Life Sciences Research for Lifelong Health

Claudia Ribeiro de Almeida

Our goal is to define the emerging role of RNA and RNA binding proteins (RBPs) in controlling B cell development and the diversification of antibody genes.

We are interested in decoding the molecular mechanisms underlying diversification of antibody genes, to gain insight into how B cells can effectively fight infections, how these responses change through our lives and the role this plays in age-related immune dysfunction.

Our research focuses on the role of RNA and RBPs as regulators of DNA deletion-recombination mechanisms occurring at antibody genes. Previous findings on the RNA helicase DDX1 have shown that RBPs can directly regulate RNA function and be part of antibody gene recombination mechanisms (Ribeiro de Almeida et al, 2018). Other RBPs have been shown to control different steps of mRNA metabolism, thereby causing gene expression changes that accompany B cell developmental-stage transitions when antibody genes diversification occurs. RBPs are important to regulate RNA fate and function, and our understanding of their roles in B cells is only emerging.

We use a number of cellular and molecular biology tools together with mouse genetics, cellular model systems and in vitro biochemical assays, to investigate the function of RBPs in B cells. We also employ state-of-the-art genomics and proteomics approaches to identify novel RBPs important for developmental stages when B cells undergo recombination mechanisms at their antibody genes.


Latest Publications

Biosynthesis of histone messenger RNA employs a specific 3' end endonuclease.
Pettinati I, Grzechnik P, Ribeiro de Almeida C, Brem J, McDonough MA, Dhir S, Proudfoot NJ, Schofield CJ

Replication-dependent (RD) core histone mRNA produced during S-phase is the only known metazoan protein-coding mRNA presenting a 3' stem-loop instead of the otherwise universal polyA tail. A metallo β-lactamase (MBL) fold enzyme, cleavage and polyadenylation specificity factor 73 (CPSF73), is proposed to be the sole endonuclease responsible for 3' end processing of both mRNA classes. We report cellular, genetic, biochemical, substrate selectivity, and crystallographic studies providing evidence that an additional endoribonuclease, MBL domain containing protein 1 (MBLAC1), is selective for 3' processing of RD histone pre-mRNA during the S-phase of the cell cycle. Depletion of MBLAC1 in cells significantly affects cell cycle progression thus identifying MBLAC1 as a new type of S-phase-specific cancer target.

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eLife, 7, 2050-084X, , 2018

PMID: 30507380

Deregulated Expression of Mammalian lncRNA through Loss of SPT6 Induces R-Loop Formation, Replication Stress, and Cellular Senescence.
Nojima T, Tellier M, Foxwell J, Ribeiro de Almeida C, Tan-Wong SM, Dhir S, Dujardin G, Dhir A, Murphy S, Proudfoot NJ

Extensive tracts of the mammalian genome that lack protein-coding function are still transcribed into long noncoding RNA. While these lncRNAs are generally short lived, length restricted, and non-polyadenylated, how their expression is distinguished from protein-coding genes remains enigmatic. Surprisingly, depletion of the ubiquitous Pol-II-associated transcription elongation factor SPT6 promotes a redistribution of H3K36me3 histone marks from active protein coding to lncRNA genes, which correlates with increased lncRNA transcription. SPT6 knockdown also impairs the recruitment of the Integrator complex to chromatin, which results in a transcriptional termination defect for lncRNA genes. This leads to the formation of extended, polyadenylated lncRNAs that are both chromatin restricted and form increased levels of RNA:DNA hybrid (R-loops) that are associated with DNA damage. Additionally, these deregulated lncRNAs overlap with DNA replication origins leading to localized DNA replication stress and a cellular senescence phenotype. Overall, our results underline the importance of restricting lncRNA expression.

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Molecular cell, 72, 1097-4164, 970-984.e7, 2018

PMID: 30449723

RNA Helicase DDX1 Converts RNA G-Quadruplex Structures into R-Loops to Promote IgH Class Switch Recombination.
Ribeiro de Almeida C, Dhir S, Dhir A, Moghaddam AE, Sattentau Q, Meinhart A, Proudfoot NJ

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 occur co-transcriptionally between nascent RNA and template DNA, we now show that they also form as part of a post-transcriptional mechanism targeting AID to IgH S-regions. This depends on the RNA helicase DDX1 that is also required for CSR in vivo. DDX1 binds to G-quadruplex (G4) structures present in intronic switch transcripts and converts them into S-region R-loops. This in turn targets the cytidine deaminase enzyme AID to S-regions so promoting CSR. Notably R-loop levels over S-regions are diminished by chemical stabilization of G4 RNA or by the expression of a DDX1 ATPase-deficient mutant that acts as a dominant-negative protein to reduce CSR efficiency. In effect, we provide evidence for how S-region transcripts interconvert between G4 and R-loop structures to promote CSR in the IgH locus.

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Molecular cell, 70, 1097-4164, 650-662.e8, 2018

PMID: 29731414

Group Members

Latest Publications

Biosynthesis of histone messenger RNA employs a specific 3' end endonuclease.

Pettinati I, Grzechnik P, Ribeiro de Almeida C

7 2050-084X: (2018)

PMID: 30507380

RNA Helicase DDX1 Converts RNA G-Quadruplex Structures into R-Loops to Promote IgH Class Switch Recombination.

Ribeiro de Almeida C, Dhir S, Dhir A

Molecular cell
70 1097-4164:650-662.e8 (2018)

PMID: 29731414

Dynamic Control of Long-Range Genomic Interactions at the Immunoglobulin κ Light-Chain Locus.

Ribeiro de Almeida C, Hendriks RW, Stadhouders R

Advances in immunology
128 1557-8445:183-271 (2015)

PMID: 26477368

The DNA-binding factor Ctcf critically controls gene expression in macrophages.

Nikolic T, Movita D, Lambers ME

Cellular & molecular immunology
11 2042-0226:58-70 (2014)

PMID: 24013844

Allelic exclusion of the immunoglobulin heavy chain locus is independent of its nuclear localization in mature B cells.

Holwerda SJ, van de Werken HJ, Ribeiro de Almeida C

Nucleic acids research
41 1362-4962:6905-16 (2013)

PMID: 23748562

DNA-binding factor CTCF and long-range gene interactions in V(D)J recombination and oncogene activation.

Ribeiro de Almeida C, Stadhouders R, Thongjuea S

119 1528-0020:6209-18 (2012)

PMID: 22538856

Gene expression profiling in mice with enforced Gata3 expression reveals putative targets of Gata3 in double positive thymocytes.

van Hamburg JP, de Bruijn MJ, Ribeiro de Almeida C

Molecular immunology
46 1872-9142:3251-60 (2009)

PMID: 19729201

Critical role for the transcription regulator CCCTC-binding factor in the control of Th2 cytokine expression.

Ribeiro de Almeida C, Heath H, Krpic S

Journal of immunology (Baltimore, Md. : 1950)
182 1550-6606:999-1010 (2009)

PMID: 19124743

CTCF regulates cell cycle progression of alphabeta T cells in the thymus.

Heath H, Ribeiro de Almeida C, Sleutels F

The EMBO journal
27 1460-2075:2839-50 (2008)

PMID: 18923423