Coding and noncoding transcriptomes of NODULIN HOMEOBOX (NDX)-deficient Arabidopsis inflorescence

Feró, Orsolya; Karányi, Zsolt; Nagy, Éva; Mosolygó-L, Ágnes; Szaker, Henrik Mihály; Csorba, Tibor; Székvölgyi, Lóránt

doi:10.1038/s41597-023-02279-9

Cited by 2 publications

(1 citation statement)

References 20 publications

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“…Finally, we concentrated the samples to 30 μL using a speed vacuum concentrator and measured the concentration using the Qubit dsDNA HS Assay Kit. NGS library preparation and sequencing was performed as described 36 , 37 using the Illumina TruSeq ChIP Sample Preparation protocol. Briefly, DRIP DNA was end-repaired and indexed adapters were ligated to the inserts.…”

Section: Methodsmentioning

confidence: 99%

DNA methylome, R-loop and clinical exome profiling of patients with sporadic amyotrophic lateral sclerosis

Feró,

Varga,

Nagy

et al. 2024

Sci Data

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Amyotrophic lateral sclerosis (ALS) is a fatal neurodegenerative disorder characterized by the death of motor neurons, the aetiology of which is essentially unknown. Here, we present an integrative epigenomic study in blood samples from seven clinically characterised sporadic ALS patients to elucidate molecular factors associated with the disease. We used clinical exome sequencing (CES) to study DNA variants, DNA-RNA hybrid immunoprecipitation sequencing (DRIP-seq) to assess R-loop distribution, and reduced representation bisulfite sequencing (RRBS) to examine DNA methylation changes. The above datasets were combined to create a comprehensive repository of genetic and epigenetic changes associated with the ALS cases studied. This repository is well-suited to unveil new correlations within individual patients and across the entire patient cohort. The molecular attributes described here are expected to guide further mechanistic studies on ALS, shedding light on the underlying genetic causes and facilitating the development of new epigenetic therapies to combat this life-threatening disease.

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Section: Methodsmentioning

confidence: 99%

DNA methylome, R-loop and clinical exome profiling of patients with sporadic amyotrophic lateral sclerosis

Feró,

Varga,

Nagy

et al. 2024

Sci Data

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Chromosomal R-loops: who R they?

Székvölgyi

2024

BIOLOGIA FUTURA

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R-loops, composed of DNA–RNA hybrids and displaced single-stranded DNA, are known to pose a severe threat to genome integrity. Therefore, extensive research has focused on identifying regulatory proteins involved in controlling R-loop levels. These proteins play critical roles in preventing R-loop accumulation and associated genome instability. Herein I summarize recent knowledge on R-loop regulators affecting R-loop homeostasis, involving a wide array of R-loop screening methods that have enabled their characterization, from forward genetic and siRNA-based screens to proximity labeling and machine learning. These approaches not only deepen our understanding on R-loop formation processes, but also hold promise to find new targets in R-loop dysregulation associated with human pathologies.

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Coding and noncoding transcriptomes of NODULIN HOMEOBOX (NDX)-deficient Arabidopsis inflorescence

Cited by 2 publications

References 20 publications

DNA methylome, R-loop and clinical exome profiling of patients with sporadic amyotrophic lateral sclerosis

DNA methylome, R-loop and clinical exome profiling of patients with sporadic amyotrophic lateral sclerosis

Chromosomal R-loops: who R they?

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