer, Simon AU - Laue, Ernest AU - Farlik, Matthias AU - Bock, Christoph AU - Beyer, Andreas AU - Perry, Anthony C.F. AU - Leeb, Martin ID - 9601 IS - 1 JF - Nature Communications TI - Genomic imprinting in mouse blastocysts is predominantly associated with H3K27me3 VL - 12 ER - TY - JOUR AB - Endometriosis is a common gynecological disorder characterized by ectopic growth of endometrium outside the uterus and is associated with chronic pain and infertility. We investigated the role of the long intergenic noncoding RNA 01133 (LINC01133) in endometriosis, an lncRNA that has been implicated in several types of cancer. We found that LINC01133 is upregulated in ectopic endometriotic lesions. As expression appeared higher in the epithelial endometrial layer, we performed a siRNA knockdown of LINC01133 in an endometriosis epithelial cell line. Phenotypic assays indicated that LINC01133 may promote proliferation and suppress cellular migration, and affect the cytoskeleton and morphology of the cells. Gene ontology analysis of differentially expressed genes indicated that cell proliferation and migration pathways were affected in line with the observed phenotype. We validated upregulation of p21 and downregulation of Cyclin A at the protein level, which together with the quantification of the DNA content using fluorescence-activated cell sorting (FACS) analysis indicated that the observed effects on cellular proliferation may be due to changes in cell cycle. Further, we found testis-specific protein kinase 1 (TESK1) kinase upregulation corresponding with phosphorylation and inactivation of actin severing protein Cofilin, which could explain changes in the cytoskeleton and cellular migration. These results indicate that endometriosis is associated with LINC01133 upregulation, which may affect pathogenesis via the cellular proliferation and migration pathways. AU - Yotova, Iveta AU - Hudson, Quanah J. AU - Pauler, Florian AU - Proestling, Katharina AU - Haslinger, Isabella AU - Kuessel, Lorenz AU - Perricos, Alexandra AU - Husslein, Heinrich AU - Wenzl, René ID - 9906 IS - 16 JF - International Journal of Molecular Sciences SN - 16616596 TI - LINC01133 inhibits invasion and promotes proliferation in an endometriosis epithelial cell line VL - 22 ER - TY - JOUR AB - Scientific research is to date largely restricted to wealthy laboratories in developed nations due to the necessity of complex and expensive equipment. This inequality limits the capacity of science to be used as a diplomatic channel. Maker movements use open-source technologies including additive manufacturing (3D printing) and laser cutting, together with low-cost computers for developing novel products. This movement is setting the groundwork for a revolution, allowing scientific equipment to be sourced at a fraction of the cost and has the potential to increase the availability of equipment for scientists around the world. Science education is increasingly recognized as another channel for science diplomacy. In this perspective, we introduce the idea that the Maker movement and open-source technologies have the potential to revolutionize science, technology, engineering and mathematics (STEM) education worldwide. We present an open-source STEM didactic tool called SCOPES (Sparking Curiosity through Open-source Platforms in Education and Science). SCOPES is self-contained, independent of local resources, and cost-effective. SCOPES can be adapted to communicate complex subjects from genetics to neurobiology, perform real-world biological experiments and explore digitized scientific samples. We envision such platforms will enhance science diplomacy by providing a means for scientists to share their findings with classrooms and for educators to incorporate didactic concepts into STEM lessons. By providing students the opportunity to design, perform, and share scientific experiments, students also experience firsthand the benefits of a multinational scientific community. We provide instructions on how to build and use SCOPES on our webpage: http://scopeseducation.org. AU - Beattie, Robert J AU - Hippenmeyer, Simon AU - Pauler, Florian ID - 7814 JF - Frontiers in Education SN - 2504-284X TI - SCOPES: Sparking curiosity through Open-Source platforms in education and science VL - 5 ER - TY - JOUR AB - Mosaic analysis with double markers (MADM) technology enables concomitant fluorescent cell labeling and induction of uniparental chromosome disomy (UPD) with