Cargando…

High resolution mapping of modified DNA nucleobases using excision repair enzymes

The incorporation and creation of modified nucleobases in DNA have profound effects on genome function. We describe methods for mapping positions and local content of modified DNA nucleobases in genomic DNA. We combined in vitro nucleobase excision with massively parallel DNA sequencing (Excision-se...

Descripción completa

Detalles Bibliográficos
Autores principales:	Bryan, D. Suzi, Ransom, Monica, Adane, Biniam, York, Kerri, Hesselberth, Jay R.
Formato:	Online Artículo Texto
Lenguaje:	English
Publicado:	Cold Spring Harbor Laboratory Press 2014
Materias:	Method
Acceso en línea:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4158761/ https://www.ncbi.nlm.nih.gov/pubmed/25015380 http://dx.doi.org/10.1101/gr.174052.114

Ejemplares similares

Global analysis of RNA cleavage by 5′-hydroxyl RNA sequencing
por: Peach, Sally E., et al.
Publicado: (2015)

Genetic bypass of essential RNA repair enzymes in budding yeast
por: Cherry, Patrick D., et al.
Publicado: (2018)

Nucleobase modification by an RNA enzyme
por: Poudyal, Raghav R., et al.
Publicado: (2017)

A new technique for genome-wide mapping of nucleotide excision repair without immunopurification of damaged DNA
por: Wu, Sizhong, et al.
Publicado: (2022)

Recovery and analysis of transcriptome subsets from pooled single-cell RNA-seq libraries
por: Riemondy, Kent A, et al.
Publicado: (2019)

New synthetic substrates of mammalian nucleotide excision repair system
por: Evdokimov, Alexey, et al.
Publicado: (2013)

Base-Resolution Analysis of Deoxyuridine at the Genome Scale Based on the Artificial Incorporation Modified Nucleobase
por: Wang, Yafen, et al.
Publicado: (2021)

Localization of Cdc7 Protein Kinase During DNA Replication in Saccharomyces cerevisiae
por: Rossbach, Daniel, et al.
Publicado: (2017)

Fluorescent probes for the analysis of DNA strand scission in base excision repair
por: Matsumoto, Naoyuki, et al.
Publicado: (2010)

High-resolution mapping demonstrates inhibition of DNA excision repair by transcription factors
por: Duan, Mingrui, et al.
Publicado: (2022)

High-resolution mapping, characterization, and optimization of autonomously replicating sequences in yeast
por: Liachko, Ivan, et al.
Publicado: (2013)

A Comprehensive, High-Resolution Map of a Gene’s Fitness Landscape
por: Firnberg, Elad, et al.
Publicado: (2014)

Genome-wide mapping of promoter-anchored interactions with close to single-enhancer resolution
por: Sahlén, Pelin, et al.
Publicado: (2015)

PASTMUS: mapping functional elements at single amino acid resolution in human cells
por: Zhang, Xinyi, et al.
Publicado: (2019)

Simultaneous measurement of biochemical phenotypes and gene expression in single cells
por: Richer, Amanda L, et al.
Publicado: (2020)

A homolog of lariat-debranching enzyme modulates turnover of branched RNA
por: Garrey, Stephen M., et al.
Publicado: (2014)

Small-scale extracts for the study of nucleotide excision repair and non-homologous end joining
por: Smeaton, Michael B., et al.
Publicado: (2007)

RRHP: a tag-based approach for 5-hydroxymethylcytosine mapping at single-site resolution
por: Petterson, Adam, et al.
Publicado: (2014)

Hidden Markov models lead to higher resolution maps of mutation signature activity in cancer
por: Wojtowicz, Damian, et al.
Publicado: (2019)

Pandora: nucleotide-resolution bacterial pan-genomics with reference graphs
por: Colquhoun, Rachel M., et al.
Publicado: (2021)

Comparative assessment of plasmid and oligonucleotide DNA substrates in measurement of in vitro base excision repair activity
por: Hou, Esther W., et al.
Publicado: (2007)

A panel of colorimetric assays to measure enzymatic activity in the base excision DNA repair pathway
por: Healing, Eleanor, et al.
Publicado: (2019)

Structured nucleosome fingerprints enable high-resolution mapping of chromatin architecture within regulatory regions
por: Schep, Alicia N., et al.
Publicado: (2015)

INSERT-seq enables high-resolution mapping of genomically integrated DNA using Nanopore sequencing
por: Ivančić, Dimitrije, et al.
Publicado: (2022)

SLIC-CAGE: high-resolution transcription start site mapping using nanogram-levels of total RNA
por: Cvetesic, Nevena, et al.
Publicado: (2018)

Highly specific and sensitive method for measuring nucleotide excision repair kinetics of ultraviolet photoproducts in human cells
por: Choi, Jun-Hyuk, et al.
Publicado: (2014)

Estimating absolute methylation levels at single-CpG resolution from methylation enrichment and restriction enzyme sequencing methods
por: Stevens, Michael, et al.
Publicado: (2013)

Nucleobase deaminases: a potential enzyme system for new therapies
por: Gaded, Vandana, et al.
Publicado: (2018)

Mapping and modeling the genomic basis of differential RNA isoform expression at single-cell resolution with LR-Split-seq
por: Rebboah, Elisabeth, et al.
Publicado: (2021)

SapTrap assembly of repair templates for Cas9-triggered homologous recombination with a self-excising cassette
por: Dickinson, Daniel J., et al.
Publicado: (2018)

High-throughput sequencing of EcoWI restriction fragments maps the genome-wide landscape of phosphorothioate modification at base resolution
por: Yang, Weiwei, et al.
Publicado: (2022)

A Modified T-test Feature Selection Method and Its Application on the HapMap Genotype Data
por: Zhou, Nina, et al.
Publicado: (2007)

BIND&MODIFY: a long-range method for single-molecule mapping of chromatin modifications in eukaryotes
por: Weng, Zhe, et al.
Publicado: (2023)

High spatial resolution nanoslit SERS for single-molecule nucleobase sensing
por: Chen, Chang, et al.
Publicado: (2018)

Mapping global and local coevolution across 600 species to identify novel homologous recombination repair genes
por: Sherill-Rofe, Dana, et al.
Publicado: (2019)

Modification mapping by nanopore sequencing
por: White, Laura K., et al.
Publicado: (2022)

Enzymatic synthesis of nucleobase-modified UDP-sugars: scope and limitations
por: Wagstaff, Ben A., et al.
Publicado: (2015)

Synthesis of Nucleobase-Modified RNA Oligonucleotides by Post-Synthetic Approach
por: Bartosik, Karolina, et al.
Publicado: (2020)

A blind deconvolution approach to high-resolution mapping of transcription factor binding sites from ChIP-seq data
por: Lun, Desmond S, et al.
Publicado: (2009)

Complementation of aprataxin deficiency by base excision repair enzymes
por: Çağlayan, Melike, et al.
Publicado: (2015)

Cannot write session to /tmp/vufind_sessions/sess_n48b7a6goa8eptdt0635dokfcu