Attractive and repulsive cues guiding retinal horizontal cells´ lamination
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ABSTRACT:
PROVIDER: PRJEB80557 | ENA |
REPOSITORIES: ENA
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Project description:Transcription factors have been implicated in the specification and differentiation of all cells in the mammalian retina with several transcription factors controlling the development of multiple neuronal subclasses. Horizontal cells and cone photoreceptors share a particularly intimate functional relationship but have been previously thought to develop through separate and distinct intrinsic molecular processes. We demonstrate that the zinc finger transcription factor Sall3 regulates development of both S-cone photoreceptors and horizontal cells. Our data shows that loss of function of Sall3 down-regulates the horizontal cell specific transcription factor Lhx1 and subsequently causes ectopic formation of horizontal-like wide-field amacrine cells partially phenocopying Lhx1-/- mice. Additionally, horizontal cells which laminate appropriately in Sall3 knockout mice show abnormal horizontal cell gene expression and failures in dendritic arborization. Over-expression of Sall3 also partially re-specifies cells to a horizontal-like wide-field amacrine fate. Intriguingly, Sall3 loss of function experiments also generated a massive reduction in the number of S-cone photoreceptors with remaining S-cones showing deficiencies in S-cone gene expression and morphology. Conversely, over-expression of Sall3 resulted in the ectopic expression of the S-cone specific genes S-opsin (Sop) and cone arrestin (Arr3) in electroporated cells. Our studies reveal that Sall3 regulates aspects of horizontal cell development in two ways: first, by maintaining Lhx1 expression, and second, by directly regulating expression of horizontal cell specific genes. We also show that Sall3 is an essential regulator of S-cone development in the mammalian retina and a potent activator of Sop and Arr3.
2011-09-10 | GSE24083 | GEO
Project description:Transcription factors have been implicated in the specification and differentiation of all cells in the mammalian retina with several transcription factors controlling the development of multiple neuronal subclasses. Horizontal cells and cone photoreceptors share a particularly intimate functional relationship but have been previously thought to develop through separate and distinct intrinsic molecular processes. We demonstrate that the zinc finger transcription factor Sall3 regulates development of both S-cone photoreceptors and horizontal cells. Our data shows that loss of function of Sall3 down-regulates the horizontal cell specific transcription factor Lhx1 and subsequently causes ectopic formation of horizontal-like wide-field amacrine cells partially phenocopying Lhx1-/- mice. Additionally, horizontal cells which laminate appropriately in Sall3 knockout mice show abnormal horizontal cell gene expression and failures in dendritic arborization. Over-expression of Sall3 also partially re-specifies cells to a horizontal-like wide-field amacrine fate. Intriguingly, Sall3 loss of function experiments also generated a massive reduction in the number of S-cone photoreceptors with remaining S-cones showing deficiencies in S-cone gene expression and morphology. Conversely, over-expression of Sall3 resulted in the ectopic expression of the S-cone specific genes S-opsin (Sop) and cone arrestin (Arr3) in electroporated cells. Our studies reveal that Sall3 regulates aspects of horizontal cell development in two ways: first, by maintaining Lhx1 expression, and second, by directly regulating expression of horizontal cell specific genes. We also show that Sall3 is an essential regulator of S-cone development in the mammalian retina and a potent activator of Sop and Arr3. Sall3 wild-type and knockout retinas used for explant cultures were extracted by microdissection at P0 in sterile PBS. Four cuts were made using micro-dissection scissors and the retinas were transferred to Nucleopore Track-Etch membrane filters (Whatman) and the tissue flattened out evenly. Filters were then floated on DMEM/F12, 10% FBS, 1X penicillin/streptomycin in 12 well plates and incubated at 37oC, 5% CO2 for 7 days. Three retinas (Sall3 knockout or wild-type) were pooled and RNA extracted using the Qiagen RNeasy kit. This was performed in triplicate for both wild-type and Sall3 knockouts retinas. A total of three replicates of Sall3 knockout and Sall3 wild-type RNA were analysed (six total samples).
2011-09-09 | E-GEOD-24083 | biostudies-arrayexpress
Project description:This dataset was acquired to identify the gene expression profile of developing retinal cell types at 42 hours post fertilization (hpf): retinal ganglion cells, photoreceptors, inhibitory neurons (amacrine cells and horizontal cells) and progenitor cells.
