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 …

RNA polymerase II speed: a key player in controlling and adapting transcriptome composition

L Muniz, E Nicolas, D Trouche - The EMBO journal, 2021 - embopress.org
Abstract RNA polymerase II (RNA Pol II) speed or elongation rate, ie, the number of
nucleotides synthesized per unit of time, is a major determinant of transcriptome …

The code and beyond: transcription regulation by the RNA polymerase II carboxy-terminal domain

KM Harlen, LS Churchman - Nature reviews Molecular cell biology, 2017 - nature.com
The carboxy-terminal domain (CTD) extends from the largest subunit of RNA polymerase II
(Pol II) as a long, repetitive and largely unstructured polypeptide chain. Throughout the …

Splicing and transcription touch base: co-transcriptional spliceosome assembly and function

L Herzel, DSM Ottoz, T Alpert… - Nature reviews Molecular …, 2017 - nature.com
Several macromolecular machines collaborate to produce eukaryotic messenger RNA. RNA
polymerase II (Pol II) translocates along genes that are up to millions of base pairs in length …

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 …

Lysine/RNA-interactions drive and regulate biomolecular condensation

T Ukmar-Godec, S Hutten, MP Grieshop… - Nature …, 2019 - nature.com
Cells form and use biomolecular condensates to execute biochemical reactions. The
molecular properties of non-membrane-bound condensates are directly connected to the …

Transcription shapes genome-wide histone acetylation patterns

BJE Martin, J Brind'Amour, A Kuzmin… - Nature …, 2021 - nature.com
Histone acetylation is a ubiquitous hallmark of transcription, but whether the link between
histone acetylation and transcription is causal or consequential has not been addressed …

CDK12 loss in cancer cells affects DNA damage response genes through premature cleavage and polyadenylation

M Krajewska, R Dries, AV Grassetti, S Dust… - Nature …, 2019 - nature.com
Abstract Cyclin-dependent kinase 12 (CDK12) modulates transcription elongation by
phosphorylating the carboxy-terminal domain of RNA polymerase II and selectively affects …

Structure of a transcribing RNA polymerase II–U1 snRNP complex

S Zhang, S Aibara, SM Vos, DE Agafonov, R Lührmann… - Science, 2021 - science.org
To initiate cotranscriptional splicing, RNA polymerase II (Pol II) recruits the U1 small nuclear
ribonucleoprotein particle (U1 snRNP) to nascent precursor messenger RNA (pre-mRNA) …

The pol II CTD: new twists in the tail

J Zaborowska, S Egloff, S Murphy - Nature structural & molecular …, 2016 - nature.com
The C-terminal domain (CTD) of the large subunit of RNA polymerase (pol) II comprises
conserved heptad repeats, and post-translational modification of the CTD regulates …