eLife assessment: Genome-wide mapping of native co-localized G4s and R-loops in living cells DOI Open Access
Andrés Aguilera

Опубликована: Июль 22, 2024

The non-B DNA structures can act as dynamic functional genomic elements regulating gene expression. Among them, G4s and R-loops are two of the best studied. interplay between emerging in repair, replication transcription. A comprehensive picture native co-localized living cells is currently lacking. Here, we describe development HepG4-seq an optimized HBD-seq methods, which robustly capture R-loops, respectively, cells. We successfully employed these methods to establish maps human HEK293 mouse embryonic stem (mESCs). discovered that dynamically altered a cell type-dependent manner largely localized at active promoters enhancers transcriptional genes. further demonstrated helicase Dhx9 direct major regulator modulates formation resolution R-loops. Depletion impaired self-renewal differentiation capacities mESCs by altering transcription - associated Taken together, our work established endogenous prevalently persisted regulatory regions genes involved regulation their linked genes, opening door for exploring broader roles disease.

Язык: Английский

The hidden architects of the genome: a comprehensive review of R-loops DOI

Chetna Yadav,

Ritu Yadav,

Smiti Nanda

и другие.

Molecular Biology Reports, Год журнала: 2024, Номер 51(1)

Опубликована: Окт. 26, 2024

Язык: Английский

Процитировано

1
Established and Emerging Roles of DEAD/H‐Box Helicases in Regulating Infection and Immunity DOI Creative Commons
Mark R. Parthun, Matthew E. Long, Emily A. Hemann

и другие.

Immunological Reviews, Год журнала: 2024, Номер unknown

Опубликована: Дек. 2, 2024

ABSTRACT The sensing of nucleic acids by DEAD/H‐box helicases, specifically retinoic acid‐inducible gene I (RIG‐I) and melanoma differentiation‐associated protein 5 (MDA5), plays a critical role in inducing antiviral immunity following infection. However, this helicase family includes many additional proteins whose immune functions have not been investigated. While numerous helicases contribute to immunity, they employ diverse mechanisms beyond the direct acids. Some members also identified play proviral (promoting virus replication/propagation) roles during infections, regulate other non‐viral regulation autoimmunity cancer. This review synthesizes known emerging broader highlights ongoing efforts target these therapeutically.

Язык: Английский

Процитировано

1
AAV-mediated genome editing is influenced by the formation of R-loops DOI Creative Commons
Francesco Puzzo, Magdalena P. Crossley, Aranyak Goswami

и другие.

bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2024, Номер unknown

Опубликована: Май 9, 2024

Recombinant adeno-associated viral vectors (rAAV) hold an intrinsic ability to stimulate homologous recombination (AAV-HR) and are the most used in clinical settings for

Язык: Английский

Процитировано

0
Genome-wide mapping of native co-localized G4s and R-loops in living cells DOI Creative Commons
Ting Liu,

Xing Shen,

Yijia Ren

и другие.

bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2024, Номер unknown

Опубликована: Июнь 4, 2024

Abstract The non-B DNA structures can act as dynamic functional genomic elements regulating gene expression. Among them, G4s and R-loops are two of the best studied. interplay between emerging in repair, replication transcription. A comprehensive picture native co-localized living cells is currently lacking. Here, we describe development HepG4-seq an optimized HBD-seq methods, which robustly capture R-loops, respectively, cells. We successfully employed these methods to establish maps human HEK293 mouse embryonic stem (mESCs). discovered that dynamically altered a cell type-dependent manner largely localized at active promoters enhancers transcriptional genes. further demonstrated helicase Dhx9 direct major regulator modulates formation resolution R-loops. Depletion impaired self-renewal differentiation capacities mESCs by altering transcription - associated Taken together, our work established endogenous prevalently persisted regulatory regions genes involved regulation their linked genes, opening door for exploring broader roles disease.

Язык: Английский

Процитировано

0
eLife assessment: Genome-wide mapping of native co-localized G4s and R-loops in living cells DOI Open Access
Andrés Aguilera

Опубликована: Июль 22, 2024

The non-B DNA structures can act as dynamic functional genomic elements regulating gene expression. Among them, G4s and R-loops are two of the best studied. interplay between emerging in repair, replication transcription. A comprehensive picture native co-localized living cells is currently lacking. Here, we describe development HepG4-seq an optimized HBD-seq methods, which robustly capture R-loops, respectively, cells. We successfully employed these methods to establish maps human HEK293 mouse embryonic stem (mESCs). discovered that dynamically altered a cell type-dependent manner largely localized at active promoters enhancers transcriptional genes. further demonstrated helicase Dhx9 direct major regulator modulates formation resolution R-loops. Depletion impaired self-renewal differentiation capacities mESCs by altering transcription - associated Taken together, our work established endogenous prevalently persisted regulatory regions genes involved regulation their linked genes, opening door for exploring broader roles disease.

Язык: Английский

Процитировано

0