Identifying and mitigating bias in next-generation sequencing methods for chromatin biology
Next-generation sequencing (NGS) technologies have been used in diverse ways to
investigate various aspects of chromatin biology by identifying genomic loci that are bound …
investigate various aspects of chromatin biology by identifying genomic loci that are bound …
Transcriptional regulation of human UDP-glucuronosyltransferase genes
Glucuronidation is an important metabolic pathway for many small endogenous and
exogenous lipophilic compounds, including bilirubin, steroid hormones, bile acids …
exogenous lipophilic compounds, including bilirubin, steroid hormones, bile acids …
RNA-seq and ChIP-seq as complementary approaches for comprehension of plant transcriptional regulatory mechanism
II Muhammad, SL Kong, SN Akmar Abdullah… - International journal of …, 2019 - mdpi.com
The availability of data produced from various sequencing platforms offer the possibility to
answer complex questions in plant research. However, drawbacks can arise when there are …
answer complex questions in plant research. However, drawbacks can arise when there are …
Defining bacterial regulons using ChIP-seq
Chromatin immunoprecipitation followed by high-throughput sequencing (ChIP-seq) is a
powerful method that identifies protein–DNA binding sites in vivo. Recent studies have …
powerful method that identifies protein–DNA binding sites in vivo. Recent studies have …
Impact of anaerobiosis on expression of the iron-responsive Fur and RyhB regulons
Iron, a major protein cofactor, is essential for most organisms. Despite the well-known effects
of O2 on the oxidation state and solubility of iron, the impact of O2 on cellular iron …
of O2 on the oxidation state and solubility of iron, the impact of O2 on cellular iron …
Balanced cell division is secured by two different regulatory sites in OxyS RNA
M Elgrably-Weiss, F Hussain, J Georg, B Shraiteh… - RNA, 2024 - rnajournal.cshlp.org
The hydrogen peroxide-induced small RNA OxyS has been proposed to originate from the
3′ UTR of a peroxide mRNA. Unexpectedly, phylogenetic OxyS targetome predictions …
3′ UTR of a peroxide mRNA. Unexpectedly, phylogenetic OxyS targetome predictions …
Decoding ChIP-seq with a double-binding signal refines binding peaks to single-nucleotides and predicts cooperative interaction
The comprehension of protein and DNA binding in vivo is essential to understand gene
regulation. Chromatin immunoprecipitation followed by sequencing (ChIP-seq) provides a …
regulation. Chromatin immunoprecipitation followed by sequencing (ChIP-seq) provides a …
ChIP-seq for genome-scale analysis of bacterial DNA-binding proteins
RP Bonocora, JT Wade - Bacterial Transcriptional Control: Methods and …, 2015 - Springer
Protein–DNA interactions are central to many basic biological processes, including
transcription regulation, DNA replication, and DNA repair. Chromatin Immunoprecipitation …
transcription regulation, DNA replication, and DNA repair. Chromatin Immunoprecipitation …
MOSAiCS-HMM: A model-based approach for detecting regions of histone modifications from ChIP-seq data
Chromatin immunoprecipitation followed by high throughput sequencing (ChIP-seq)
experiments are routinely utilized for studying epigenomics of transcriptional regulation. We …
experiments are routinely utilized for studying epigenomics of transcriptional regulation. We …
Systematic evaluation of the impact of ChIP-seq read designs on genome coverage, peak identification, and allele-specific binding detection
Background Chromatin immunoprecipitation followed by sequencing (ChIP-seq)
experiments revolutionized genome-wide profiling of transcription factors and histone …
experiments revolutionized genome-wide profiling of transcription factors and histone …