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Papers by Ruth Ashery-Padan

Research paper thumbnail of The LHX2-OTX2 transcriptional regulatory module controls retinal pigmented epithelium differentiation and underlies genetic risk for age-related macular degeneration

PLOS Biology

Tissue-specific transcription factors (TFs) control the transcriptome through an association with... more Tissue-specific transcription factors (TFs) control the transcriptome through an association with noncoding regulatory regions (cistromes). Identifying the combination of TFs that dictate specific cell fate, their specific cistromes and examining their involvement in complex human traits remain a major challenge. Here, we focus on the retinal pigmented epithelium (RPE), an essential lineage for retinal development and function and the primary tissue affected in age-related macular degeneration (AMD), a leading cause of blindness. By combining mechanistic findings in stem-cell-derived human RPE, in vivo functional studies in mice and global transcriptomic and proteomic analyses, we revealed that the key developmental TFs LHX2 and OTX2 function together in transcriptional module containing LDB1 and SWI/SNF (BAF) to regulate the RPE transcriptome. Importantly, the intersection between the identified LHX2-OTX2 cistrome with published expression quantitative trait loci, ATAC-seq data fro...

Research paper thumbnail of Retinal pigmented epithelium development from the perspective of transcription factors and cis‐regulatory elements

Research paper thumbnail of Cell fate decisions, transcription factors and signaling during early retinal development

Progress in Retinal and Eye Research

Research paper thumbnail of Pax6 directly binds a <i>Trpm3</i> enhancer sequence <i>in vitro</i> and <i>in vivo.</i>

<p>(A) Schematic diagram of the murine <i>Trpm3</i> locus. Three transcription ... more <p>(A) Schematic diagram of the murine <i>Trpm3</i> locus. Three transcription start sites (TSS, black arrows) are distributed across 600 kb. The black rectangles represent <i>Trpm3</i> exons. The red rectangle represents the <i>miR-204</i>-encoding sequence in intron 6. (B) Area downstream of TSS2. Ellipses represent real-time qRT-PCR amplicons. Gray circle represents the location of EMSA probe Trpm3.4. (C) <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1003357#s2&quot; target="_blank">Results</a> of real-time qRT-PCR on DNA from newborn lens ChIP experiment. Y-axis represents relative quantity of template DNA divided by the amount of template of the same reaction in 1% of input DNA. <i>P</i>-values for A1 = 0.0043, A2 = 0.0098, error bars indicate SD. (D) Acrylamide gel of radioactive EMSA probe Trpm3.4. Pax6CON is an oligonucleotide with the consensus binding site of Pax6.. For the Trpm3.4 probe, the first lane is Trpm3.4 probe only, lane 2 is probe+1∶10 flag-Pax6, lane 3 is probe+Pax6-flag, lane 4 is probe with Pax6-flag and competition by cold probe.</p

Research paper thumbnail of Lack of centrioles and primary cilia in <i>STIL<sup>−/−</sup></i> mouse embryos

Although most animal cells contain centrosomes, consisting of a pair of centrioles, their precise... more Although most animal cells contain centrosomes, consisting of a pair of centrioles, their precise contribution to cell division and embryonic development is unclear. Genetic ablation of STIL, an essential component of the centriole replication machinery in mammalian cells, causes embryonic lethality in mice around mid gestation associated with defective Hedgehog signaling. Here, we describe, by focused ion beam scanning electron microscopy, that STIL ¡/¡ mouse embryos do not contain centrioles or primary cilia, suggesting that these organelles are not essential for mammalian development until mid gestation. We further show that the lack of primary cilia explains the absence of Hedgehog signaling in STIL ¡/¡ cells. Exogenous re-expression of STIL or STIL microcephaly mutants compatible with human survival, induced non-templated, de novo generation of centrioles in STIL ¡/¡ cells. Thus, while the abscence of centrioles is compatible with mammalian gastrulation, lack of centrioles and primary cilia impairs Hedgehog signaling and further embryonic development.

