Live-cell imaging unveils distinct R-loop populations with heterogeneous dynamics

Martin, Robert M; de Almeida, Madalena R; Gameiro, Eduardo; de Almeida, Sérgio F

doi:10.1093/nar/gkad812

Cited by 4 publications

(1 citation statement)

References 42 publications

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“…While studies have implicated various factors in the regulation of R‐loop dynamics, such as transcriptional activity, chromatin state, and DNA damage signaling, the underlying molecular mechanisms remain incompletely understood. Time‐resolved studies using live‐cell imaging or single‐molecule techniques (Malig et al., 2020; Martin et al., 2023) can provide insights into the temporal dynamics of R‐loop formation, resolution, and turnover in different cellular contexts, shedding light on their regulatory pathways and functional outcomes. A recent study using single molecule tracking has successfully established the ability of RNA polymerase to form R‐loops at double stranded breaks, independent of other factors (G. Lim et al., 2023).…”

Section: Discussionmentioning

confidence: 99%

Approaches for Mapping and Analysis of R‐loops

Mukhopadhyay,

Miller,

Stoja

et al. 2024

Current Protocols

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R‐loops are nucleic acid structures composed of a DNA:RNA hybrid with a displaced non‐template single‐stranded DNA. Current approaches to identify and map R‐loop formation across the genome employ either an antibody targeted against R‐loops (S9.6) or a catalytically inactivated form of RNase H1 (dRNH1), a nuclease that can bind and resolve DNA:RNA hybrids via RNA exonuclease activity. This overview article outlines several ways to map R‐loops using either methodology, explaining the differences and similarities among the approaches. Bioinformatic analysis of R‐loops involves several layers of quality control and processing before visualizing the data. This article provides resources and tools that can be used to accurately process R‐loop mapping data and explains the advantages and disadvantages of the resources as compared to one another. © 2024 Wiley Periodicals LLC.

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Section: Discussionmentioning

confidence: 99%

Approaches for Mapping and Analysis of R‐loops

Mukhopadhyay,

Miller,

Stoja

et al. 2024

Current Protocols

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TERRA and the alternative lengthening of telomeres: a dangerous affair

Azzalin

2024

FEBS Letters

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Eukaryotic telomeres are transcribed into the long noncoding RNA TERRA. A fraction of TERRA remains associated with telomeres by forming RNA:DNA hybrids dubbed telR‐loops. TERRA and telR‐loops are essential to promote telomere elongation in human cancer cells that maintain telomeres through a homology‐directed repair pathway known as alternative lengthening of telomeres or ALT. However, TERRA and telR‐loops compromise telomere integrity and cell viability if their levels are not finely tuned. The study of telomere transcription in ALT cells will enormously expand our understanding of the ALT mechanism and of how genome integrity is maintained. Moreover, telomere transcription, TERRA and telR‐loops are likely to become exceptionally suited targets for the development of novel anti‐cancer therapies.

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Beyond the Synapse: FMR1 and FMRP Molecular Mechanisms in the Nucleus

Hansen,

Dischler,

Dias

2024

IJMS

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FMR1 (Fragile X messenger ribonucleoprotein 1), located on the X-chromosome, encodes the multi-functional FMR1 protein (FMRP), critical to brain development and function. Trinucleotide CGG repeat expansions at this locus cause a range of neurological disorders, collectively referred to as Fragile X-related conditions. The most well-known of these is Fragile X syndrome, a neurodevelopmental disorder associated with syndromic facial features, autism, intellectual disabilities, and seizures. However, CGG expansions of different sizes also confer a risk of neuropsychiatric and neurodegenerative disorders throughout the lifespan, through distinct molecular mechanisms. Although Fragile X syndrome is associated with downstream synaptic deficits and neuronal hyperexcitability, work in the past decade has demonstrated that both the causative FMR1 trinucleotide repeat expansion and FMRP itself play important roles in nuclear function and regulation, including non-canonical nucleic acid structure formation and chromatin dynamics. These effects are critical to cellular pathophysiology, although the full extent of their contribution to clinical phenotypes is only just emerging. Here, we present a focused review on some of the nuclear consequences of FMR1/FMRP dysregulation, including parallels in other repeat expansion disorders, ranging from studies in model systems to human cells and tissues.

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Live-cell imaging unveils distinct R-loop populations with heterogeneous dynamics

Cited by 4 publications

References 42 publications

Approaches for Mapping and Analysis of R‐loops

Approaches for Mapping and Analysis of R‐loops

TERRA and the alternative lengthening of telomeres: a dangerous affair

Beyond the Synapse: FMR1 and FMRP Molecular Mechanisms in the Nucleus

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