Deciphering molecular interactions by proximity labeling

W Qin, KF Cho, PE Cavanagh, AY Ting - Nature methods, 2021 - nature.com
Many biological processes are executed and regulated through the molecular interactions of
proteins and nucleic acids. Proximity labeling (PL) is a technology for tagging the …

DamID as a versatile tool for understanding gene regulation

GN Aughey, SW Cheetham, TD Southall - Development, 2019 - journals.biologists.com
The interaction of proteins and RNA with chromatin underlies the regulation of gene
expression. The ability to profile easily these interactions is fundamental for understanding …

[HTML][HTML] Hepatocellular cystathionine γ lyase/hydrogen sulfide attenuates nonalcoholic fatty liver disease by activating farnesoid X receptor

W Xu, C Cui, C Cui, Z Chen, H Zhang, Q Cui, G Xu… - Hepatology, 2022 - journals.lww.com
Conclusions FXR sulfhydration is a post‐translational modification affected by hepatic
endogenous CSE/H 2 S that may promote FXR activity and attenuate NAFLD. Hepatic CSE …

Tn5 DNA transposase in multi-omics research

D Penkov, E Zubkova, Y Parfyonova - Methods and Protocols, 2023 - mdpi.com
Tn5 transposase use in biotechnology has substantially advanced the sequencing
applications of genome-wide analysis of cells. This is mainly due to the ability of Tn5 …

[图书][B] Next-generation sequencing data analysis

X Wang - 2016 - taylorfrancis.com
Next-generation DNA and RNA sequencing has revolutionized biology and medicine. With
sequencing costs continuously dropping and our ability to generate large datasets rising …

Nucleosomal embedding reshapes the dynamics of abasic sites

E Bignon, VEP Claerbout, T Jiang, C Morell, N Gillet… - Scientific reports, 2020 - nature.com
Apurinic/apyrimidinic (AP) sites are the most common DNA lesions, which benefit from a
most efficient repair by the base excision pathway. The impact of losing a nucleobase on the …

Mass Spectrometry for Assessing Protein–Nucleic Acid Interactions

X He, X Chen, Y Wang - Analytical chemistry, 2023 - ACS Publications
Protein− nucleic acid interactions, including the interac-tions of proteins with DNA, RNA, and
DNA/RNA hybrid, often confer important biological consequences to targeted nucleic acids …

Induced proximity labeling and editing for epigenetic research

C Zhou, S Wagner, FS Liang - Cell Chemical Biology, 2024 - cell.com
Epigenetic regulation plays a pivotal role in various biological and disease processes. Two
key lines of investigation have been pursued that aim to unravel endogenous epigenetic …

[HTML][HTML] CSSQ: a ChIP-seq signal quantifier pipeline

A Kumar, MY Hu, Y Mei, Y Fan - Frontiers in Cell and Developmental …, 2023 - frontiersin.org
Chromatin immunoprecipitation followed by sequencing (ChIP-seq) has revolutionized the
studies of epigenomes and the massive increase in ChIP-seq datasets calls for robust and …

Measuring RNA polymerase activity genome-wide with high-resolution run-on-based methods

A Jordán-Pla, ME Pérez-Martínez, JE Pérez-Ortín - Methods, 2019 - Elsevier
The biogenesis of RNAs is a multi-layered and highly regulated process that involves a
diverse set of players acting in an orchestrated manner throughout the transcription cycle …