Research paper thumbnail of Cerebral Cortex doi:10.1093/cercor/bhp057 In Vivo MRI of Altered Brain Anatomy and Fiber Connectivity in Adult Pax6 Deficient Mice

The impact of developmental ablation of Pax6 function on morphology and functional connectivity o... more The impact of developmental ablation of Pax6 function on morphology and functional connectivity of the adult cerebrum was studied in cortex-specific Pax6 knockout mice (Pax6cKO) using structural magnetic resonance imaging (MRI), manganese-enhanced MRI, and diffusion tensor MRI in conjunction with fiber tractography. Mutants presented with decreased volumes of total brain and olfactory bulb, reduced cortical thickness, and altered layering of the piriform cortex. Tracking of major neuronal fiber bundles revealed a disorganization of callosal fibers with an almost complete lack of interhemispheric connectivity. In Pax6cKO mice intrahemispheric callosal fibers as well as intracortical fibers were predominantly directed along a rostrocaudal orientation instead of a left--right and dorsoventral orientation found in controls. Fiber disorganization also involved the septohippocampal connection targeting mostly the lateral septal nucleus. The hippocampus was rostrally extended and its volum...

Research paper thumbnail of The Roles of Pax6 in Development of the Ocular Lens

Investigative Ophthalmology & Visual Science, 2007

Research paper thumbnail of Targeted deletion of AP-2 alpha in the corneal epithelium results in defects in Bowman's layer and subsequent activation of stromal fibroblasts

Investigative Ophthalmology & Visual Science, 2004

Research paper thumbnail of Role of ERK2 in Lens Cell Proliferation and Differentiation during Development

Investigative Ophthalmology & Visual Science, 2011

Research paper thumbnail of Transcription factors of the RPE play a role in choroid vascularization

Investigative Ophthalmology & Visual Science, 2017

Research paper thumbnail of Investigation Of Pax6 Function In Mouse Ocular Surface Mesenchyme Using A Tissue Specific Mouse Model, Wnt1cre+/Pax6flox/RosamTmG

Investigative Ophthalmology & Visual Science, 2011

Research paper thumbnail of Lysine Acetyltransferases CBP and EP300 are Essential for Histone H3 K18 and K27 Acetylation in the Lens Placode and to Determine the Fate of Lens Progenitor Cells

Investigative Ophthalmology & Visual Science, 2013

Research paper thumbnail of Targeted Deletion of FGF Receptor-2 Identifies a Role for FGF Signaling in Lens Growth

Investigative Ophthalmology & Visual Science, 2002

Research paper thumbnail of Pax6 Is Required for the Differentiation of the Lens Fiber-Cells

Investigative Ophthalmology & Visual Science, 2009

Research paper thumbnail of Roles of LIM homeodomain 2 (Lhx2) in the differentiation of mammalian retinal pigmented epithelium

Acta Ophthalmologica, 2019

Research paper thumbnail of mSWI/SNF (BAF) Complexes Are Indispensable for the Neurogenesis and Development of Embryonic Olfactory Epithelium

PLoS genetics, Sep 1, 2016

Neurogenesis is a key developmental event through which neurons are generated from neural stem/pr... more Neurogenesis is a key developmental event through which neurons are generated from neural stem/progenitor cells. Chromatin remodeling BAF (mSWI/SNF) complexes have been reported to play essential roles in the neurogenesis of the central nervous system. However, whether BAF complexes are required for neuron generation in the olfactory system is unknown. Here, we identified onscBAF and ornBAF complexes, which are specifically present in olfactory neural stem cells (oNSCs) and olfactory receptor neurons (ORNs), respectively. We demonstrated that BAF155 subunit is highly expressed in both oNSCs and ORNs, whereas high expression of BAF170 subunit is observed only in ORNs. We report that conditional deletion of BAF155, a core subunit in both onscBAF and ornBAF complexes, causes impaired proliferation of oNSCs as well as defective maturation and axonogenesis of ORNs in the developing olfactory epithelium (OE), while the high expression of BAF170 is important for maturation of ORNs. Interes...

