scholarly journals Functional anatomy of distant-acting mammalian enhancers

2013 ◽  
Vol 368 (1620) ◽  
pp. 20120359 ◽  
Author(s):  
D. E. Dickel ◽  
A. Visel ◽  
L. A. Pennacchio
Keyword(s):  
Cultured Cells ◽  
Functional Anatomy ◽  
Transcriptional Enhancers ◽  
Genome Wide ◽  
Multiple Transcription Factor ◽  
Cell Type Specific ◽  
Specific Regulation ◽  
Architectural Characteristics ◽  
The Impact

Transcriptional enhancers are a major class of functional element embedded in the vast non-coding portion of the human genome. Acting over large genomic distances, enhancers play critical roles in the tissue and cell type-specific regulation of genes, and there is mounting evidence that they contribute to the aetiology of many human diseases. Methods for genome-wide mapping of enhancer regions are now available, but the functional architecture contained within human enhancer elements remains unclear. Here, we review recent approaches aimed at understanding the functional anatomy of individual enhancer elements, using systematic qualitative and quantitative assessments of mammalian enhancer variants in cultured cells and in vivo . These studies provide direct insight into common architectural characteristics of enhancers including the presence of multiple transcription factor-binding sites and the mixture of both transcriptionally activating and repressing domains within the same enhancer. Despite such progress in understanding the functional composition of enhancers, the inherent complexities of enhancer anatomy continue to limit our ability to predict the impact of sequence changes on in vivo enhancer function. While providing an initial glimpse into the mutability of mammalian enhancers, these observations highlight the continued need for experimental enhancer assessment as genome sequencing becomes routine in the clinic.

scholarly journals MITO-Tag Mice enable rapid isolation and multimodal profiling of mitochondria from specific cell types in vivo

2018 ◽  
Vol 116 (1) ◽  
pp. 303-312 ◽  
Author(s):  
Erol C. Bayraktar ◽  
Lou Baudrier ◽  
Ceren Özerdem ◽  
Caroline A. Lewis ◽  
Sze Ham Chan ◽  
...  
Keyword(s):  
Metabolite Profiling ◽  
Cultured Cells ◽  
Transgenic Animals ◽  
Cell Types ◽  
Tissue Level ◽  
Specific Cell ◽  
Mammalian Tissues ◽  
Cell Type Specific ◽  
Untargeted Metabolite Profiling

Mitochondria are metabolic organelles that are essential for mammalian life, but the dynamics of mitochondrial metabolism within mammalian tissues in vivo remains incompletely understood. While whole-tissue metabolite profiling has been useful for studying metabolism in vivo, such an approach lacks resolution at the cellular and subcellular level. In vivo methods for interrogating organellar metabolites in specific cell types within mammalian tissues have been limited. To address this, we built on prior work in which we exploited a mitochondrially localized 3XHA epitope tag (MITO-Tag) for the fast isolation of mitochondria from cultured cells to generate MITO-Tag Mice. Affording spatiotemporal control over MITO-Tag expression, these transgenic animals enable the rapid, cell-type-specific immunoisolation of mitochondria from tissues, which we verified using a combination of proteomic and metabolomic approaches. Using MITO-Tag Mice and targeted and untargeted metabolite profiling, we identified changes during fasted and refed conditions in a diverse array of mitochondrial metabolites in hepatocytes and found metabolites that behaved differently at the mitochondrial versus whole-tissue level. MITO-Tag Mice should have utility for studying mitochondrial physiology, and our strategy should be generally applicable for studying other mammalian organelles in specific cell types in vivo.

scholarly journals MITO-Tag Mice enable rapid isolation and multimodal profiling of mitochondria from specific cell types in vivo

2018 ◽  
Author(s):  
Erol Can Bayraktar ◽  
Lou Baudrier ◽  
Ceren Özerdem ◽  
Caroline A. Lewis ◽  
Sze Ham Chan ◽  
...  
Keyword(s):  
Metabolite Profiling ◽  
Cultured Cells ◽  
Transgenic Animals ◽  
Cell Types ◽  
Tissue Level ◽  
Specific Cell ◽  
Mammalian Tissues ◽  
Cell Type Specific ◽  
Untargeted Metabolite Profiling

