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Literature DB >> 25591929

Base-resolution maps of 5-formylcytosine and 5-carboxylcytosine reveal genome-wide DNA demethylation dynamics.

Xingyu Lu¹, Dali Han¹, Boxuan Simen Zhao¹, Chun-Xiao Song¹, Li-Sheng Zhang¹, Louis C Doré¹, Chuan He¹.

Abstract

Entities: Chemical

Mesh：

Substances：

Year: 2015 PMID： 25591929 PMCID： PMC4349244 DOI： 10.1038/cr.2015.5

Source DB: PubMed Journal: Cell Res ISSN： 1001-0602 Impact factor: 25.617

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15 in total

1. Embryonic lethal phenotype reveals a function of TDG in maintaining epigenetic stability.

Authors: Daniel Cortázar; Christophe Kunz; Jim Selfridge; Teresa Lettieri; Yusuke Saito; Eilidh MacDougall; Annika Wirz; David Schuermann; Angelika L Jacobs; Fredy Siegrist; Roland Steinacher; Josef Jiricny; Adrian Bird; Primo Schär
Journal: Nature Date: 2011-01-30 Impact factor: 49.962

2. The discovery of 5-formylcytosine in embryonic stem cell DNA.

Authors: Toni Pfaffeneder; Benjamin Hackner; Matthias Truss; Martin Münzel; Markus Müller; Christian A Deiml; Christian Hagemeier; Thomas Carell
Journal: Angew Chem Int Ed Engl Date: 2011-06-30 Impact factor: 15.336

3. Thymine DNA glycosylase is essential for active DNA demethylation by linked deamination-base excision repair.

Authors: Salvatore Cortellino; Jinfei Xu; Mara Sannai; Robert Moore; Elena Caretti; Antonio Cigliano; Madeleine Le Coz; Karthik Devarajan; Andy Wessels; Dianne Soprano; Lara K Abramowitz; Marisa S Bartolomei; Florian Rambow; Maria Rosaria Bassi; Tiziana Bruno; Maurizio Fanciulli; Catherine Renner; Andres J Klein-Szanto; Yoshihiro Matsumoto; Dominique Kobi; Irwin Davidson; Christophe Alberti; Lionel Larue; Alfonso Bellacosa
Journal: Cell Date: 2011-06-30 Impact factor: 41.582

4. Simple combinations of lineage-determining transcription factors prime cis-regulatory elements required for macrophage and B cell identities.

Authors: Sven Heinz; Christopher Benner; Nathanael Spann; Eric Bertolino; Yin C Lin; Peter Laslo; Jason X Cheng; Cornelis Murre; Harinder Singh; Christopher K Glass
Journal: Mol Cell Date: 2010-05-28 Impact factor: 17.970

5. Genome-wide analysis reveals TET- and TDG-dependent 5-methylcytosine oxidation dynamics.

Authors: Li Shen; Hao Wu; Dinh Diep; Shinpei Yamaguchi; Ana C D'Alessio; Ho-Lim Fung; Kun Zhang; Yi Zhang
Journal: Cell Date: 2013-04-18 Impact factor: 41.582

6. Genome-wide profiling of 5-formylcytosine reveals its roles in epigenetic priming.

Authors: Chun-Xiao Song; Keith E Szulwach; Qing Dai; Ye Fu; Shi-Qing Mao; Li Lin; Craig Street; Yujing Li; Mickael Poidevin; Hao Wu; Juan Gao; Peng Liu; Lin Li; Guo-Liang Xu; Peng Jin; Chuan He
Journal: Cell Date: 2013-04-18 Impact factor: 41.582

7. Conversion of 5-methylcytosine to 5-hydroxymethylcytosine in mammalian DNA by MLL partner TET1.

Authors: Mamta Tahiliani; Kian Peng Koh; Yinghua Shen; William A Pastor; Hozefa Bandukwala; Yevgeny Brudno; Suneet Agarwal; Lakshminarayan M Iyer; David R Liu; L Aravind; Anjana Rao
Journal: Science Date: 2009-04-16 Impact factor: 47.728

