Alkyladenine DNA glycosylase associates with transcription elongation to coordinate DNA repair with gene expression.

Base excision repair (BER) initiated by alkyladenine DNA glycosylase (AAG) is essential for removal of aberrantly methylated DNA bases. Genome instability and accumulation of aberrant bases accompany multiple diseases, including cancer and neurological disorders. While BER is well studied on naked DNA, it remains unclear how BER efficiently operates on chromatin. Here, we show that AAG binds to chromatin and forms complex with RNA polymerase (pol) II. This occurs through direct interaction with Elongator and results in transcriptional co-regulation. Importantly, at co-regulated genes, aberrantly methylated bases accumulate towards the 3'end in regions enriched for BER enzymes AAG and APE1, Elongator and active RNA pol II. Active transcription and functional Elongator are further crucial to ensure efficient BER, by promoting AAG and APE1 chromatin recruitment. Our findings provide insights into genome stability maintenance in actively transcribing chromatin and reveal roles of aberrantly methylated bases in regulation of gene expression.

Hidden α-helical propensity segments within disordered regions of the transcriptional activator CHOP.

C/EBP-homologous protein (CHOP) is a key determinant of the apoptotic response to endoplasmic reticulum stress or DNA damage. As a member of the C/EBP family, CHOP contains a low complexity N-terminal region involved in transcriptional activation, followed by a bZIP that binds DNA after dimerization. However, in contrast to other C/EBPs, CHOP directs binding to non-canonical C/EBP sites due to unique substitutions in its DNA-binding domain. Herein, we show that the N-terminal region of CHOP is intrinsically unstructured but contains two segments presenting α-helical propensity. One of these segments is conserved in other C/EBPs and mediates essential roles of CHOP, including regulation through phosphorylation. The second segment is placed within a proteolytic-resistant portion of the protein and exhibits reduced flexibility. Moreover, the DNA-binding region of CHOP also contains a segment with α-helical character towards its most N-terminal part. Our results suggest that structure-prone segments scattered within disordered regions may be critical for macromolecular recognition during CHOP-mediated transcriptional activation.

Impact of ribonucleotide incorporation by DNA polymerases ß and λ on oxidative base excision repair.

Oxidative stress is a very frequent source of DNA damage. Many cellular DNA polymerases (Pols) can incorporate ribonucleotides (rNMPs) during DNA synthesis. However, whether oxidative stress-triggered DNA repair synthesis contributes to genomic rNMPs incorporation is so far not fully understood. Human specialized Pols ß and λ are the important enzymes involved in the oxidative stress tolerance, acting both in base excision repair and in translesion synthesis past the very frequent oxidative lesion 7,8-dihydro-8-oxoguanine (8-oxo-G). We found that Pol ß, to a greater extent than Pol λ can incorporate rNMPs opposite normal bases or 8-oxo-G, and with a different fidelity. Further, the incorporation of rNMPs opposite 8-oxo-G delays repair by DNA glycosylases. Studies in Pol ß- and λ-deficient cell extracts suggest that Pol ß levels can greatly affect rNMP incorporation opposite oxidative DNA lesions.

Quantitative enzyme-linked immunosorbent assay determination of an abundant hemoglobin-derived anti-infective peptide in human placenta.

A fragment of the human beta-chain of hemoglobin (HEM), hHEMbeta111-146, was shown to have broad antimicrobial properties. The 3.9-kDa peptide was postulated to occur in high concentrations in placenta tissue. We established a reliable method to quantify hHEMbeta111-146 in placenta tissue. Our methodology consists of a tissue extraction step (step 1), a chromatographic enrichment step (step 2), and a final quantification step (step 3) by enzyme-linked immunosorbent assay (ELISA). The specificity of the ELISA reaction was confirmed by parallel analysis of the samples via Western blot (step 4). The ELISA measured the absorbance of a tetramethylbenzidine substrate at 450nm. It showed no cross-reactivity with the corresponding gamma- and alpha-HEM regions and low cross-reactivity with the beta-HEM region and full-length HEM. The sample preparation procedure enabled a prepurification of hHEMbeta111-146, completely eliminating cross-reactive proteins and HEM peptides. The linear range of detection in step 3 was 20-200ng/well (200-2000microg/L) with a limit of quantification of 23ng/well (230microg/L) and a limit of detection of 7ng/well (70microg/L). The assay was characterized by good linearity (r(2)>0.99), intraday precision (coefficient of variation [CV]=2.2-8.3%), interday precision (CV=1.8-9.1%), and accuracy (76-109%). The mean recovery of the ELISA was determined to be 97%, and the overall recovery during steps 1-3 was found to be 40.3+/-2.5%. We measured concentrations from 0.28 to 0.74mg/g placenta tissue of the hHEMbeta111-146 in different placenta samples with an average concentration of 0.57mg/g. This abundant concentration supports an important physiological role of hHEMbeta111-146 in the placenta infective barrier.