Research paper thumbnail of Nature Neuroscience Suppl Info 2013

Research paper thumbnail of Sensory cortex limits cortical maps and drives top-down plasticity in thalamocortical circuits

Nature Neuroscience, 2013

The primary somatosensory cortex (S1) contains a complete body map that mirrors the subcortical m... more The primary somatosensory cortex (S1) contains a complete body map that mirrors the subcortical maps developed by peripheral sensory input projecting to the sensory hindbrain, the thalamus and then S1. Peripheral changes during development alter these maps through 'bottom-up' plasticity. Unknown is how S1 size influences map organization and whether an altered S1 map feeds back to affect subcortical maps. We show that the size of S1 in mice is significantly reduced by cortex-specific deletion of Pax6, resulting in a reduced body map and loss of body representations by an exclusion of later-differentiating sensory thalamocortical input. An initially normal sensory thalamus was repatterned to match the aberrant S1 map by apoptotic deletion of thalamic neurons representing body parts with axons excluded from S1. Deleted representations were rescued by altering competition between thalamocortical axons using sensory deprivation or increasing the size of S1. Thus, S1 size determined the resolution and completeness of body maps and engaged 'top-down' plasticity that repatterned the sensory thalamus to match S1.

Research paper thumbnail of Somatic gene targeting in the developing and adult mouse retina

Methods, 2002

Retinogenesis is a developmental process that is tightly regulated both temporally and spatially ... more Retinogenesis is a developmental process that is tightly regulated both temporally and spatially and is therefore an excellent model system for studying the molecular and cellular mechanisms of neurogenesis in the central nervous system. Understanding of these events in vivo is greatly facilitated by the availability of mouse mutant models, including those with natural or targeted mutations and those with conditional knockout or forced expression of genes. This article reviews these genetic modifications and their contribution to the study of retinogenesis in mammals, with special emphasis on conditional gene targeting approaches.

Research paper thumbnail of Distinct Regions Specify the Targeting of Otefin to the Nucleoplasmic Side of the Nuclear Envelope

Journal of Biological Chemistry, 1997

Research paper thumbnail of The LHX2-OTX2 transcriptional regulatory module controls retinal pigmented epithelium differentiation and underlies genetic risk for age-related macular degeneration

PLOS Biology

Tissue-specific transcription factors (TFs) control the transcriptome through an association with... more Tissue-specific transcription factors (TFs) control the transcriptome through an association with noncoding regulatory regions (cistromes). Identifying the combination of TFs that dictate specific cell fate, their specific cistromes and examining their involvement in complex human traits remain a major challenge. Here, we focus on the retinal pigmented epithelium (RPE), an essential lineage for retinal development and function and the primary tissue affected in age-related macular degeneration (AMD), a leading cause of blindness. By combining mechanistic findings in stem-cell-derived human RPE, in vivo functional studies in mice and global transcriptomic and proteomic analyses, we revealed that the key developmental TFs LHX2 and OTX2 function together in transcriptional module containing LDB1 and SWI/SNF (BAF) to regulate the RPE transcriptome. Importantly, the intersection between the identified LHX2-OTX2 cistrome with published expression quantitative trait loci, ATAC-seq data fro...

Research paper thumbnail of Retinal pigmented epithelium development from the perspective of transcription factors and cis‐regulatory elements

Research paper thumbnail of Cell fate decisions, transcription factors and signaling during early retinal development

Progress in Retinal and Eye Research

Research paper thumbnail of Pax6 directly binds a <i>Trpm3</i> enhancer sequence <i>in vitro</i> and <i>in vivo.</i>

