scholarly journals Chromatin accessibility analysis reveals regulatory dynamics of developing human retina and hiPSC-derived retinal organoids

2020 ◽  
Vol 6 (6) ◽  
pp. eaay5247 ◽  
Author(s):  
Haohuan Xie ◽  
Wen Zhang ◽  
Mei Zhang ◽  
Tasneem Akhtar ◽  
Young Li ◽  
...  
Keyword(s):  
Transcriptional Regulatory Network ◽  
Retinal Development ◽  
Chromatin Accessibility ◽  
Mouse Retina ◽  
Transcriptional Dynamics ◽  
Transcriptional Regulatory ◽  
Regulatory Dynamics ◽  
Induced Pluripotent

Retinal organoids (ROs) derived from human induced pluripotent stem cells (hiPSCs) provide potential opportunities for studying human retinal development and disorders; however, to what extent ROs recapitulate the epigenetic features of human retinal development is unknown. In this study, we systematically profiled chromatin accessibility and transcriptional dynamics over long-term human retinal and RO development. Our results showed that ROs recapitulated the human retinogenesis to a great extent, but divergent chromatin features were also discovered. We further reconstructed the transcriptional regulatory network governing human and RO retinogenesis in vivo. Notably, NFIB and THRA were identified as regulators in human retinal development. The chromatin modifications between developing human and mouse retina were also cross-analyzed. Notably, we revealed an enriched bivalent modification of H3K4me3 and H3K27me3 in human but not in murine retinogenesis, suggesting a more dedicated epigenetic regulation on human genome.

scholarly journals Chromatin accessibility and translational landscapes of tea plants under chilling stress

2021 ◽  
Vol 8 (1) ◽  
Author(s):  
Pengjie Wang ◽  
Shan Jin ◽  
Xuejin Chen ◽  
Liangyu Wu ◽  
Yucheng Zheng ◽  
...  
Keyword(s):  
Regulatory Network ◽  
Transcriptional Regulatory Network ◽  
Chilling Stress ◽  
Chromatin Accessibility ◽  
Open Reading Frames ◽  
Translation Efficiency ◽  
Limited Information ◽  
Transcriptional Regulatory ◽  
Tea Plants

AbstractPlants have evolved regulatory mechanisms at multiple levels to regulate gene expression in order to improve their cold adaptability. However, limited information is available regarding the stress response at the chromatin and translational levels. Here, we characterize the chromatin accessibility, transcriptional, and translational landscapes of tea plants in vivo under chilling stress for the first time. Chilling stress significantly affected both the transcription and translation levels as well as the translation efficiency of tea plants. A total of 3010 genes that underwent rapid and independent translation under chilling stress were observed, and they were significantly enriched in the photosynthesis-antenna protein and phenylpropanoid biosynthesis pathways. A set of genes that were significantly responsive to cold at the transcription and translation levels, including four (+)-neomenthol dehydrogenases (MNDs) and two (E)-nerolidol synthases (NESs) arranged in tandem on the chromosomes, were also found. We detected potential upstream open reading frames (uORFs) on 3082 genes and found that tea plants may inhibit the overall expression of genes by enhancing the translation of uORFs under chilling stress. In addition, we identified distal transposase hypersensitive sites (THSs) and proximal THSs and constructed a transcriptional regulatory network for tea plants under chilling stress. We also identified 13 high-confidence transcription factors (TFs) that may play a crucial role in cold regulation. These results provide valuable information regarding the potential transcriptional regulatory network in plants and help to clarify how plants exhibit flexible responses to chilling stress.

scholarly journals Transcriptional regulatory networks that promote and restrict identities and functions of intestinal innate lymphoid cells

2018 ◽  
Author(s):  
Maria Pokrovskii ◽  
Jason A. Hall ◽  
David E. Ochayon ◽  
Ren Yi ◽  
Natalia S. Chaimowitz ◽  
...  
Keyword(s):  
Regulatory Networks ◽  
Inflammatory Diseases ◽  
Innate Lymphoid Cells ◽  
Chromatin Accessibility ◽  
Immune Defense ◽  
Lymphoid Cells ◽  
Transcriptional Regulatory Networks ◽  
Transcriptional Regulatory

