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1

Syding, Linn Amanda, Petr Nickl, Petr Kasparek, and Radislav Sedlacek. "CRISPR/Cas9 Epigenome Editing Potential for Rare Imprinting Diseases: A Review." Cells 9, no. 4 (2020): 993. http://dx.doi.org/10.3390/cells9040993.

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Imprinting diseases (IDs) are rare congenital disorders caused by aberrant dosages of imprinted genes. Rare IDs are comprised by a group of several distinct disorders that share a great deal of homology in terms of genetic etiologies and symptoms. Disruption of genetic or epigenetic mechanisms can cause issues with regulating the expression of imprinted genes, thus leading to disease. Genetic mutations affect the imprinted genes, duplications, deletions, and uniparental disomy (UPD) are reoccurring phenomena causing imprinting diseases. Epigenetic alterations on methylation marks in imprinting
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Nakamura, Muneaki, Alexis E. Ivec, Yuchen Gao, and Lei S. Qi. "Durable CRISPR-Based Epigenetic Silencing." BioDesign Research 2021 (July 1, 2021): 1–8. http://dx.doi.org/10.34133/2021/9815820.

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Development of CRISPR-based epigenome editing tools is important for the study and engineering of biological behavior. Here, we describe the design of a reporter system for quantifying the ability of CRISPR epigenome editors to produce a stable gene repression. We characterize the dynamics of durable gene silencing and reactivation, as well as the induced epigenetic changes of this system. We report the creation of single-protein CRISPR constructs bearing combinations of three epigenetic editing domains, termed KAL, that can stably repress the gene expression. This system should allow for the
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Fang, Yongxing, Wladislaw Stroukov, Toni Cathomen, and Claudio Mussolino. "Chimerization Enables Gene Synthesis and Lentiviral Delivery of Customizable TALE-Based Effectors." International Journal of Molecular Sciences 21, no. 3 (2020): 795. http://dx.doi.org/10.3390/ijms21030795.

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Designer effectors based on the DNA binding domain (DBD) of Xanthomonas transcription activator-like effectors (TALEs) are powerful sequence-specific tools with an excellent reputation for their specificity in editing the genome, transcriptome, and more recently the epigenome in multiple cellular systems. However, the repetitive structure of the TALE arrays composing the DBD impedes their generation as gene synthesis product and prevents the delivery of TALE-based genes using lentiviral vectors (LVs), a widely used system for human gene therapy. To overcome these limitations, we aimed at chime
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Roman Azcona, Maria Silvia, Yongxing Fang, Antonio Carusillo, Toni Cathomen, and Claudio Mussolino. "A versatile reporter system for multiplexed screening of effective epigenome editors." Nature Protocols 15, no. 10 (2020): 3410–40. http://dx.doi.org/10.1038/s41596-020-0380-y.

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Willyard, Cassandra. "The epigenome editors: How tools such as CRISPR offer new details about epigenetics." Nature Medicine 23, no. 8 (2017): 900–903. http://dx.doi.org/10.1038/nm0817-900.

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O’Geen, Henriette, Marketa Tomkova, Jacquelyn A. Combs, Emma K. Tilley, and David J. Segal. "Determinants of heritable gene silencing for KRAB-dCas9 + DNMT3 and Ezh2-dCas9 + DNMT3 hit-and-run epigenome editing." Nucleic Acids Research 50, no. 6 (2022): 3239–53. http://dx.doi.org/10.1093/nar/gkac123.

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Abstract Precision epigenome editing has gained significant attention as a method to modulate gene expression without altering genetic information. However, a major limiting factor has been that the gene expression changes are often transient, unlike the life-long epigenetic changes that occur frequently in nature. Here, we systematically interrogate the ability of CRISPR/dCas9-based epigenome editors (Epi-dCas9) to engineer persistent epigenetic silencing. We elucidated cis regulatory features that contribute to the differential stability of epigenetic reprogramming, such as the active transc
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7

Psatha, Nikoletta, Kiriaki Paschoudi, Anastasia Papadopoulou, and Evangelia Yannaki. "In Vivo Hematopoietic Stem Cell Genome Editing: Perspectives and Limitations." Genes 13, no. 12 (2022): 2222. http://dx.doi.org/10.3390/genes13122222.

