Acta Chimica Sinica Cover

Cover for Acta Chimica Sinica vol 70 nº 20 based on paper by Zhang Liang, Yu Miao, He Chuan. Mouse Tet1 Protein can Oxidize 5mC to 5hmC and 5caC on Single-stranded DNA. The paper shows that Tet proteins can oxidize 5-methylcytosine (5mC) to 5-methylhydroxicytosine (5hmC) and 5hmC to 5-Carboxylcytosine (5caC) on single-stranded DNA as well […]

Base resolution sequencing 5-hydroxymethylcytosine cell cover proposal

The study of 5-hydroxylmethylcytosines (5hmC) has been hampered by the lack of a method to map it at single-base resolution on a genome-wide scale. Affinity purification-based methods cannot precisely locate 5hmC nor accurately determine its relative abundance at each modified site. We here present a genome-wide approach, Tet-assisted bisulfite sequencing (TAB-Seq), that when combined with traditional bisulfite sequencing can be used for mapping 5hmC at base resolution and quantifying the relative abundance of 5hmC as well as 5mC. Application of this method to embryonic stem cells not only confirms widespread distribution of 5hmC in the mammalian genome but also reveals sequence bias and strand asymmetry at 5hmC sites. We observe high levels of 5hmC and reciprocally low levels of 5mC near but not on transcription factor-binding sites. Additionally, the relative abundance of 5hmC varies significantly among distinct functional sequence elements, suggesting different mechanisms for 5hmC deposition and maintenance.

Base-Resolution Analysis of 5-Hydroxymethylcytosine in the Mammalian Genome. Miao Yu, Gary C. Hon, Keith E. Szulwach, Chun-Xiao Song, Liang Zhang, Audrey Kim, Xuekun Li, Qing Dai, Yin Shen, Beomseok Park, Jung-Hyun Min, Peng Jinsend email, Bing Rensend email, Chuan He. Cell, Volume 149, Issue 6, 1368-1380, 17 May 2012 The image shows the concept of […]

N6-methyladenosine-dependent RNA structural switches regulate RNA–protein interactions

Nature proposal cover hnRNP decipher RNP code dph N6mA methyl adenosin RNA 3Dciencia

Molecular biology: RNA modification does a regulatory two-step. The m6A structural modification of RNA regulates gene expression. It has now been found to mediate an unusual control mechanism: by altering the structure of RNA, m6A allows a regulatory protein to bind to that RNA. REFERENCIAS N6-methyladenosine-dependent RNA structural switches regulate RNA–protein interactions. Nian Liu, Qing […]

Pathogenic bacteria fight versus oxidative stress

cell host microbe proposal h2o2 bacterial proteome cover 3dciencia web

Thiol-group oxidation of active and allosteric cysteines is a widespread regulatory posttranslational protein modification. Pathogenic bacteria, including Pseudomonas aeruginosa and Staphylococcus aureus, use regulatory cysteine oxidation to respond to and overcome reactive oxygen species (ROS) encountered in the host environment. REFERENCES Proteome-wide Quantification and Characterization of Oxidation-Sensitive Cysteines in Pathogenic Bacteria. Xin Deng · Eranthie […]

Alpha Carbonic Anydrase Zinc active center

Carbonic anhydrases catalyze the reversible hydration of CO2. Since the discovery of this zinc (Zn) metalloenzyme in erythrocytes over 65 years ago, carbonic anhydrase has not only been found in virtually all mammalian tissues but is also abundant in plants and green unicellular algae. The enzyme is important to many eukaryotic physiological processes such as […]

Nature Chemical Biology. Human Thymine DNA glycosylase specifically recognizes 5-carboxylcytosine-modified DNA

Human thymine DNA glycosylase (hTDG) efficiently excises 5-carboxylcytosine (5caC), a key oxidation product of 5-methylcytosine in genomic DNA, in a recently discovered cytosine demethylation pathway. We present here the crystal structures of the hTDG catalytic domain in complex with duplex DNA containing either 5caC or a fluorinated analog. These structures, together with biochemical and computational […]