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 …

Causes and consequences of RNA polymerase II stalling during transcript elongation

M Noe Gonzalez, D Blears, JQ Svejstrup - Nature reviews Molecular …, 2021 - nature.com
The journey of RNA polymerase II (Pol II) as it transcribes a gene is anything but a smooth
ride. Transcript elongation is discontinuous and can be perturbed by intrinsic regulatory …

Transcription elongation can affect genome 3D structure

S Heinz, L Texari, MGB Hayes, M Urbanowski… - Cell, 2018 - cell.com
How transcription affects genome 3D organization is not well understood. We found that
during influenza A (IAV) infection, rampant transcription rapidly reorganizes host cell …

Knowing when to stop: Transcription termination on protein-coding genes by eukaryotic RNAPII

JB Rodríguez-Molina, S West, LA Passmore - Molecular cell, 2023 - cell.com
Gene expression is controlled in a dynamic and regulated manner to allow for the consistent
and steady expression of some proteins as well as the rapidly changing production of other …

3′-end processing of eukaryotic mRNA: machinery, regulation, and impact on gene expression

V Boreikaitė, LA Passmore - Annual review of biochemistry, 2023 - annualreviews.org
Formation of the 3′ end of a eukaryotic mRNA is a key step in the production of a mature
transcript. This process is mediated by a number of protein factors that cleave the pre …

Nascent RNA analyses: tracking transcription and its regulation

EM Wissink, A Vihervaara, ND Tippens… - Nature Reviews …, 2019 - nature.com
The programmes that direct an organism's development and maintenance are encoded in its
genome. Decoding of this information begins with regulated transcription of genomic DNA …

Integrator recruits protein phosphatase 2A to prevent pause release and facilitate transcription termination

KL Huang, D Jee, CB Stein, ND Elrod, T Henriques… - Molecular cell, 2020 - cell.com
Efficient release of promoter-proximally paused RNA Pol II into productive elongation is
essential for gene expression. Recently, we reported that the Integrator complex can bind …

The integrator complex attenuates promoter-proximal transcription at protein-coding genes

ND Elrod, T Henriques, KL Huang, DC Tatomer… - Molecular cell, 2019 - cell.com
The transition of RNA polymerase II (Pol II) from initiation to productive elongation is a
central, regulated step in metazoan gene expression. At many genes, Pol II pauses stably in …

Elevated pre-mRNA 3′ end processing activity in cancer cells renders vulnerability to inhibition of cleavage and polyadenylation

Y Cui, L Wang, Q Ding, J Shin, J Cassel, Q Liu… - Nature …, 2023 - nature.com
Cleavage and polyadenylation (CPA) is responsible for 3′ end processing of eukaryotic
poly (A)+ RNAs and preludes transcriptional termination. JTE-607, which targets CPSF-73 …

Control of RNA Pol II speed by PNUTS-PP1 and Spt5 dephosphorylation facilitates termination by a “sitting duck torpedo” mechanism

MA Cortazar, RM Sheridan, B Erickson, N Fong… - Molecular cell, 2019 - cell.com
Control of transcription speed, which influences many co-transcriptional processes, is poorly
understood. We report that PNUTS-PP1 phosphatase is a negative regulator of RNA …