2022-01-24 | GSE194158 | GEO
Project description:To comprehensively profile cell types in the human retina, we performed single cell RNA-sequencing on 20,009 cells obtained post-mortem from three donors and compiled a reference transcriptome atlas. Using unsupervised clustering analysis, we identified 18 transcriptionally distinct clusters representing all known retinal cells: rod photoreceptors, cone photoreceptors, Müller glia cells, bipolar cells, amacrine cells, retinal ganglion cells, horizontal cells, retinal astrocytes and microglia.
2019-08-21 | E-MTAB-7316 | biostudies-arrayexpress
Project description:Using our newly designed C. acetobutylicum arrays we analyzed the mRNA changes during a time course experiment (up to 66 h) paying special attention on the study of the late timepoints. Keywords: time course Samples were taken from a Bioflow II reactor at 6, 7, 8, 9, 10, 12, 14, 16, 18, 20, 22, 24, 26, 28, 30, 32, 34, 36, 38, 40, 44, 48, 54, 58, and 66 hrs after bioreactor inoculation. Two slides per timepoint were hybridized on a dye swap configuration. The control mRNA was generated by combining samples taken at 8, 10, 12, 14, 16, 18, 20, 22, 24, 26, 28, 30, 32, 34, 36, 38, 40, 44, 48, 54, 58, and 66 hrs after bioreactor inoculation. For timepoints 6, 8, 14, 32, 38, 66 our internal quality control check suggested a larger than normal variation of the intensities in the control channel and a third slide was hybridized. The discarded slides are GSM141189, GSM141203, GSM141222, GSM141229 and GSM141242.
2010-05-25 | E-GEOD-6094 | biostudies-arrayexpress
Project description:The lineage of the horizontal basal cells (HBC) stem cells and other Sox2eGFP-positive cells from the olfactory epithelium were profiled by single-cell RNA-Seq to identify differentiated cells types, intermediate stages, transition states, and to infer the lineage trajectories.
2017-04-14 | GSE95601 | GEO
Project description:Experimental horizontal gene transfer in Vibrio cholerae
| PRJNA447902 | ENA
Project description:Plasmid fitness is directed by two orthogonal processes—vertical transfer through cell division and horizontal transfer through conjugation. When considered individually, improvements in either mode of transfer can promote how well a plasmid spreads and persists. Together, however, the metabolic cost of conjugation could create a tradeoff that constrains plasmid evolution. Here we present evidence for the presence, consequences, and molecular basis of a conjugation-growth tradeoff across 40 plasmids derived from clinical E. coli pathogens. We discover that most plasmids operate below a conjugation efficiency threshold for major growth effects, indicating strong natural selection for vertical transfer. Below this threshold, E. coli demonstrates a remarkable growth tolerance to over four orders of magnitude change in conjugation efficiency. This tolerance fades as nutrients become scarce and horizontal transfer attracts a greater share of host resources. Our results provide insight into evolutionary constraints directing plasmid fitness and strategies to combat the spread of antibiotic resistance.
2022-12-23 | GSE219270 | GEO
Project description:As the light-sensing part of the visual system, the retina is comprised of five classes of neurons, including photoreceptors, horizontal, amacrine, bipolar, and retinal ganglion cells, along with several non-neuronal cell types such as Muller glia. These major cell classes can be further classified into hundreds of distinct cell subtypes. The development of the retina is under tight temporal control where multipotent progenitor cells differentiate into specific mature cell types in a sequential, but overlapping, order. Additionally, the developmental process is under tight spatial control, with cells at the central retina developing earlier than cells at the periphery. To provide a comprehensive view of the human fetal retina at the molecular level and investigate transcriptional regulatory mechanisms controlling the differentiation process, we profiled more than 300,000 single nuclei of the human fetal retina from 12 donors spanning post conception week 10 and 23 with Multiome RNA-seq and ATAC-seq.
2024-05-30 | GSE268630 | GEO
Project description:The lineage of the horizontal basal cells (HBC) stem cells and their descendants from the olfactory epithelium were profiled by single-cell RNA-Seq to identify differentiated cell types, intermediate stages, transition states, and to infer the lineage trajectories.
2017-10-30 | GSE99251 | GEO