Cargando…

Understanding the structural and dynamic consequences of DNA epigenetic modifications: Computational insights into cytosine methylation and hydroxymethylation

We report a series of molecular dynamics (MD) simulations of up to a microsecond combined simulation time designed to probe epigenetically modified DNA sequences. More specifically, by monitoring the effects of methylation and hydroxymethylation of cytosine in different DNA sequences, we show, for t...

Descripción completa

Detalles Bibliográficos
Autores principales:	Carvalho, Alexandra T P, Gouveia, Leonor, Kanna, Charan Raju, Wärmländer, Sebastian K T S, Platts, Jamie A, Kamerlin, Shina Caroline Lynn
Formato:	Online Artículo Texto
Lenguaje:	English
Publicado:	Taylor & Francis 2015
Materias:	Research Papers
Acceso en línea:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4622728/ https://www.ncbi.nlm.nih.gov/pubmed/25625845 http://dx.doi.org/10.4161/15592294.2014.988043

Ejemplares similares

Theoretical modelling of epigenetically modified DNA sequences
por: Carvalho, Alexandra Teresa Pires, et al.
Publicado: (2015)

Hydroxymethylated cytosine in development and disease
por: Pfeifer, Gerd P
Publicado: (2013)

Enzymatic approaches for profiling cytosine methylation and hydroxymethylation
por: Wang, Tong, et al.
Publicado: (2021)

Cytosine methylation and hydroxymethylation mark DNA for elimination in Oxytricha trifallax
por: Bracht, John R, et al.
Publicado: (2012)

Cytosine methylation and hydroxymethylation mark DNA for elimination in Oxytricha trifallax
por: Bracht, John R, et al.
Publicado: (2013)

Recognition and potential mechanisms for replication and erasure of cytosine hydroxymethylation
por: Hashimoto, Hideharu, et al.
Publicado: (2012)

Hydroxymethylated Cytosines Are Associated with Elevated C to G Transversion Rates
por: Supek, Fran, et al.
Publicado: (2014)

Epigenetic Modification of Cytosines in Hematopoietic Differentiation and Malignant Transformation
por: An, Jungeun, et al.
Publicado: (2023)

Association of 5-hydroxymethylation and 5-methylation of DNA cytosine with tissue-specific gene expression
por: Ponnaluri, V. K. Chaithanya, et al.
Publicado: (2016)

Genome-wide characterization of cytosine-specific 5-hydroxymethylation in normal breast tissue
por: Wilkins, Owen M., et al.
Publicado: (2019)

Recent Advances in Understanding Biological GTP Hydrolysis through Molecular Simulation
por: Calixto, Ana Rita, et al.
Publicado: (2020)

Tet-dependent 5-hydroxymethyl-Cytosine modification of mRNA regulates the axon guidance genes robo2 and slit in Drosophila
por: Singh, Badri Nath, et al.
Publicado: (2023)

Cytosine modifications exhibit circadian oscillations that are involved in epigenetic diversity and aging
por: Oh, Gabriel, et al.
Publicado: (2018)

Epigenetic modification of cytosines fine tunes the stability of i-motif DNA
por: Wright, Elisé P, et al.
Publicado: (2020)

Epigenetic Regulators of DNA Cytosine Modification: Promising Targets for Cancer Therapy
por: Jung, Inkyung, et al.
Publicado: (2023)

Cell Cycle-Dependent Turnover of 5-Hydroxymethyl Cytosine in Mouse Embryonic Stem Cells
por: Otani, Junji, et al.
Publicado: (2013)

Cytosine 5-hydroxymethylation regulates VHL gene expression in renal clear cell carcinoma
por: Ma, En-Guang, et al.
Publicado: (2017)

Association between the Cytosine Hydroxymethylation and the Expression of microRNA in Multiple Sclerosis in Polish Population
por: Basak, Justyna, et al.
Publicado: (2023)

Hydroxymethylation of DNA: an epigenetic marker
por: Richa, Rajneesh, et al.
Publicado: (2014)

Where are the female science professors? A personal perspective
por: Kamerlin, Shina Caroline Lynn
Publicado: (2016)

DNA cytosine hydroxymethylation levels are distinct among non-overlapping classes of peripheral blood leukocytes
por: Hohos, Natalie M., et al.
Publicado: (2016)

Circadian oscillations of cytosine modification in humans contribute to epigenetic variability, aging, and complex disease
por: Oh, Gabriel, et al.
Publicado: (2019)

An all-to-all approach to the identification of sequence-specific readers for epigenetic DNA modifications on cytosine
por: Song, Guang, et al.
Publicado: (2021)

Epigenetic Regulation of HIV-1 Latency by Cytosine Methylation
por: Kauder, Steven E., et al.
Publicado: (2009)

Epigenetic signatures of methylated DNA cytosine in Alzheimer’s disease
por: Fetahu, Irfete S., et al.
Publicado: (2019)

Structural consequence of the most frequently recurring cancer-associated substitution in DNA polymerase ε
por: Parkash, Vimal, et al.
Publicado: (2019)

Ascorbate content of clinical glioma tissues is related to tumour grade and to global levels of 5-hydroxymethyl cytosine
por: Crake, Rebekah L. I., et al.
Publicado: (2022)

Epigenetic Modifications in the Biology of Nonalcoholic Fatty Liver Disease: The Role of DNA Hydroxymethylation and TET Proteins
por: Pirola, Carlos J., et al.
Publicado: (2015)

Cytosine epigenetic modification modulates the formation of an unprecedented G4 structure in the WNT1 promoter
por: Wang, Zi-Fu, et al.
Publicado: (2020)

A Structural View into the Complexity of Carbon Dioxide Fixation
por: Kourist, Robert, et al.
Publicado: (2022)

Co-Localization of DNA i-Motif-Forming Sequences and 5-Hydroxymethyl-cytosines in Human Embryonic Stem Cells
por: Bhavsar-Jog, Yogini P., et al.
Publicado: (2019)

Author Correction: An all-to-all approach to the identification of sequence-specific readers for epigenetic DNA modifications on cytosine
por: Song, Guang, et al.
Publicado: (2021)

Chemical Methods for Decoding Cytosine Modifications in DNA
por: Booth, Michael J., et al.
Publicado: (2014)

The Impact of the HydroxyMethylCytosine epigenetic signature on DNA structure and function
por: Battistini, Federica, et al.
Publicado: (2021)

Uncovering plant epigenetics: new insights into cytosine methylation in rye genomes
por: Kaur, Navneet, et al.
Publicado: (2023)

Understanding thio-effects in simple phosphoryl systems: role of solvent effects and nucleophile charge
por: Carvalho, Alexandra T. P., et al.
Publicado: (2015)

Hydroxymethylation and Epigenetic Drugs: New Insights into the Diagnosis and Treatment in Epigenetics of Hepatocellular Carcinoma
por: Ouyang, Wei, et al.
Publicado: (2023)

Concerted or Stepwise: How Much Do Free-Energy Landscapes Tell Us about the Mechanisms of Elimination Reactions?
por: Duarte, Fernanda, et al.
Publicado: (2014)

Development and Application of a Nonbonded Cu(2+) Model That Includes the Jahn–Teller Effect
por: Liao, Qinghua, et al.
Publicado: (2015)

Similar Active Sites and Mechanisms Do Not Lead to Cross-Promiscuity in Organophosphate Hydrolysis: Implications for Biotherapeutic Engineering
por: Purg, Miha, et al.
Publicado: (2017)

Cannot write session to /tmp/vufind_sessions/sess_glsmielbi8bdmsg42140u784dr