SummaryInnate lymphoid cells (ILCs) can be subdivided into several distinct cytokine-secreting lineages that promote tissue homeostasis and immune defense but also contribute to inflammatory diseases. Accumulating evidence suggests that ILCs, similarly to other immune populations, are capable of phenotypic and functional plasticity in response to infectious or environmental stimuli. Yet the transcriptional circuits that control ILC identity and function are largely unknown. Here we integrate gene expression and chromatin accessibility data to infer transcriptional regulatory networks within intestinal type 1, 2, and 3 ILCs. We predict the “core” sets of transcription-factor (TF) regulators driving each ILC subset identity, among which only a few TFs were previously known. To assist in the interpretation of these networks, TFs were organized into cooperative clusters, or modules that control gene programs with distinct functions. The ILC network reveals extensive alternative-lineage-gene repression, whose regulation may explain reported plasticity between ILC subsets. We validate new roles for c-MAF and BCL6 as regulators affecting the type 1 and type 3 ILC lineages. Manipulation of TF pathways identified here might provide a novel means to selectively regulate ILC effector functions to alleviate inflammatory disease or enhance host tolerance to pathogenic microbes or noxious stimuli. Our results will enable further exploration of ILC biology, while our network approach will be broadly applicable to identifying key cell state regulators in otherin vivocell populations.

scholarly journals Hematopoietic stem/progenitor cells, generation of induced pluripotent stem cells, and isolation of endothelial progenitors from 21- to 23.5-year cryopreserved cord blood

Blood ◽  
2011 ◽  
Vol 117 (18) ◽  
pp. 4773-4777 ◽  
Author(s):  
Hal E. Broxmeyer ◽  
Man-Ryul Lee ◽  
Giao Hangoc ◽  
Scott Cooper ◽  
Nutan Prasain ◽  
...  
Keyword(s):  
Stem Cells ◽  
Cord Blood ◽  
Progenitor Cells ◽  
Proliferative Potential ◽  
Hematopoietic Stem ◽  
Immunodeficient Mice ◽  
Induced Pluripotent

Abstract Cryopreservation of hematopoietic stem cells (HSCs) and hematopoietic progenitor cells (HPCs) is crucial for cord blood (CB) banking and transplantation. We evaluated recovery of functional HPC cryopreserved as mononuclear or unseparated cells for up to 23.5 years compared with prefreeze values of the same CB units. Highly efficient recovery (80%-100%) was apparent for granulocyte-macrophage and multipotential hematopoietic progenitors, although some collections had reproducible low recovery. Proliferative potential, response to multiple cytokines, and replating of HPC colonies was extensive. CD34+ cells isolated from CB cryopreserved for up to 21 years had long-term (≥ 6 month) engrafting capability in primary and secondary immunodeficient mice reflecting recovery of long-term repopulating, self-renewing HSCs. We recovered functionally responsive CD4+ and CD8+ T lymphocytes, generated induced pluripotent stem (iPS) cells with differentiation representing all 3 germ cell lineages in vitro and in vivo, and detected high proliferative endothelial colony forming cells, results of relevance to CB biology and banking.

The anemia of the newborn induces erythropoietin expression in the developing mouse retina

2010 ◽  
Vol 299 (1) ◽  
pp. R111-R118 ◽  
Author(s):  
N. Scheerer ◽  
N. Dünker ◽  
S. Imagawa ◽  
M. Yamamoto ◽  
N. Suzuki ◽  
...  
Keyword(s):  
Transforming Growth Factor ◽  
Fluorescent Protein ◽  
Ganglion Cells ◽  
Retinal Development ◽  
Transforming Growth Factor Β ◽  
Neuroprotective Activity ◽  
Mouse Retina ◽  
Mrna Levels ◽  
Neuroprotective Effects

The hematopoietic hormone erythropoietin (Epo), regularly produced by the kidneys and the liver, is also expressed in neuronal tissue, where it has been found to mediate paracrine neuroprotective effects. In most studies exploring the rescue effects of Epo, apoptosis was exogenously induced by different cell death stimuli. Herein, we set out to study the expression and function of Epo in physiologically occurring apoptosis in a model of retinal development. We made use of an organotypic retinal wholemount culture system that resembles the physiological in vivo situation with cell connections still retained. Epo mRNA expression in the retina, liver, and kidney showed a significant increase during early development, coinciding with the anemia of the newborn. In the retina of Epo-green fluorescent protein transgenic mice, Epo-expressing cells were identified and found to be distributed in the retinal ganglion cell layer. Treatment of retinal wholemount cultures with recombinant Epo resulted in a significant decrease of apoptotic ganglion cells as well as photoreceptor cells throughout retinal development. Moreover, transforming growth factor-β-induced apoptosis was completely antagonized by Epo when both factors were simultaneously applied. Investigations on the signaling pathway revealed a decrease in Bax mRNA levels in Epo-treated retinal cells. We conclude that Epo exerts wide and prolonged neuroprotective activity in physiologically occurring apoptosis and thus contributes to proper retinal development.