8. Quantitative sequencing of 5-formylcytosine in DNA at single-base resolution.

Authors: Michael J Booth; Giovanni Marsico; Martin Bachman; Dario Beraldi; Shankar Balasubramanian
Journal: Nat Chem Date: 2014-03-23 Impact factor: 24.427

9. The nuclear DNA base 5-hydroxymethylcytosine is present in Purkinje neurons and the brain.

Authors: Skirmantas Kriaucionis; Nathaniel Heintz
Journal: Science Date: 2009-04-16 Impact factor: 47.728

10. Genome-wide distribution of 5-formylcytosine in embryonic stem cells is associated with transcription and depends on thymine DNA glycosylase.

Authors: Eun-Ang Raiber; Dario Beraldi; Gabriella Ficz; Heather E Burgess; Miguel R Branco; Pierre Murat; David Oxley; Michael J Booth; Wolf Reik; Shankar Balasubramanian
Journal: Genome Biol Date: 2012-08-17 Impact factor: 13.583

33 in total

1. A Highly Sensitive and Robust Method for Genome-wide 5hmC Profiling of Rare Cell Populations.

Authors: Dali Han; Xingyu Lu; Alan H Shih; Ji Nie; Qiancheng You; Meng Michelle Xu; Ari M Melnick; Ross L Levine; Chuan He
Journal: Mol Cell Date: 2016-07-28 Impact factor: 17.970

2. Simple and Efficient Room-Temperature Release of Biotinylated Nucleic Acids from Streptavidin and Its Application to Selective Molecular Detection.

Authors: Samuel Bearden; Fanny Wang; Adam R Hall
Journal: Anal Chem Date: 2019-06-12 Impact factor: 6.986

Base-resolution maps of 5-formylcytosine and 5-carboxylcytosine reveal genome-wide DNA demethylation dynamics.

1. Embryonic lethal phenotype reveals a function of TDG in maintaining epigenetic stability.

2. The discovery of 5-formylcytosine in embryonic stem cell DNA.

3. Thymine DNA glycosylase is essential for active DNA demethylation by linked deamination-base excision repair.

4. Simple combinations of lineage-determining transcription factors prime cis-regulatory elements required for macrophage and B cell identities.

5. Genome-wide analysis reveals TET- and TDG-dependent 5-methylcytosine oxidation dynamics.

6. Genome-wide profiling of 5-formylcytosine reveals its roles in epigenetic priming.

7. Conversion of 5-methylcytosine to 5-hydroxymethylcytosine in mammalian DNA by MLL partner TET1.

8. Quantitative sequencing of 5-formylcytosine in DNA at single-base resolution.

9. The nuclear DNA base 5-hydroxymethylcytosine is present in Purkinje neurons and the brain.

10. Genome-wide distribution of 5-formylcytosine in embryonic stem cells is associated with transcription and depends on thymine DNA glycosylase.

1. A Highly Sensitive and Robust Method for Genome-wide 5hmC Profiling of Rare Cell Populations.

2. Simple and Efficient Room-Temperature Release of Biotinylated Nucleic Acids from Streptavidin and Its Application to Selective Molecular Detection.

3. Base-resolution profiling of active DNA demethylation using MAB-seq and caMAB-seq.

Review 4. Role of base excision repair in maintaining the genetic and epigenetic integrity of CpG sites.

Review 5. TET-mediated active DNA demethylation: mechanism, function and beyond.

Review 6. Detecting and interpreting DNA methylation marks.

Review 7. Role of Base Excision "Repair" Enzymes in Erasing Epigenetic Marks from DNA.

8. Charting oxidized methylcytosines at base resolution.

9. Tet3 Reads 5-Carboxylcytosine through Its CXXC Domain and Is a Potential Guardian against Neurodegeneration.

Review 10. Nucleic Acid Modifications in Regulation of Gene Expression.