<p>(A) Schematic diagram of the murine <i>Trpm3</i> locus. Three transcription ... more <p>(A) Schematic diagram of the murine <i>Trpm3</i> locus. Three transcription start sites (TSS, black arrows) are distributed across 600 kb. The black rectangles represent <i>Trpm3</i> exons. The red rectangle represents the <i>miR-204</i>-encoding sequence in intron 6. (B) Area downstream of TSS2. Ellipses represent real-time qRT-PCR amplicons. Gray circle represents the location of EMSA probe Trpm3.4. (C) <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1003357#s2&quot; target="_blank">Results</a> of real-time qRT-PCR on DNA from newborn lens ChIP experiment. Y-axis represents relative quantity of template DNA divided by the amount of template of the same reaction in 1% of input DNA. <i>P</i>-values for A1 = 0.0043, A2 = 0.0098, error bars indicate SD. (D) Acrylamide gel of radioactive EMSA probe Trpm3.4. Pax6CON is an oligonucleotide with the consensus binding site of Pax6.. For the Trpm3.4 probe, the first lane is Trpm3.4 probe only, lane 2 is probe+1∶10 flag-Pax6, lane 3 is probe+Pax6-flag, lane 4 is probe with Pax6-flag and competition by cold probe.</p

Research paper thumbnail of Lack of centrioles and primary cilia in <i>STIL<sup>−/−</sup></i> mouse embryos

Although most animal cells contain centrosomes, consisting of a pair of centrioles, their precise... more Although most animal cells contain centrosomes, consisting of a pair of centrioles, their precise contribution to cell division and embryonic development is unclear. Genetic ablation of STIL, an essential component of the centriole replication machinery in mammalian cells, causes embryonic lethality in mice around mid gestation associated with defective Hedgehog signaling. Here, we describe, by focused ion beam scanning electron microscopy, that STIL ¡/¡ mouse embryos do not contain centrioles or primary cilia, suggesting that these organelles are not essential for mammalian development until mid gestation. We further show that the lack of primary cilia explains the absence of Hedgehog signaling in STIL ¡/¡ cells. Exogenous re-expression of STIL or STIL microcephaly mutants compatible with human survival, induced non-templated, de novo generation of centrioles in STIL ¡/¡ cells. Thus, while the abscence of centrioles is compatible with mammalian gastrulation, lack of centrioles and primary cilia impairs Hedgehog signaling and further embryonic development.

Research paper thumbnail of Cerebral Cortex doi:10.1093/cercor/bhp057 In Vivo MRI of Altered Brain Anatomy and Fiber Connectivity in Adult Pax6 Deficient Mice

The impact of developmental ablation of Pax6 function on morphology and functional connectivity o... more The impact of developmental ablation of Pax6 function on morphology and functional connectivity of the adult cerebrum was studied in cortex-specific Pax6 knockout mice (Pax6cKO) using structural magnetic resonance imaging (MRI), manganese-enhanced MRI, and diffusion tensor MRI in conjunction with fiber tractography. Mutants presented with decreased volumes of total brain and olfactory bulb, reduced cortical thickness, and altered layering of the piriform cortex. Tracking of major neuronal fiber bundles revealed a disorganization of callosal fibers with an almost complete lack of interhemispheric connectivity. In Pax6cKO mice intrahemispheric callosal fibers as well as intracortical fibers were predominantly directed along a rostrocaudal orientation instead of a left--right and dorsoventral orientation found in controls. Fiber disorganization also involved the septohippocampal connection targeting mostly the lateral septal nucleus. The hippocampus was rostrally extended and its volum...

Research paper thumbnail of The Roles of Pax6 in Development of the Ocular Lens

Investigative Ophthalmology & Visual Science, 2007

Research paper thumbnail of Targeted deletion of AP-2 alpha in the corneal epithelium results in defects in Bowman's layer and subsequent activation of stromal fibroblasts

Investigative Ophthalmology & Visual Science, 2004

Research paper thumbnail of Role of ERK2 in Lens Cell Proliferation and Differentiation during Development

Investigative Ophthalmology & Visual Science, 2011

Research paper thumbnail of Transcription factors of the RPE play a role in choroid vascularization

Investigative Ophthalmology & Visual Science, 2017

Research paper thumbnail of Investigation Of Pax6 Function In Mouse Ocular Surface Mesenchyme Using A Tissue Specific Mouse Model, Wnt1cre+/Pax6flox/RosamTmG