ABSTRACTMitochondria are metabolic organelles that are essential for mammalian life, but the dynamics of mitochondrial metabolism within mammalian tissues in vivo remains incompletely understood. While whole-tissue metabolite profiling has been useful for studying metabolism in vivo, such an approach lacks resolution at the cellular and subcellular level. In vivo methods for interrogating organellar metabolites in specific cell-types within mammalian tissues have been limited. To address this, we built on prior work in which we exploited a mitochondrially-localized 3XHA epitope-tag (“MITO-Tag”) for the fast isolation of mitochondria from cultured cells to now generate “MITO-Tag Mice.” Affording spatiotemporal control over MITO-Tag expression, these transgenic animals enable the rapid, cell-type-specific immunoisolation of mitochondria from tissues, which we verified using a combination of proteomic and metabolomic approaches. Using MITO-Tag Mice and targeted and untargeted metabolite profiling, we identified changes during fasted and refed conditions in a diverse array of mitochondrial metabolites in hepatocytes and found metabolites that behaved differently at the mitochondrial versus whole-tissue level. MITO-Tag Mice should have utility for studying mitochondrial physiology and our strategy should be generally applicable for studying other mammalian organelles in specific cell-types in vivo.

scholarly journals The endosomal sorting adaptor HD-PTP is required for ephrin-B:EphB signalling in cell collapse and motor axon guidance

2018 ◽  
Author(s):  
Sylvie Lahaie ◽  
Daniel Morales ◽  
Halil Bagci ◽  
Noumeira Hamoud ◽  
Charles-Etienne Castonguay ◽  
...  
Keyword(s):  
Cultured Cells ◽  
Cell Communication ◽  
Adaptor Protein ◽  
Tyrosine Kinase Receptor ◽  
Kinase Activation ◽  
Surface Receptors ◽  
Endosomal Sorting ◽  
Mediate Cell ◽  
The Impact

AbstractThe signalling output of many transmembrane receptors that mediate cell-cell communication is restricted by the endosomal sorting complex required for transport (ESCRT), but the impact of this machinery on Eph tyrosine kinase receptor function is unknown. We identified the ESCRT-associated adaptor protein HD-PTP as part of an EphB2 BioID interactome, and confirmed this association using co-immunoprecipitation. Although HD-PTP loss does not change EphB2 expression, it attenuates the ephrin-B2:EphB2 signalling-induced collapse of cultured cells and axonal growth cones, and results in aberrant guidance of chick spinal motor neuron axons in vivo HD-PTP depletion abrogates ligand-induced EphB2 clustering, and EphB2 and Src family kinase activation. HD-PTP deficiency also accelerates ligand-induced EphB2 degradation, contrasting the phenotypes reported for other cell surface receptors. Our results link Eph signalling to the ESCRT machinery and demonstrate a role for HD-PTP in the earliest steps of ephrin-B:EphB signalling, as well as in obstructing premature receptor depletion.

scholarly journals Hyperinsulinemia promotes aberrant histone acetylation in triple negative breast cancer

2018 ◽  
Author(s):  
Parijat Senapati ◽  
Christine Thai ◽  
Angelica Sanchez ◽  
Emily J Gallagher ◽  
Derek LeRoith ◽  
...  
Keyword(s):  
Breast Cancer ◽  
Histone Acetylation ◽  
Triple Negative Breast Cancer ◽  
Triple Negative ◽  
Prognostic Indicator ◽  
Gene Promoters ◽  
Genome Wide ◽  
Altered Gene ◽  
The Impact