scholarly journals Modeling gene regulation from paired expression and chromatin accessibility data

2017 ◽  
Vol 114 (25) ◽  
pp. E4914-E4923 ◽  
Author(s):  
Zhana Duren ◽  
Xi Chen ◽  
Rui Jiang ◽  
Yong Wang ◽  
Wing Hung Wong
Keyword(s):  
Gene Expression ◽  
Target Genes ◽  
Transcriptional Regulatory Network ◽  
Joint Modeling ◽  
Regulatory Elements ◽  
Chromatin Accessibility ◽  
Exciting Opportunity ◽  
Transcriptional Regulatory ◽  
Dna Elements ◽  
Context Specific

The rapid increase of genome-wide datasets on gene expression, chromatin states, and transcription factor (TF) binding locations offers an exciting opportunity to interpret the information encoded in genomes and epigenomes. This task can be challenging as it requires joint modeling of context-specific activation of cis-regulatory elements (REs) and the effects on transcription of associated regulatory factors. To meet this challenge, we propose a statistical approach based on paired expression and chromatin accessibility (PECA) data across diverse cellular contexts. In our approach, we model (i) the localization to REs of chromatin regulators (CRs) based on their interaction with sequence-specific TFs, (ii) the activation of REs due to CRs that are localized to them, and (iii) the effect of TFs bound to activated REs on the transcription of target genes (TGs). The transcriptional regulatory network inferred by PECA provides a detailed view of how trans- and cis-regulatory elements work together to affect gene expression in a context-specific manner. We illustrate the feasibility of this approach by analyzing paired expression and accessibility data from the mouse Encyclopedia of DNA Elements (ENCODE) and explore various applications of the resulting model.

scholarly journals Quantitative dissection of transcription in development yields evidence for transcription factor-driven chromatin accessibility

2020 ◽  
Author(s):  
Elizabeth Eck ◽  
Jonathan Liu ◽  
Maryam Kazemzadeh-Atoufi ◽  
Sydney Ghoreishi ◽  
Shelby Blythe ◽  
...  
Keyword(s):  
Transcription Factor ◽  
Predictive Power ◽  
Molecular Mechanisms ◽  
Thermal Fluctuations ◽  
Chromatin Accessibility ◽  
Dna Accessibility ◽  
Transcriptional Regulatory ◽  
Regulatory Dynamics ◽  
Predictive Understanding ◽  
Developmental Decision

AbstractThermodynamic models of gene regulation can predict transcriptional regulation in bacteria, but in eukaryotes chromatin accessibility and energy expenditure may call for a different framework. Here we systematically tested the predictive power of models of DNA accessibility based on the Monod-Wyman-Changeux (MWC) model of allostery, which posits that chromatin fluctuates between accessible and inaccessible states. We dissected the regulatory dynamics of hunchback by the activator Bicoid and the pioneer-like transcription factor Zelda in living Drosophila embryos and showed that no thermodynamic or non-equilibrium MWC model can recapitulate hunchback transcription. Therefore, we explored a model where DNA accessibility is not the result of thermal fluctuations but is catalyzed by Bicoid and Zelda, possibly through histone acetylation, and found that this model can predict hunchback dynamics. Thus, our theory-experiment dialogue uncovered potential molecular mechanisms of transcriptional regulatory dynamics, a key step toward reaching a predictive understanding of developmental decision-making.

scholarly journals PAX3-FOXO1 coordinates enhancer architecture, eRNA transcription, and RNA polymerase pause release at select gene targets

2021 ◽  
Author(s):  
Susu Zhang ◽  
Jing Wang ◽  
Qi Liu ◽  
W Hayes McDonald ◽  
Monica Bomber ◽  
...  
Keyword(s):  
Rna Polymerase ◽  
Transcriptional Control ◽  
Transcriptional Regulatory Network ◽  
Chromatin Accessibility ◽  
Single Element ◽  
Core Network ◽  
Chemical Genetic ◽  
Super Enhancer ◽  
Transcriptional Regulatory ◽  
Time Courses