Investigative Ophthalmology & Visual Science, 2011

Research paper thumbnail of Lysine Acetyltransferases CBP and EP300 are Essential for Histone H3 K18 and K27 Acetylation in the Lens Placode and to Determine the Fate of Lens Progenitor Cells

Investigative Ophthalmology & Visual Science, 2013

Research paper thumbnail of Targeted Deletion of FGF Receptor-2 Identifies a Role for FGF Signaling in Lens Growth

Investigative Ophthalmology & Visual Science, 2002

Research paper thumbnail of Pax6 Is Required for the Differentiation of the Lens Fiber-Cells

Investigative Ophthalmology & Visual Science, 2009

Research paper thumbnail of Roles of LIM homeodomain 2 (Lhx2) in the differentiation of mammalian retinal pigmented epithelium

Acta Ophthalmologica, 2019

Research paper thumbnail of mSWI/SNF (BAF) Complexes Are Indispensable for the Neurogenesis and Development of Embryonic Olfactory Epithelium

PLoS genetics, Sep 1, 2016

Neurogenesis is a key developmental event through which neurons are generated from neural stem/pr... more Neurogenesis is a key developmental event through which neurons are generated from neural stem/progenitor cells. Chromatin remodeling BAF (mSWI/SNF) complexes have been reported to play essential roles in the neurogenesis of the central nervous system. However, whether BAF complexes are required for neuron generation in the olfactory system is unknown. Here, we identified onscBAF and ornBAF complexes, which are specifically present in olfactory neural stem cells (oNSCs) and olfactory receptor neurons (ORNs), respectively. We demonstrated that BAF155 subunit is highly expressed in both oNSCs and ORNs, whereas high expression of BAF170 subunit is observed only in ORNs. We report that conditional deletion of BAF155, a core subunit in both onscBAF and ornBAF complexes, causes impaired proliferation of oNSCs as well as defective maturation and axonogenesis of ORNs in the developing olfactory epithelium (OE), while the high expression of BAF170 is important for maturation of ORNs. Interes...

Research paper thumbnail of Nature Neuroscience Suppl Info 2013

Research paper thumbnail of Sensory cortex limits cortical maps and drives top-down plasticity in thalamocortical circuits

Nature Neuroscience, 2013

The primary somatosensory cortex (S1) contains a complete body map that mirrors the subcortical m... more The primary somatosensory cortex (S1) contains a complete body map that mirrors the subcortical maps developed by peripheral sensory input projecting to the sensory hindbrain, the thalamus and then S1. Peripheral changes during development alter these maps through 'bottom-up' plasticity. Unknown is how S1 size influences map organization and whether an altered S1 map feeds back to affect subcortical maps. We show that the size of S1 in mice is significantly reduced by cortex-specific deletion of Pax6, resulting in a reduced body map and loss of body representations by an exclusion of later-differentiating sensory thalamocortical input. An initially normal sensory thalamus was repatterned to match the aberrant S1 map by apoptotic deletion of thalamic neurons representing body parts with axons excluded from S1. Deleted representations were rescued by altering competition between thalamocortical axons using sensory deprivation or increasing the size of S1. Thus, S1 size determined the resolution and completeness of body maps and engaged 'top-down' plasticity that repatterned the sensory thalamus to match S1.

Research paper thumbnail of Somatic gene targeting in the developing and adult mouse retina

Methods, 2002

Retinogenesis is a developmental process that is tightly regulated both temporally and spatially ... more Retinogenesis is a developmental process that is tightly regulated both temporally and spatially and is therefore an excellent model system for studying the molecular and cellular mechanisms of neurogenesis in the central nervous system. Understanding of these events in vivo is greatly facilitated by the availability of mouse mutant models, including those with natural or targeted mutations and those with conditional knockout or forced expression of genes. This article reviews these genetic modifications and their contribution to the study of retinogenesis in mammals, with special emphasis on conditional gene targeting approaches.

Research paper thumbnail of Distinct Regions Specify the Targeting of Otefin to the Nucleoplasmic Side of the Nuclear Envelope

Journal of Biological Chemistry, 1997