AbstractExcess levels of insulin relative to glucose in the blood, or hyperinsulinemia, is considered to be a poor prognostic indicator for patients with triple negative breast cancer (TNBC). While this association has been recognized for some time, the mechanistic role of hyperinsulinemia in promoting TNBC remains unclear. We show that insulin treatment leads to genome-wide increase in histone acetylation, in particular at H3K9, through the PI3K/AKT/mTOR pathway in MDA-MB-231 cells. Genome-wide analysis showed that the increase in histone acetylation occurs primarily at gene promoters. In addition, insulin induces higher levels of reactive oxygen species and DNA damage foci in cells. In vivo, hyperinsulinemia also enhances growth of MDA-MB-231 derived tumors through increased histone acetylation. These results demonstrate the impact of hyperinsulinemia on altered gene regulation through chromatin and the importance of targeting hyperinsulinemia-induced processes that lead to chromatin dysfunction in TNBC.

scholarly journals A simplified transposon mutagenesis method to perform phenotypic forward genetic screens in cultured cells

2019 ◽  
Author(s):  
Charlotte R. Feddersen ◽  
Lexy S. Wadsworth ◽  
Eliot Y. Zhu ◽  
Hayley R. Vaughn ◽  
Andrew P. Voigt ◽  
...  
Keyword(s):  
Cultured Cells ◽  
Sequence Data ◽  
Sleeping Beauty ◽  
Transposon Mutagenesis ◽  
Loss Of Function ◽  
Genetic Screens ◽  
Sleeping Beauty Transposon ◽  
Genome Wide ◽  
Forward Genetic Screens ◽  
The Impact

AbstractThe introduction of genome-wide shRNA and CRISPR libraries has facilitated cell-based screens to identify loss-of-function mutations associated with a phenotype of interest. Approaches to perform analogous gain-of-function screens are less common, although some reports have utilized arrayed viral expression libraries or the CRISPR activation system. However, a variety of technical and logistical challenges make these approaches difficult for many labs to execute. In addition, genome-wide shRNA or CRISPR libraries typically contain of hundreds of thousands of individual engineered elements, and the associated complexity creates issues with replication and reproducibility for these methods. Here we describe a simple, reproducible approach using the Sleeping Beauty transposon system to perform phenotypic cell-based genetic screens. This approach employs only three plasmids to perform unbiased, whole-genome transposon mutagenesis. We also describe a ligation-mediated PCR method that can be used in conjunction with the included software tools to map raw sequence data, identify candidate genes associated with phenotypes of interest, and predict the impact of recurrent transposon insertions on candidate gene function. Finally, we demonstrate the high reproducibility of our approach by having three individuals perform independent replicates of a mutagenesis screen to identify drivers of vemurafenib resistance in cultured melanoma cells. Collectively, our work establishes a facile, adaptable method that can be performed by labs of any size to perform robust, genome-wide screens to identify genes that influence phenotypes of interest.

CXCR4/SDF-1 Is a Key Regulator for Leukemia Migration and Homing to the BM: Impact of AMD3100 on In Vivo Response to Chemotherapy.

Blood ◽  
2006 ◽  
Vol 108 (11) ◽  
pp. 569-569 ◽  
Author(s):  
Bruno Nervi ◽  
Pablo Ramirez ◽  
Matthew Holt ◽  
Michael P. Rettig ◽  
Julie K. Ritchey ◽  
...  
Keyword(s):  
Reporter Gene ◽  
Survival Benefit ◽  
Cultured Cells ◽  
Ex Vivo ◽  
Dual Function ◽  
Hematopoietic Stem ◽  
Response To Chemotherapy ◽  
The Impact