single-cell resolution. In UPD, imprinted genes are either overexpressed 2-fold or are not expressed. Here, the MADM platform is utilized to probe imprinting phenotypes at the transcriptional level. This protocol highlights major steps for the generation and isolation of projection neurons and astrocytes with MADM-induced UPD from mouse cerebral cortex for downstream single-cell and low-input sample RNA-sequencing experiments. For complete details on the use and execution of this protocol, please refer to Laukoter et al. (2020b). AU - Laukoter, Susanne AU - Amberg, Nicole AU - Pauler, Florian AU - Hippenmeyer, Simon ID - 8978 IS - 3 JF - STAR Protocols SN - 2666-1667 TI - Generation and isolation of single cells from mouse brain with mosaic analysis with double markers-induced uniparental chromosome disomy VL - 1 ER - TY - JOUR AB - The cyclin-dependent kinase inhibitor p57KIP2 is encoded by the imprinted Cdkn1c locus, exhibits maternal expression, and is essential for cerebral cortex development. How Cdkn1c regulates corticogenesis is however not clear. To this end we employ Mosaic Analysis with Double Markers (MADM) technology to genetically dissect Cdkn1c gene function in corticogenesis at single cell resolution. We find that the previously described growth-inhibitory Cdkn1c function is a non-cell-autonomous one, acting on the whole organism. In contrast we reveal a growth-promoting cell-autonomous Cdkn1c function which at the mechanistic level mediates radial glial progenitor cell and nascent projection neuron survival. Strikingly, the growth-promoting function of Cdkn1c is highly dosage sensitive but not subject to genomic imprinting. Collectively, our results suggest that the Cdkn1c locus regulates cortical development through distinct cell-autonomous and non-cell-autonomous mechanisms. More generally, our study highlights the importance to probe the relative contributions of cell intrinsic gene function and tissue-wide mechanisms to the overall phenotype. AU - Laukoter, Susanne AU - Beattie, Robert J AU - Pauler, Florian AU - Amberg, Nicole AU - Nakayama, Keiichi I. AU - Hippenmeyer, Simon ID - 7253 JF - Nature Communications SN - 2041-1723 TI - Imprinted Cdkn1c genomic locus cell-autonomously promotes cell survival in cerebral cortex development VL - 11 ER - TY - JOUR AB - In mammalian genomes, a subset of genes is regulated by genomic imprinting, resulting in silencing of one parental allele. Imprinting is essential for cerebral cortex development, but prevalence and functional impact in individual cells is unclear. Here, we determined allelic expression in cortical cell types and established a quantitative platform to interrogate imprinting in single cells. We created cells with uniparental chromosome disomy (UPD) containing two copies of either the maternal or the paternal chromosome; hence, imprinted genes will be 2-fold overexpressed or not expressed. By genetic labeling of UPD, we determined cellular phenotypes and transcriptional responses to deregulated imprinted gene expression at unprecedented single-cell resolution. We discovered an unexpected degree of cell-type specificity and a novel function of imprinting in the regulation of cortical astrocyte survival. More generally, our results suggest functional relevance of imprinted gene expression in glial astrocyte lineage and thus for generating cortical cell-type diversity. AU - Laukoter, Susanne AU - Pauler, Florian AU - Beattie, Robert J AU - Amberg, Nicole AU - Hansen, Andi H AU - Streicher, Carmen AU - Penz, Thomas AU - Bock, Christoph AU - Hippenmeyer, Simon ID - 8162 IS - 6 JF - Neuron SN - 0896-6273 TI - Cell-type specificity of genomic imprinting in cerebral cortex VL - 107 ER - TY - GEN AB - In mammals, chromatin marks at imprinted genes are asymmetrically inherited to control parentally-biased gene expression. This control is thought predominantly to involve parent-specific differentially methylated regions (DMR) in genomic DNA. However, neither parent-of-origin-specific transcription nor DMRs have been comprehensively mapped. We here address this by integrating transcriptomic and epigenomic approaches in mouse preimplantation embryos (blastocysts). Transcriptome-analysis identified 71 genes expressed with previously unknown parent-of-origin-specific expression in blastocysts (nBiX: novel blastocyst-imprinted expression). Uniparental expression of nBiX genes disappeared soon after implantation. Micro-whole-genome bisulfite