Biological soft matter: intrinsically disordered proteins in liquid–liquid phase separation and biomolecular condensates

AV Fonin, IA Antifeeva, IM Kuznetsova… - Essays in …, 2022 - portlandpress.com
The facts that many proteins with crucial biological functions do not have unique structures
and that many biological processes are compartmentalized into the liquid-like biomolecular …

R-loop-dependent promoter-proximal termination ensures genome stability

C Xu, C Li, J Chen, Y Xiong, Z Qiao, P Fan, C Li, S Ma… - Nature, 2023 - nature.com
The proper regulation of transcription is essential for maintaining genome integrity and
executing other downstream cellular functions,. Here we identify a stable association …

PARP1 associates with R-loops to promote their resolution and genome stability

N Laspata, P Kaur, SY Mersaoui, D Muoio… - Nucleic acids …, 2023 - academic.oup.com
PARP1 is a DNA-dependent ADP-Ribose transferase with ADP-ribosylation activity that is
triggered by DNA breaks and non-B DNA structures to mediate their resolution. PARP1 was …

Deep structural insights into RNA‐binding disordered protein regions

A Zeke, E Schad, T Horvath… - Wiley …, 2022 - Wiley Online Library
Recent efforts to identify RNA binding proteins in various organisms and cellular contexts
have yielded a large collection of proteins that are capable of RNA binding in the absence of …

Hypoxia-induced transcriptional stress is mediated by ROS-induced R-loops

TS Ma, KR Worth, C Maher, N Ng, C Beghè… - Nucleic acids …, 2023 - academic.oup.com
Hypoxia is a common feature of solid tumors and is associated with poor patient prognosis,
therapy resistance and metastasis. Radiobiological hypoxia (< 0.1% O2) is one of the few …

R-loops: emerging key regulators in plants

D Zheng, M Li, Y Yang, R Huang… - Journal of Experimental …, 2023 - academic.oup.com
The biological implications of R-loops are increasingly receiving attention in plant biology.
Compared with recent progresses in humans, the studies of R-loops in plants are lagging …

NKAPL facilitates transcription pause-release and bridges elongation to initiation during meiosis exit

Z Kang, C Xu, S Lu, J Gong, R Yan, G Luo… - Nature …, 2025 - nature.com
Transcription elongation, especially RNA polymerase II (Pol II) pause-release, is less
studied than transcription initiation in regulating gene expression during meiosis. It is also …

Epitranscriptome in action: RNA modifications in the DNA damage response

B Xhemalçe, KM Miller, N Gromak - Molecular Cell, 2024 - cell.com
Complex pathways involving the DNA damage response (DDR) contend with cell-intrinsic
and-extrinsic sources of DNA damage. DDR mis-regulation results in genome instability that …

Integrative modeling of lncRNA-chromatin interaction maps reveals diverse mechanisms of nuclear retention

S Tabe-Bordbar, S Sinha - BMC genomics, 2023 - Springer
Background Many long non-coding RNAs, known to be involved in transcriptional
regulation, are enriched in the nucleus and interact with chromatin. However, their …

Essential roles and risks of G-quadruplex regulation: recognition targets of ALS-linked TDP-43 and FUS

A Ishiguro, A Ishihama - Frontiers in Molecular Biosciences, 2022 - frontiersin.org
A non-canonical DNA/RNA structure, G-quadruplex (G4), is a unique structure formed by two
or more guanine quartets, which associate through Hoogsteen hydrogen bonding leading to …