Abstract Hematopoietic stem cells (HSC) reside in the bone marrow (BM) and interact with stroma cells and extracellular matrix. CXCR4/SDF-1 axis regulates the trafficking of HSC to and from the BM. We utilized a PML-RARα knock-in mouse model of human acute promyelocytic leukemia (APL) to study APL interaction with the normal BM. We have previously shown there is a rapid mobilization of APL cells from the BM into peripheral blood (PB) after administration of AMD3100, a competitive inhibitor of CXCR4. We hypothesize that we can sensitize these tumor cells to chemotherapy by interrupting the interaction between APL and the BM stroma. We transduced banked APL cells with a dual function reporter gene that encodes a fusion protein comprised of Click Beetle Red luciferase, a bioluminescence imaging (BLI) optical reporter gene, and EGFP for ex vivo cell sorting (Luc/EGFP). Upon iv injection into genetically compatible recipients (F1 129/B6 mice), APL rapidly migrated to the BM with increased BLI signal in the femurs, spine, ribs, and skull, at 4 days after injection, followed by spleen infiltration and death due to leukostasis by day 15. 129/B6 F1 mice (n=28) were injected iv with 106 APL cells. By day 12 all mice had ±5% APL cells in PB. 8 mice received AraC (500mg/kg/sq) on days 12 and 13, and another 8 mice received AraC+AMD (5mg/kg/sq) 1 hour before and 3 hours after each AraC injection. 6 mice received only AMD and 6 control mice were observed. Total body BLI signal, WBC, and blasts per μl of blood on days 19 and 23 were higher in AraC versus AraC+AMD (p<0.004). Median survival for control, AMD, AraC and AraC+AMD groups were 18, 19, 23 and 30 days respectively (p<0.0006). Hemoglobin, platelet and granulocyte recovery post-chemotherapy was similar in both groups. We developed an in vitro mouse stroma system to study engraftment, ex vivo mobilization and sensitivity to chemotherapy. In vitro culture of APL cells showed no difference in APL survival between AraC versus AraC+AMD as measured by flow cytometry or BLI. Stroma offered a survival benefit versus no stroma (p<0.0001). We injected 4 genetically compatible mice with 106 APL cells iv and after 14 days mice were sacrificed. Blast percentage in blood, spleen and BM was 47, 58 and 40% respectively. We cultured cells from all three compartments ex vivo with AraC (25ng/ml). After 24 hours APL survival was 25, 80 and 60% respectively (p<0.006). We repeated the same experiment, but we did, in addition, a positive selection for CD34 to purify APL cells away from surrounding cells in the BM and spleen. Survival after ex vivo AraC incubation was 32, 30, 34% respectively (p=NS). In summary, CXCR4/SDF-1 is a key regulator for leukemia migration and homing to the BM. The interaction of APL cells with the BM and splenic microenvironments provides a survival benefit. Rapid mobilization of APL cells in vivo by AMD3100 interrupts APL-stromal interactions and sensitizes APL to chemotherapy. The impact of additional mobilizing agents on APL mobilization on sensitizing APL to chemo and radiotherapy will be presented. Finally, preliminary RNA profiling studies will be presented in an attempt to identify genes in APL cell that are differentially expressed when bound to and released from the BM.

scholarly journals Elongin A regulates transcription in vivo through enhanced RNA polymerase processivity

2020 ◽  
pp. jbc.RA120.015876
Author(s):  
Yating Wang ◽  
Liming Hou ◽  
M. Behfar Ardehali ◽  
Robert E. Kingston ◽  
Brian D Dynlacht
Keyword(s):  
Rna Polymerase ◽  
Rna Polymerase Ii ◽  
Transcriptional Elongation ◽  
Rna Seq ◽  
Transcription Profiles ◽  
Genome Wide ◽  
The Impact

