Signaling via the NFκB system

S Mitchell, J Vargas, A Hoffmann - … Reviews: Systems Biology …, 2016 - Wiley Online Library
The nuclear factor kappa B (NFκB) family of transcription factors is a key regulator of immune
development, immune responses, inflammation, and cancer. The NFκB signaling system …

MYC: connecting selective transcriptional control to global RNA production

TR Kress, A Sabò, B Amati - Nature Reviews Cancer, 2015 - nature.com
Two opposing models have been proposed to describe the function of the MYC oncoprotein
in shaping cellular transcriptomes: one posits that MYC amplifies transcription at all active …

[HTML][HTML] Native elongating transcript sequencing reveals human transcriptional activity at nucleotide resolution

A Mayer, J Di Iulio, S Maleri, U Eser, J Vierstra… - Cell, 2015 - cell.com
Major features of transcription by human RNA polymerase II (Pol II) remain poorly defined
due to a lack of quantitative approaches for visualizing Pol II progress at nucleotide …

[HTML][HTML] Splicing of nascent RNA coincides with intron exit from RNA polymerase II

FC Oesterreich, L Herzel, K Straube, K Hujer, J Howard… - Cell, 2016 - cell.com
Protein-coding genes in eukaryotes are transcribed by RNA polymerase II (Pol II) and
introns are removed from pre-mRNA by the spliceosome. Understanding the time lag …

Nascent RNA and the coordination of splicing with transcription

KM Neugebauer - Cold Spring Harbor Perspectives in …, 2019 - cshperspectives.cshlp.org
At each active protein-encoding gene, nascent RNA is tethered to the DNA axis by
elongating RNA polymerase II (Pol II) and is continuously altered by splicing and other …

Perfect timing: splicing and transcription rates in living cells

T Alpert, L Herzel… - Wiley Interdisciplinary …, 2017 - Wiley Online Library
An important step toward understanding gene regulation is the elucidation of the time
necessary for the completion of individual steps. Measurement of reaction rates can reveal …

[HTML][HTML] Global donor and acceptor splicing site kinetics in human cells

L Wachutka, L Caizzi, J Gagneur, P Cramer - Elife, 2019 - elifesciences.org
RNA splicing is an essential part of eukaryotic gene expression. Although the mechanism of
splicing has been extensively studied in vitro, in vivo kinetics for the two-step splicing …

The determinants of alternative RNA splicing in human cells

TV Ramanouskaya, VV Grinev - Molecular Genetics and Genomics, 2017 - Springer
Alternative splicing represents an important level of the regulation of gene function in
eukaryotic organisms. It plays a critical role in virtually every biological process within an …

[HTML][HTML] Position-dependent effects of RNA-binding proteins in the context of co-transcriptional splicing

T Horn, A Gosliga, C Li, M Enculescu… - npj Systems Biology and …, 2023 - nature.com
Alternative splicing is an important step in eukaryotic mRNA pre-processing which increases
the complexity of gene expression programs, but is frequently altered in disease. Previous …

[HTML][HTML] Exon definition facilitates reliable control of alternative splicing in the RON proto-oncogene

M Enculescu, S Braun, ST Setty, A Busch, K Zarnack… - Biophysical …, 2020 - cell.com
Alternative splicing is a key step in eukaryotic gene expression that allows for the production
of multiple transcript and protein isoforms from the same gene. Even though splicing is …