SummaryDNA methylation at selective cytosine residues (5mC) and their removal by TET-mediated DNA demethylation are critical for setting up pluripotent states in early embryonic development 1-2 . TET enzymes successively convert 5mC to 5hmC, 5fC, and 5caC, the latter two of which are subject to removal by thymine DNA glycosylase (TDG) in conjunction with base excision repair [1][2][3][4][5][6] . Early reports indicate that 5fC and 5caC could be stably detected on enhancers, promoters, and gene bodies with distinct effects on gene expression, but the mechanisms have remained elusive 7,8 . Here we determined the X-ray crystal structure of elongating Pol II in complex with DNA template containing oxidized 5-methylcytosines (oxi-mCs), revealing specific hydrogen bonds between the 5-carboxyl group of 5caC and the conserved epi-DNA recognition loop in the polymerase. This causes a positional shift for incoming NTP thus compromising nucleotide addition. To test the in vivo significance of this structural insight, we determined the global effect of increased 5fC/5caC levels on transcription, finding that such DNA modifications indeed retarded Pol II elongation on gene bodies. These results demonstrate the functional impact of oxi-mCs on gene expression and suggest a novel role for Pol II to function as a specific and direct epigenetic sensor during transcription elongation.Epigenetic DNA methylation (5mC) is an important regulator of gene transcription recognized by several families of protein readers, such as methyl-CpG-binding domain proteins (MBDs) and ubiquitin-like PHD and RING finger domain containing proteins Users may view, print, copy, and download text and data-mine the content in such documents, for the purposes of academic research, subject always to the full Conditions of use

Diabetic nephropathy (DN) is a chronic disease characterized by proteinuria, glomerular hypertrophy, decreased glomerular filtration and renal fibrosis with loss of renal function. DN is the leading cause of end-stage renal disease, accounting for millions of deaths worldwide. Hyperglycemia is the driving force for the development of diabetic nephropathy. The exact cause of diabetic nephropathy is unknown, but various postulated mechanisms are: hyperglycemia (causing hyperfiltration and renal injury), advanced glycosylation products, activation of cytokines. In this review article, we have discussed a number of diabetes-induced metabolites such as glucose, advanced glycation end products, protein kinase C and oxidative stress and other related factors that are implicated in the pathophysiology of the DN. An understanding of the biochemical and molecular changes especially early in the DN may lead to new and effective therapies towards prevention and amelioration of DN.

In human cells, the oxidative DNA lesion 8,5′-cyclo-2'-deoxyadenosine (CydA) induces prolonged stalling of RNA polymerase II (Pol II) followed by transcriptional bypass, generating both error-free and mutant transcripts with AMP misincorporated immediately downstream from the lesion. Here, we present biochemical and crystallographic evidence for the mechanism of CydA recognition. Pol II stalling results from impaired loading of the template base (5′) next to CydA into the active site, leading to preferential AMP misincorporation. Such predominant AMP insertion, which also occurs at an abasic site, is unaffected by the identity of the 5′-templating base, indicating that it derives from nontemplated synthesis according to an A rule known for DNA polymerases and recently identified for Pol II bypass of pyrimidine dimers. Subsequent to AMP misincorporation, Pol II encounters a major translocation block that is slowly overcome. Thus, the translocation block combined with the poor extension of the dA.rA mispair reduce transcriptional mutagenesis. Moreover, increasing the active-site flexibility by mutation in the trigger loop, which increases the ability of Pol II to accommodate the bulky lesion, and addition of transacting factor TFIIF facilitate CydA bypass. Thus, blocking lesion entry to the active site, translesion A rule synthesis, and translocation block are common features of transcription across different bulky DNA lesions.RNA polymerase II | translesion transcription | oxidative DNA damage | transcriptional mutagenesis | transcription factor TFIIF A ccurate and efficient genomic DNA transcription into mRNA is crucial for cell survival under DNA damage caused by UV (ultraviolet) irradiation, oxidative stress, or chemical agents. DNA lesions interfere with replication and transcription and cause mutations that grossly affect gene expression (1). To maintain genomic integrity, cells have evolved an orchestrated interplay of various DNA repair and DNA damage tolerance mechanisms. DNA damage that causes major helical distortion, such as UVinduced cyclobutane pyrimidine dimers (CPDs) and cisplatin adducts, is primarily removed by the nucleotide excision repair (NER) pathway (2). Nonbulky and nonhelix-distorting DNA lesions are typically processed by the base excision repair (BER) pathway. Despite ongoing DNA repair, some lesions escape detection and pose a roadblock for both replication and transcription machineries. During replication, the deleterious effects of DNA lesions can be alleviated by translesion synthesis (TLS). During TLS, the high-fidelity replicative DNA polymerases are transiently replaced by specialized low-fidelity translesion DNA polymerases that can accommodate bulky lesions within their more spacious active sites, thus enabling their bypass (3, 4). RNA polymerase II (Pol II) uses a distinct mechanism to bypass DNA lesions: a conformational flexibility of its active center (the flexible trigger loop domain), allowing accommodation of bulky lesions. During transcriptional TLS (lesion bypass), Pol...