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 …

mRNAs, proteins and the emerging principles of gene expression control

C Buccitelli, M Selbach - Nature Reviews Genetics, 2020 - nature.com
Gene expression involves transcription, translation and the turnover of mRNAs and proteins.
The degree to which protein abundances scale with mRNA levels and the implications in …

H3K4me3 regulates RNA polymerase II promoter-proximal pause-release

H Wang, Z Fan, PV Shliaha, M Miele, RC Hendrickson… - Nature, 2023 - nature.com
Trimethylation of histone H3 lysine 4 (H3K4me3) is associated with transcriptional start sites
and has been proposed to regulate transcription initiation,. However, redundant functions of …

RNA sequencing: the teenage years

R Stark, M Grzelak, J Hadfield - Nature Reviews Genetics, 2019 - nature.com
Over the past decade, RNA sequencing (RNA-seq) has become an indispensable tool for
transcriptome-wide analysis of differential gene expression and differential splicing of …

SARS-CoV-2 uses a multipronged strategy to impede host protein synthesis

Y Finkel, A Gluck, A Nachshon, R Winkler, T Fisher… - Nature, 2021 - nature.com
The coronavirus SARS-CoV-2 is the cause of the ongoing pandemic of COVID-19.
Coronaviruses have developed a variety of mechanisms to repress host mRNA translation to …

Acquired resistance to anti-MAPK targeted therapy confers an immune-evasive tumor microenvironment and cross-resistance to immunotherapy in melanoma

L Haas, A Elewaut, CL Gerard, C Umkehrer… - Nature cancer, 2021 - nature.com
How targeted therapies and immunotherapies shape tumors, and thereby influence
subsequent therapeutic responses, is poorly understood. In the present study, we show, in …

TDP-43 condensation properties specify its RNA-binding and regulatory repertoire

M Hallegger, AM Chakrabarti, FCY Lee, BL Lee… - Cell, 2021 - cell.com
Mutations causing amyotrophic lateral sclerosis (ALS) often affect the condensation
properties of RNA-binding proteins (RBPs). However, the role of RBP condensation in the …

Temporal modelling using single-cell transcriptomics

J Ding, N Sharon, Z Bar-Joseph - Nature Reviews Genetics, 2022 - nature.com
Methods for profiling genes at the single-cell level have revolutionized our ability to study
several biological processes and systems including development, differentiation, response …

Rapid and accurate alignment of nucleotide conversion sequencing reads with HISAT-3N

Y Zhang, C Park, C Bennett, M Thornton… - Genome …, 2021 - genome.cshlp.org
Sequencing technologies using nucleotide conversion techniques such as cytosine to
thymine in bisulfite-seq and thymine to cytosine in SLAM seq are powerful tools to explore …

Inhibition of METTL3 results in a cell-intrinsic interferon response that enhances antitumor immunity

AA Guirguis, Y Ofir-Rosenfeld, K Knezevic, W Blackaby… - Cancer Discovery, 2023 - AACR
Therapies that enhance antitumor immunity have altered the natural history of many
cancers. Consequently, leveraging nonoverlapping mechanisms to increase …