R loops: new modulators of genome dynamics and function

JM Santos-Pereira, A Aguilera - Nature Reviews Genetics, 2015 - nature.com
R loops are nucleic acid structures composed of an RNA–DNA hybrid and a displaced
single-stranded DNA. Recently, evidence has emerged that R loops occur more often in the …

The regulation and functions of the nuclear RNA exosome complex

C Kilchert, S Wittmann, L Vasiljeva - Nature reviews Molecular cell …, 2016 - nature.com
The RNA exosome complex is the most versatile RNA-degradation machine in eukaryotes.
The exosome has a central role in several aspects of RNA biogenesis, including RNA …

Noncoding mutations cause super-enhancer retargeting resulting in protein synthesis dysregulation during B cell lymphoma progression

RJ Leeman-Neill, D Song, J Bizarro, L Wacheul… - Nature …, 2023 - nature.com
Whole-genome sequencing of longitudinal tumor pairs representing transformation of
follicular lymphoma to high-grade B cell lymphoma with MYC and BCL2 rearrangements …

Regulation of long non-coding RNAs and genome dynamics by the RNA surveillance machinery

L Nair, H Chung, U Basu - Nature reviews Molecular cell biology, 2020 - nature.com
Much of the mammalian genome is transcribed, generating long non-coding RNAs
(lncRNAs) that can undergo post-transcriptional surveillance whereby only a subset of the …

Molecular mechanisms of somatic hypermutation and class switch recombination

SP Methot, JM Di Noia - Advances in immunology, 2017 - Elsevier
In order to promote an efficient humoral immune response, germinal center B cells modify
both the antigen recognition and effector domains by programmed genetic alterations of …

AID in antibody diversification: there and back again

Y Feng, N Seija, JM Di Noia, A Martin - Trends in immunology, 2020 - cell.com
Activation-Induced cytidine Deaminase (AID) initiates affinity maturation and isotype
switching by deaminating deoxycytidines within immunoglobulin genes, leading to somatic …

RNA exosome-regulated long non-coding RNA transcription controls super-enhancer activity

E Pefanis, J Wang, G Rothschild, J Lim, D Kazadi… - Cell, 2015 - cell.com
We have ablated the cellular RNA degradation machinery in differentiated B cells and
pluripotent embryonic stem cells (ESCs) by conditional mutagenesis of core (Exosc3) and …

Targeting RNA for processing or destruction by the eukaryotic RNA exosome and its cofactors

JC Zinder, CD Lima - Genes & development, 2017 - genesdev.cshlp.org
The eukaryotic RNA exosome is an essential and conserved protein complex that can
degrade or process RNA substrates in the 3′-to-5′ direction. Since its discovery nearly …

APOBEC-induced mutagenesis in cancer

TM Mertz, CD Collins, M Dennis… - Annual Review of …, 2022 - annualreviews.org
The initiation, progression, and relapse of cancers often result from mutations occurring
within somatic cells. Consequently, processes that elevate mutation rates accelerate …

RNA helicase DDX1 converts RNA G-quadruplex structures into R-loops to promote IgH class switch recombination

CR de Almeida, S Dhir, A Dhir, AE Moghaddam… - Molecular cell, 2018 - cell.com
Class switch recombination (CSR) at the immunoglobulin heavy-chain (IgH) locus is
associated with the formation of R-loop structures over switch (S) regions. While these often …