sequencing (μWGBS) of individual uniparental blastocysts detected 859 DMRs. Only 18% of nBiXs were associated with a DMR, whereas 60% were associated with parentally-biased H3K27me3. This suggests a major role for Polycomb-mediated imprinting in blastocysts. Five nBiX-clusters contained at least one known imprinted gene, and five novel clusters contained exclusively nBiX-genes. These data suggest a complex program of stage-specific imprinting involving different tiers of regulation. AU - Santini, Laura AU - Halbritter, Florian AU - Titz-Teixeira, Fabian AU - Suzuki, Toru AU - Asami, Maki AU - Ramesmayer, Julia AU - Ma, Xiaoyan AU - Lackner, Andreas AU - Warr, Nick AU - Pauler, Florian AU - Hippenmeyer, Simon AU - Laue, Ernest AU - Farlik, Matthias AU - Bock, Christoph AU - Beyer, Andreas AU - Perry, Anthony C. F. AU - Leeb, Martin ID - 8813 T2 - bioRxiv TI - Novel imprints in mouse blastocysts are predominantly DNA methylation independent ER - TY - JOUR AB - Long non-coding (lnc) RNAs are numerous and found throughout the mammalian genome, and many are thought to be involved in the regulation of gene expression. However, the majority remain relatively uncharacterised and of uncertain function making the use of model systems to uncover their mode of action valuable. Imprinted lncRNAs target and recruit epigenetic silencing factors to a cluster of imprinted genes on the same chromosome, making them one of the best characterized lncRNAs for silencing distant genes in cis. In this study we examined silencing of the distant imprinted gene Slc22a3 by the lncRNA Airn in the Igf2r imprinted cluster in mouse. Previously we proposed that imprinted lncRNAs may silence distant imprinted genes by disrupting promoter-enhancer interactions by being transcribed through the enhancer, which we called the enhancer interference hypothesis. Here we tested this hypothesis by first using allele-specific chromosome conformation capture (3C) to detect interactions between the Slc22a3 promoter and the locus of the Airn lncRNA that silences it on the paternal chromosome. In agreement with the model, we found interactions enriched on the maternal allele across the entire Airn gene consistent with multiple enhancer-promoter interactions. Therefore, to test the enhancer interference hypothesis we devised an approach to delete the entire Airn gene. However, the deletion showed that there are no essential enhancers for Slc22a2, Pde10a and Slc22a3 within the Airn gene, strongly indicating that the Airn RNA rather than its transcription is responsible for silencing distant imprinted genes. Furthermore, we found that silent imprinted genes were covered with large blocks of H3K27me3 on the repressed paternal allele. Therefore we propose an alternative hypothesis whereby the chromosome interactions may initially guide the lncRNA to target imprinted promoters and recruit repressive chromatin, and that these interactions are lost once silencing is established. AU - Andergassen, Daniel AU - Muckenhuber, Markus AU - Bammer, Philipp C. AU - Kulinski, Tomasz M. AU - Theussl, Hans-Christian AU - Shimizu, Takahiko AU - Penninger, Josef M. AU - Pauler, Florian AU - Hudson, Quanah J. ID - 7399 IS - 7 JF - PLoS Genetics SN - 1553-7404 TI - The Airn lncRNA does not require any DNA elements within its locus to silence distant imprinted genes VL - 15 ER - TY - JOUR AB - Background: Norepinephrine (NE) signaling has a key role in white adipose tissue (WAT) functions, including lipolysis, free fatty acid liberation and, under certain conditions, conversion of white into brite (brown-in-white) adipocytes. However, acute effects of NE stimulation have not been described at the transcriptional network level. Results: We used RNA-seq to uncover a broad transcriptional response. The inference of protein-protein and protein-DNA interaction networks allowed us to identify a set of immediate-early genes (IEGs) with high betweenness, validating our approach and suggesting a hierarchical control of transcriptional regulation. In addition, we identified a transcriptional regulatory network with IEGs as master regulators, including HSF1 and NFIL3 as novel NE-induced IEG candidates. Moreover, a functional enrichment analysis and gene clustering into functional modules suggest a crosstalk between metabolic, signaling, and immune responses. Conclusions: Altogether, our network biology approach explores for the first time the immediate-early systems level response of