Transcriptional control is a highly dynamic process that changes rapidly in response to various cellular and extracellular cues1. Thus, it is difficult to achieve a mechanistic understanding of transcription factor function using traditional genetic deletion or RNAi methods, because these slow approaches make it challenging to distinguish direct from indirect transcriptional effects. Here, we used a chemical-genetic approach to rapidly degrade a canonical transcriptional activator, PAX3-FOXO12-6 to define how the t(2;13)(q35;q14) disrupts normal gene expression programs to trigger cancer. By coupling rapid protein degradation with the analysis of nascent transcription over short time courses, we identified a core transcriptional network that rapidly collapsed upon PAX3-FOXO1 degradation. Moreover, loss of PAX3-FOXO1 impaired RNA polymerase pause release and transcription elongation at regulated gene targets. The activity of PAX3-FOXO1 at enhancers controlling this core network was surprisingly selective and often only a single element within a complex super-enhancer was affected. In addition, fusion of the endogenous PAX3-FOXO1 with APEX2 identified proteins in close proximity with PAX3-FOXO1, including ARID1A and MYOD1. We found that continued expression of PAX3-FOXO1 was required to maintain chromatin accessibility and allow neighboring DNA binding proteins and chromatin remodeling complexes to associate with this small number of regulated enhancers. Overall, this work provides a detailed mechanism by which PAX3-FOXO1 maintains an oncogenic transcriptional regulatory network.

scholarly journals Leveraging chromatin accessibility for transcriptional regulatory network inference in T Helper 17 Cells

2018 ◽  
Author(s):  
Emily R. Miraldi ◽  
Maria Pokrovskii ◽  
Aaron Watters ◽  
Dayanne M. Castro ◽  
Nicholas De Veaux ◽  
...  
Keyword(s):  
Gene Expression ◽  
Regulatory Networks ◽  
Network Inference ◽  
Transcriptional Regulatory Network ◽  
Indirect Evidence ◽  
T Helper ◽  
Motif Analysis ◽  
T Helper 17 ◽  
Transcriptional Regulatory

AbstractTranscriptional regulatory networks (TRNs) provide insight into cellular behavior by describing interactions between transcription factors (TFs) and their gene targets. The Assay for Transposase Accessible Chromatin (ATAC)-seq, coupled with transcription-factor motif analysis, provides indirect evidence of chromatin binding for hundreds of TFs genome-wide. Here, we propose methods for TRN inference in a mammalian setting, using ATAC-seq data to influence gene expression modeling. We rigorously test our methods in the context of T Helper Cell Type 17 (Th17) differentiation, generating new ATAC-seq data to complement existing Th17 genomic resources (plentiful gene expression data, TF knock-outs and ChIP-seq experiments). In this resource-rich mammalian setting, our extensive benchmarking provides quantitative, genome-scale evaluation of TRN inference combining ATAC-seq and RNA-seq data. We refine and extend our previous Th17 TRN, using our new TRN inference methods to integrate all Th17 data (gene expression, ATAC-seq, TF KO, ChIP-seq). We highlight newly discovered roles for individual TFs and groups of TFs (“TF-TF modules”) in Th17 gene regulation. Given the popularity of ATAC-seq, which provides high-resolution with low sample input requirements, we anticipate that application of our methods will improve TRN inference in new mammalian systems, especially in vivo, for cells directly from humans and animal models.

scholarly journals Chromatin accessibility dynamics and single cell RNA-Seq reveal new regulators of regeneration in neural progenitors

eLife ◽  
2020 ◽  
Vol 9 ◽  
Author(s):  
Anneke Dixie Kakebeen ◽  
Alexander Daniel Chitsazan ◽  
Madison Corinne Williams ◽  
Lauren M Saunders ◽  
Andrea Elizabeth Wills
Keyword(s):  
Single Cell ◽  
Cell Fate ◽  
Neural Progenitor Cells ◽  
Cell Types ◽  
Chromatin Accessibility ◽  
Rna Seq ◽  
Tail Regeneration ◽  
Cell Fate Decisions ◽  
Transcriptional Regulatory ◽  
Regulatory Dynamics

Vertebrate appendage regeneration requires precisely coordinated remodeling of the transcriptional landscape to enable the growth and differentiation of new tissue, a process executed over multiple days and across dozens of cell types. The heterogeneity of tissues and temporally-sensitive fate decisions involved has made it difficult to articulate the gene regulatory programs enabling regeneration of individual cell types. To better understand how a regenerative program is fulfilled by neural progenitor cells (NPCs) of the spinal cord, we analyzed pax6-expressing NPCs isolated from regenerating Xenopus tropicalis tails. By intersecting chromatin accessibility data with single-cell transcriptomics, we find that NPCs place an early priority on neuronal differentiation. Late in regeneration, the priority returns to proliferation. Our analyses identify Pbx3 and Meis1 as critical regulators of tail regeneration and axon organization. Overall, we use transcriptional regulatory dynamics to present a new model for cell fate decisions and their regulators in NPCs during regeneration.

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