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The tremendous evolution of genome-editing tools in the last two decades has provided innovative and effective approaches for gene therapy of congenital and acquired diseases. Zinc-finger nucleases (ZFNs), transcription activator- like effector nucleases (TALENs) and CRISPR-Cas9 have been already applied by ex vivo hematopoietic stem cell (HSC) gene therapy in genetic diseases (i.e., Hemoglobinopathies, Fanconi anemia and hereditary Immunodeficiencies) as well as infectious diseases (i.e., HIV), and the recent development of CRISPR-Cas9-based systems using base and prime editors as well as epi
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Dehshahri, Ali, Alessio Biagioni, Hadi Bayat, et al. "Editing SOX Genes by CRISPR-Cas: Current Insights and Future Perspectives." International Journal of Molecular Sciences 22, no. 21 (2021): 11321. http://dx.doi.org/10.3390/ijms222111321.

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Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) and its associated proteins (Cas) is an adaptive immune system in archaea and most bacteria. By repurposing these systems for use in eukaryote cells, a substantial revolution has arisen in the genome engineering field. In recent years, CRISPR-Cas technology was rapidly developed and different types of DNA or RNA sequence editors, gene activator or repressor, and epigenome modulators established. The versatility and feasibility of CRISPR-Cas technology has introduced this system as the most suitable tool for discovering and stud
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9

Szyf, Moshe. "The Epigenome: Molecular Hide and Seek. Stephan Beck and Alexander Olek, editors. Weinheim, Germany: Wiley-VCH GmbH Co. KGaA, 2003, 188 pp., $35.00, softcover. ISBN 3-527-30494-0." Clinical Chemistry 49, no. 9 (2003): 1566–67. http://dx.doi.org/10.1373/49.9.1566.

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10

Brane, Andrew, Madeline Sutko, and Trygve O. Tollefsbol. "p21 Promoter Methylation Is Vital for the Anticancer Activity of Withaferin A." International Journal of Molecular Sciences 26, no. 3 (2025): 1210. https://doi.org/10.3390/ijms26031210.

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Breast cancer (BC) is a widespread malignancy that affects the lives of millions of women each year, and its resulting financial and healthcare hardships cannot be overstated. These issues, in combination with side effects and obstacles associated with the current standard of care, generate considerable interest in new potential targets for treatment as well as means for BC prevention. One potential preventive compound is Withaferin A (WFA), a traditional medicinal compound found in winter cherries. WFA has shown promise as an anticancer agent and is thought to act primarily through its effect
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11

Zaenker, Kurt. "Editorial From Editor-in-Chief: The Epigenome." Epigenetic Diagnosis & Therapy 1, no. 1 (2015): 2. http://dx.doi.org/10.2174/221408320101150417114249.

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Goodrich, Jaclyn. "Insights on exposure-induced disease susceptibility: an interview with Jaclyn Goodrich." Epigenomics 14, no. 6 (2022): 319–21. http://dx.doi.org/10.2217/epi-2022-0046.

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In this interview, Dr Jaclyn Goodrich speaks with Storm Johnson, Commissioning Editor for Epigenomics, on her work to date on environmental epigenetics and the impact of toxic exposures on susceptible populations. Jaclyn Goodrich is a research assistant professor of environmental health sciences at the University of Michigan School of Public Health (Ann Arbor, MI, USA). She obtained a doctorate in toxicology and completed postdoctoral training in environmental epigenomics at the University of Michigan. The overarching goal of her current research program is to identify environmental factors th
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13

Yusuf, Abdurrahman Pharmacy, Murtala Bello Abubakar, Ibrahim Malami, et al. "Zinc Metalloproteins in Epigenetics and Their Crosstalk." Life 11, no. 3 (2021): 186. http://dx.doi.org/10.3390/life11030186.

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More than half a century ago, zinc was established as an essential micronutrient for normal human physiology. In silico data suggest that about 10% of the human proteome potentially binds zinc. Many proteins with zinc-binding domains (ZBDs) are involved in epigenetic modifications such as DNA methylation and histone modifications, which regulate transcription in physiological and pathological conditions. Zinc metalloproteins in epigenetics are mainly zinc metalloenzymes and zinc finger proteins (ZFPs), which are classified into writers, erasers, readers, editors, and feeders. Altogether, these
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14

Gupta, Pravesh, Dapeng Hao, Krishna Bojja Bojja, et al. "833 The epigenomic landscape of human glioma-associated myeloid cells." Journal for ImmunoTherapy of Cancer 8, Suppl 3 (2020): A885. http://dx.doi.org/10.1136/jitc-2020-sitc2020.0833.

