Mechanisms of lncRNA biogenesis as revealed by nascent transcriptomics

T Nojima, NJ Proudfoot - Nature reviews Molecular cell biology, 2022 - nature.com
Mammalian genomes express two principal gene categories through RNA polymerase II-
mediated transcription: protein-coding transcription units and non-coding RNA transcription …

Long noncoding RNAs in plants

AT Wierzbicki, T Blevins… - Annual Review of Plant …, 2021 - annualreviews.org
Plants have an extraordinary diversity of transcription machineries, including five nuclear
DNA-dependent RNA polymerases. Four of these enzymes are dedicated to the production …

[HTML][HTML] Epigenetic regulation of abiotic stress memory: maintaining the good things while they last

V Oberkofler, L Pratx, I Bäurle - Current opinion in plant biology, 2021 - Elsevier
As sessile organisms, plants have evolved sophisticated ways to constantly gauge and
adapt to changing environmental conditions including extremes that may be harmful to their …

Native elongation transcript sequencing reveals temperature dependent dynamics of nascent RNAPII transcription in Arabidopsis

P Kindgren, M Ivanov, S Marquardt - Nucleic Acids Research, 2020 - academic.oup.com
Temperature profoundly affects the kinetics of biochemical reactions, yet how large
molecular complexes such as the transcription machinery accommodate changing …

Natural temperature fluctuations promote COOLAIR regulation of FLC

Y Zhao, P Zhu, J Hepworth, R Bloomer… - Genes & …, 2021 - genesdev.cshlp.org
Plants monitor many aspects of their fluctuating environments to help align their
development with seasons. Molecular understanding of how noisy temperature cues are …

Histone chaperone ASF1 mediates H3. 3-H4 deposition in Arabidopsis

Z Zhong, Y Wang, M Wang, F Yang, QA Thomas… - Nature …, 2022 - nature.com
Histone chaperones and chromatin remodelers control nucleosome dynamics, which are
essential for transcription, replication, and DNA repair. The histone chaperone Anti …

LncRNA FLAIL affects alternative splicing and represses flowering in Arabidopsis

Y Jin, M Ivanov, AN Dittrich, ADL Nelson… - The EMBO …, 2023 - embopress.org
How the noncoding genome affects cellular functions is a key biological question. A
particular challenge is to distinguish the effects of noncoding DNA elements from long …

Cotranscriptional RNA processing and modification in plants

S Marquardt, E Petrillo, PA Manavella - The Plant Cell, 2023 - academic.oup.com
The activities of RNA polymerases shape the epigenetic landscape of genomes with
profound consequences for genome integrity and gene expression. A fundamental event …

Transcript elongation by RNA polymerase II in plants: factors, regulation and impact on gene expression

S Obermeyer, H Kapoor, H Markusch… - The Plant …, 2024 - Wiley Online Library
Transcriptional elongation by RNA polymerase II (RNAPII) through chromatin is a dynamic
and highly regulated step of eukaryotic gene expression. A combination of transcript …

Inositol hexakisphosphate is required for Integrator function

MH Lin, MK Jensen, ND Elrod, KL Huang… - Nature …, 2022 - nature.com
Integrator is a multi-subunit protein complex associated with RNA polymerase II (Pol II), with
critical roles in noncoding RNA 3′-end processing and transcription attenuation of a broad …