human adipocytes to acute sympathetic activation, thereby providing a first network basis of early cell fate programs and crosstalks between metabolic and transcriptional networks required for proper WAT function. AU - Higareda Almaraz, Juan AU - Karbiener, Michael AU - Giroud, Maude AU - Pauler, Florian AU - Gerhalter, Teresa AU - Herzig, Stephan AU - Scheideler, Marcel ID - 20 IS - 1 JF - BMC Genomics SN - 1471-2164 TI - Norepinephrine triggers an immediate-early regulatory network response in primary human white adipocytes VL - 19 ER - TY - GEN AB - Table S1. Genes with highest betweenness. Table S2. Local and Master regulators up-regulated. Table S3. Local and Master regulators down-regulated (XLSX 23 kb). AU - Higareda Almaraz, Juan AU - Karbiener, Michael AU - Giroud, Maude AU - Pauler, Florian AU - Gerhalter, Teresa AU - Herzig, Stephan AU - Scheideler, Marcel ID - 9807 TI - Additional file 1: Of Norepinephrine triggers an immediate-early regulatory network response in primary human white adipocytes ER - TY - GEN AB - Table S4. Counts per Gene per Million Reads Mapped. (XLSX 2751 kb). AU - Higareda Almaraz, Juan AU - Karbiener, Michael AU - Giroud, Maude AU - Pauler, Florian AU - Gerhalter, Teresa AU - Herzig, Stephan AU - Scheideler, Marcel ID - 9808 TI - Additional file 3: Of Norepinephrine triggers an immediate-early regulatory network response in primary human white adipocytes ER - TY - JOUR AB - To determine the dynamics of allelic-specific expression during mouse development, we analyzed RNA-seq data from 23 F1 tissues from different developmental stages, including 19 female tissues allowing X chromosome inactivation (XCI) escapers to also be detected. We demonstrate that allelic expression arising from genetic or epigenetic differences is highly tissue-specific. We find that tissue-specific strain-biased gene expression may be regulated by tissue-specific enhancers or by post-transcriptional differences in stability between the alleles. We also find that escape from X-inactivation is tissue-specific, with leg muscle showing an unexpectedly high rate of XCI escapers. By surveying a range of tissues during development, and performing extensive validation, we are able to provide a high confidence list of mouse imprinted genes including 18 novel genes. This shows that cluster size varies dynamically during development and can be substantially larger than previously thought, with the Igf2r cluster extending over 10 Mb in placenta. AU - Andergassen, Daniel AU - Dotter, Christoph AU - Wenzel, Dyniel AU - Sigl, Verena AU - Bammer, Philipp AU - Muckenhuber, Markus AU - Mayer, Daniela AU - Kulinski, Tomasz AU - Theussl, Hans AU - Penninger, Josef AU - Bock, Christoph AU - Barlow, Denise AU - Pauler, Florian AU - Hudson, Quanah ID - 713 JF - eLife SN - 2050084X TI - Mapping the mouse Allelome reveals tissue specific regulation of allelic expression VL - 6 ER - TY - JOUR AB - The concerted production of neurons and glia by neural stem cells (NSCs) is essential for neural circuit assembly. In the developing cerebral cortex, radial glia progenitors (RGPs) generate nearly all neocortical neurons and certain glia lineages. RGP proliferation behavior shows a high degree of non-stochasticity, thus a deterministic characteristic of neuron and glia production. However, the cellular and molecular mechanisms controlling RGP behavior and proliferation dynamics in neurogenesis and glia generation remain unknown. By using mosaic analysis with double markers (MADM)-based genetic paradigms enabling the sparse and global knockout with unprecedented single-cell resolution, we identified Lgl1 as a critical regulatory component. We uncover Lgl1-dependent tissue-wide community effects required for embryonic cortical neurogenesis and novel cell-autonomous Lgl1 functions controlling RGP-mediated glia genesis and postnatal NSC behavior. These results suggest that NSC-mediated neuron and glia production is tightly regulated through the concerted interplay of sequential Lgl1-dependent global and cell intrinsic mechanisms. AU - Beattie, Robert J AU - Postiglione, Maria P AU - Burnett, Laura AU - Laukoter, Susanne AU - Streicher, Carmen AU - Pauler, Florian AU - Xiao, Guanxi AU - Klezovitch, Olga AU - Vasioukhin, Valeri AU - Ghashghaei, Troy AU - Hippenmeyer, Simon ID - 944 IS - 3 JF - Neuron SN - 08966273 TI - Mosaic analysis with double markers reveals distinct sequential functions of Lgl1 in neural stem cells VL - 94 ER -