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BackgroundGliomas are recalcitrant tumors of the central nervous system. The tumor immune microenvironment (TIME) in gliomas is considered immunosuppressive and making it difficult to treat these tumors with conventional immunotherapy approaches, therefore a better characterization of the immune cell repertoire is needed to fully understand the tumor immune contexture. While single-cell RNA-sequencing (scRNA-seq) approaches have revealed the transcriptional heterogeneity, the gene regulatory landscape at the chromatin level is quintessential for a deeper understanding of lineage and signal-dep
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15

Jirtle, Randy L. "The science of hope: an interview with Randy Jirtle." Epigenomics 14, no. 6 (2022): 299–302. http://dx.doi.org/10.2217/epi-2022-0048.

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In this interview, Professor Randy L Jirtle speaks with Storm Johnson, Commissioning Editor for Epigenomics, on his work on genomic imprinting, environmental epigenomics and the fetal origins of disease susceptibility. Professor Randy Jirtle joined the Duke University Department of Radiology in 1977 and headed the Epigenetics and Imprinting Laboratory until 2012. He is now Professor of Epigenetics in the Department of Biological Sciences at North Carolina State University, Raleigh, NC, USA. Jirtle's research interests are in epigenetics, genomic imprinting and the fetal origins of disease susc
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Laird, Peter W. "How epigenomics broke the mold: an interview with Peter W Laird." Epigenomics 14, no. 6 (2022): 303–8. http://dx.doi.org/10.2217/epi-2022-0066.

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In this interview, Professor Peter W Laird speaks with Storm Johnson, Commissioning Editor for Epigenomics, on his work to date in the field of cancer epigenetics. Dr Peter W Laird is a Professor at Van Andel Institute (VAI) in Grand Rapids, Michigan. He earned his B.S. and M.S., Cum Laude, from the University of Leiden, The Netherlands. He trained for his PhD with Dr Piet Borst, The Netherlands Cancer Institute, and as a postdoc with Dr Anton Berns, The Netherlands Cancer Institute, and with Dr Rudolf Jaenisch, at the Whitehead Institute for Biomedical Research in Cambridge, MA, USA. He joine
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Goel, Ajay. "The era of biomarkers and precision medicine in colorectal cancer: an interview with Ajay Goel." Epigenomics 14, no. 6 (2022): 345–49. http://dx.doi.org/10.2217/epi-2022-0010.

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In this interview, Professor Ajay Goel speaks with Storm Johnson, Commissioning Editor for Epigenomics, on his work to date in the field of epigenetic biomarkers in colorectal cancer. Ajay Goel, PhD, is a Professor and Founding Chair of the Department of Molecular Diagnostics, at the Beckman Research Institute and Associate Director of Basic Science at the City of Hope comprehensive Cancer Center. He also serves as Director of Biotech Innovations at the City of Hope, Duarte, CA, USA. Dr Goel has spent more than 25 years researching cancer and has been the lead author or contributor to more tha
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18

"Fine-tuning epigenome editors." Nature Biotechnology 40, no. 3 (2022): 281. http://dx.doi.org/10.1038/s41587-022-01270-w.

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19

Cappelluti, Martino Alfredo, Valeria Mollica Poeta, Sara Valsoni, et al. "Durable and efficient gene silencing in vivo by hit-and-run epigenome editing." Nature, February 28, 2024. http://dx.doi.org/10.1038/s41586-024-07087-8.

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AbstractPermanent epigenetic silencing using programmable editors equipped with transcriptional repressors holds great promise for the treatment of human diseases1–3. However, to unlock its full therapeutic potential, an experimental confirmation of durable epigenetic silencing after the delivery of transient delivery of editors in vivo is needed. To this end, here we targeted Pcsk9, a gene expressed in hepatocytes that is involved in cholesterol homeostasis. In vitro screening of different editor designs indicated that zinc-finger proteins were the best-performing DNA-binding platform for eff
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Yahsi, Berkay, Fahreddin Palaz, and Pervin Dincer. "Applications of CRISPR Epigenome Editors in Tumor Immunology and Autoimmunity." ACS Synthetic Biology, January 31, 2024. http://dx.doi.org/10.1021/acssynbio.3c00524.