Elongin is an RNA polymerase II (RNAPII)-associated factor that has been shown to stimulate transcriptional elongation in vitro. The Elongin complex is thought to be required for transcriptional induction in response to cellular stimuli and to ubiquitinate RNAPII in response to DNA damage. Yet the impact of the Elongin complex on transcription in vivo has not been well studied. Here, we performed comprehensive studies of the role of Elongin A, the largest subunit of the Elongin complex, on RNAPII transcription genome-wide. Our results suggest that Elongin A localizes to actively transcribed regions and potential enhancers, and the level of recruitment correlated with transcription levels. We also identified a large group of factors involved in transcription as Elongin A-associated factors. In addition, we found that loss of Elongin A leads to dramatically reduced levels of Ser2-phosphorylated, but not total, RNAPII, and cells depleted of Elongin A show stronger promoter RNAPII pausing, suggesting that Elongin A may be involved in the release of paused RNAPII. Our RNA-seq studies suggest that loss of Elongin A did not alter global transcription, and unlike prior in vitro studies, we did not observe a dramatic impact on RNAPII elongation rates in our cell-based nascent RNA-seq experiments upon Elongin A depletion. Taken together, our studies provide the first comprehensive analysis of the role of Elongin A in regulating transcription in vivo. Our studies also revealed that unlike prior in vitro findings, depletion of Elongin A has little impact on global transcription profiles and transcription elongation in vivo.

scholarly journals Cell-type–specific, multicolor labeling of endogenous proteins with split fluorescent protein tags in Drosophila

2021 ◽  
Vol 118 (23) ◽  
pp. e2024690118
Author(s):  
Rie Kamiyama ◽  
Kota Banzai ◽  
Peiwei Liu ◽  
Abhijit Marar ◽  
Ryo Tamura ◽  
...  
Keyword(s):  
Tandem Repeats ◽  
Fluorescent Protein ◽  
Protein Localization ◽  
Fluorescence Signal ◽  
Cell Type ◽  
Genomic Locus ◽  
Cell Type Specific ◽  
Endogenous Proteins ◽  
The Impact

The impact of the Drosophila experimental system on studies of modern biology cannot be understated. The ability to tag endogenously expressed proteins is essential to maximize the use of this model organism. Here, we describe a method for labeling endogenous proteins with self-complementing split fluorescent proteins (split FPs) in a cell-type–specific manner in Drosophila. A short fragment of an FP coding sequence is inserted into a specific genomic locus while the remainder of the FP is expressed using an available GAL4 driver line. In consequence, complementation fluorescence allows examination of protein localization in particular cells. Besides, when inserting tandem repeats of the short FP fragment at the same genomic locus, we can substantially enhance the fluorescence signal. The enhanced signal is of great value in live-cell imaging at the subcellular level. We can also accomplish a multicolor labeling system with orthogonal split FPs. However, other orthogonal split FPs do not function for in vivo imaging besides split GFP. Through protein engineering and in vivo functional studies, we report a red split FP that we can use for duplexed visualization of endogenous proteins in intricate Drosophila tissues. Using the two orthogonal split FP systems, we have simultaneously imaged proteins that reside in distinct subsynaptic compartments. Our approach allows us to study the proximity between and localization of multiple proteins endogenously expressed in essentially any cell type in Drosophila.

scholarly journals Altered hippocampal interneuron activity precedes ictal onset

2016 ◽  
Author(s):  
Mitra L. Miri ◽  
Martin Vinck ◽  
Rima Pant ◽  
Jessica A. Cardin
Keyword(s):  
Inhibitory Interneuron ◽  
Seizure Disorders ◽  
Hippocampal Interneuron ◽  
Ictal Activity ◽  
Cell Type Specific ◽  
Hippocampal Network ◽  
The Impact ◽  
Interneuron Activity ◽  
Rapid Shift

SummaryAlthough failure of GABAergic inhibition is a commonly hypothesized mechanism underlying seizure disorders, the series of events that precipitate a rapid shift from healthy to ictal activity remain unclear. Furthermore, the diversity of inhibitory interneuron populations poses a challenge for understanding local circuit interactions during seizure initiation. Using a combined optogenetic and electrophysiological approach, we examined the activity of two identified hippocampal interneuron classes during seizure induction in vivo. We identified cell type-specific differences in preictal firing patterns and input sensitivity of parvalbumin- and somatostatin-expressing interneurons. Surprisingly, the impact of both sources of inhibition remained intact throughout the preictal period and into the early ictal phase. Our findings suggest that the onset of ictal activity is not due to a failure of inhibition, but is instead associated with a decoupling of inhibitory cells from their normal relationship with the local hippocampal network.

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