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Dhakate, Priyanka, Deepmala Sehgal, Samantha Vaishnavi, et al. "Comprehending the evolution of gene editing platforms for crop trait improvement." Frontiers in Genetics 13 (August 23, 2022). http://dx.doi.org/10.3389/fgene.2022.876987.

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CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats)/Cas (CRISPR-associated) system was initially discovered as an underlying mechanism for conferring adaptive immunity to bacteria and archaea against viruses. Over the past decade, this has been repurposed as a genome-editing tool. Numerous gene editing-based crop improvement technologies involving CRISPR/Cas platforms individually or in combination with next-generation sequencing methods have been developed that have revolutionized plant genome-editing methodologies. Initially, CRISPR/Cas nucleases replaced the earlier used sequ
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Verma, Vipasha, Akhil Kumar, Mahinder Partap, Meenakshi Thakur, and Bhavya Bhargava. "CRISPR-Cas: A robust technology for enhancing consumer-preferred commercial traits in crops." Frontiers in Plant Science 14 (February 7, 2023). http://dx.doi.org/10.3389/fpls.2023.1122940.

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The acceptance of new crop varieties by consumers is contingent on the presence of consumer-preferred traits, which include sensory attributes, nutritional value, industrial products and bioactive compounds production. Recent developments in genome editing technologies provide novel insight to identify gene functions and improve the various qualitative and quantitative traits of commercial importance in plants. Various conventional as well as advanced gene-mutagenesis techniques such as physical and chemical mutagenesis, CRISPR-Cas9, Cas12 and base editors are used for the trait improvement in
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23

Bode, Daniel, Alyssa H. Cull, Juan A. Rubio-Lara, and David G. Kent. "Exploiting Single-Cell Tools in Gene and Cell Therapy." Frontiers in Immunology 12 (July 12, 2021). http://dx.doi.org/10.3389/fimmu.2021.702636.

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Single-cell molecular tools have been developed at an incredible pace over the last five years as sequencing costs continue to drop and numerous molecular assays have been coupled to sequencing readouts. This rapid period of technological development has facilitated the delineation of individual molecular characteristics including the genome, transcriptome, epigenome, and proteome of individual cells, leading to an unprecedented resolution of the molecular networks governing complex biological systems. The immense power of single-cell molecular screens has been particularly highlighted through
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Conroy, Gemma. "‘Epigenome editor’ silences gene that causes deadly brain disorders." Nature, June 27, 2024. http://dx.doi.org/10.1038/d41586-024-02115-z.

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"An interview with Peter Rugg-Gunn." Development 151, no. 14 (2024). http://dx.doi.org/10.1242/dev.204218.

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Peter Rugg-Gunn is a Group Leader and Head of Public Engagement at the Babraham Institute in Cambridge, UK, interested in the epigenome during early human development. Peter is scientific lead of the Human Developmental Biology Initiative (HDBI), a member of the Scientific and Clinical Advances Advisory Committee of the Human Fertilisation and Embryology Authority (HFEA), and is active in UK and international efforts to establish guidance in stem cell-based embryo models. We spoke to Peter about his career path, his interest in public dialogue and his role as an Editor for Development.
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Zahir, Farah R. "Understanding environmental epigenomics in autism spectrum disorder: an interview with Farah R Zahir." Epigenomics, September 23, 2021. http://dx.doi.org/10.2217/epi-2021-0319.

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In this interview, Dr Farah R Zahir speaks with Storm Johnson, Commissioning Editor for Epigenomics, on her work to date in the field of epigenomics, autism and intellectual disability. Dr Farah R Zahir specializes in the identification of novel genetic and epigenetic causes for neurodevelopmental diseases. Her PhD, awarded in 2011 by the University of British Columbia (UBC), resulted in the characterization of new intellectual disability (ID) syndromes, as well as discovery of several new causative genes for the disorder. She was awarded the prestigious James Miller Memorial Prize for integra
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