David P. Bartel

The molecular determinants of PABPC-mediated deadenylation rate

This study investigates how PABPC1 binding and 3' UTR sequences influence deadenylation rates, revealing two mechanisms by which UTR sequences modulate deadenylation kinetics.

Dissection of Poly(A)-binding protein (PABPC) cellular function using degron-mediated depletion with replacement

This paper develops a protein-replacement platform to study PABPC function by degrading endogenous PABPC1/4 and expressing engineered variants, revealing domain-specific roles and functional divergence.

The spliceosome assembles on excised linear introns to protect them from degradation

The paper shows that spliceosomes protect linear introns from degradation by assembling on them, and this process is conserved across stress and unstress conditions.

The E3 ubiquitin ligase mechanism specifying target-directed microRNA degradation

This paper identifies how a human AGO-miRNA-trigger complex binds ZSWIM8 for CUL3-mediated polyubiquitylation, leading to target-directed miRNA degradation.

Derepression of a single microRNA target causes female infertility in mice

This study shows that derepression of Zeb1, a target of miR-200a/b, causes infertility in mice by disrupting pituitary hormone production and gene expression.

mRNA 3' UTRs direct microRNA degradation to participate in imprinted gene networks and regulate growth

The paper identifies and validates new TDMD-triggering sites in mouse models, showing their role in microRNA degradation and growth regulation through imprinted gene networks.

Functional microRNA targeting without seed pairing

The paper shows that microRNA targeting can occur without seed pairing, as 3'-only sites bind and repress mRNAs similarly to canonical sites, though with different kinetics and conformational effects.

mRNA poly(A)-tail length is a battleground for coronavirus-host competition

This study shows coronavirus infection limits PABPC1 activity, destabilizing short-tailed host mRNAs and enabling viral mRNAs to maintain specific poly(A)-tail lengths through synthesis and capping mechanisms.

Lysosomal RNA profiling reveals targeting of specific types of RNAs for degradation

This study identifies lysosomal RNases and shows specific RNA types are targeted for degradation via autophagy-dependent mechanisms.

PAL-AI reveals genetic determinants that control poly(A)-tail length during oocyte maturation, with relevance to human fertility

PAL-AI predicts poly(A)-tail length changes in oocytes, identifies genetic variants under negative selection linked to human fertility.

Global inhibition of deadenylation stabilizes the transcriptome in mitotic cells

The paper shows that during prolonged mitotic arrest, the transcriptome is stabilized through increased mRNA half-lives and reduced deadenylation, dependent on PABPC1 and PABPC4.

5' untranslated regions tune Toxoplasma translation

This study identifies how 5' UTR features and upstream AUGs regulate translation efficiency in Toxoplasma gondii using ribosome profiling and synthetic reporter assays.

The structural basis for RNA slicing by human Argonaute2

This paper presents the cryo-EM structure of a human AGO-guide complex bound to a fully paired target, revealing structural rearrangements that enable slicing-competent conformation and explain RNA slicing mechanism.

Nuclear release of eIF1 globally increases stringency of start-codon selection to preserve mitotic arrest physiology

The paper shows that eIF1 release during mitosis increases start-codon selection stringency, altering translation and affecting mitotic cell survival.

Widespread destabilization of C. elegans microRNAs by the E3 ubiquitin ligase EBAX-1

The paper identifies 22 C. elegans miRNAs destabilized by EBAX-1 loss, showing TDMD is a major miRNA-destabilization pathway with variable 3' sequence dependence.

The G3BP stress-granule proteins reinforce the integrated-stress-response translation program

This study shows that G3BP proteins and stress granules prioritize translation of stress-resistant mRNAs and suppress cytosolic translation during stress.

Control of poly(A)-tail length and translation in vertebrate oocytes and early embryos

The paper identifies regulatory elements that control mRNA poly(A)-tail length and translation in vertebrate oocytes and embryos, showing conservation across species.

The widespread influence of ZSWIM8 on microRNAs during mouse embryonic development

The paper investigates the role of ZSWIM8 in miRNA degradation during mouse embryonic development, finding that its loss leads to developmental defects and altered miRNA accumulation.

A statistical approach for identifying primary substrates of ZSWIM8-mediated microRNA degradation in small-RNA sequencing data

The paper introduces a statistical model to identify primary substrates of ZSWIM8-mediated microRNA degradation using small-RNA sequencing data, showing improved robustness and consistency compared to previous methods.

The molecular basis of coupling between poly(A)-tail length and translational efficiency

The paper investigates how poly(A)-tail length influences translational efficiency in oocytes and embryos, showing that PABPC availability and mRNA stability mechanisms determine this coupling.

Xrn1p Acts at Multiple Steps in the Budding-Yeast RNAi Pathway to Enhance the Efficiency of Silencing

The paper identifies Xrn1p as a cofactor in the budding-yeast RNAi pathway, showing it enhances silencing through multiple functions.

The Dynamics of Cytoplasmic mRNA Metabolism

The paper examines mRNA metabolism dynamics in mouse fibroblasts, finding that deadenylation rates determine cytoplasmic mRNA stability and degradation.

MicroRNAs Cause Accelerated Decay of Short-Tailed Target mRNAs

The paper shows miRNAs accelerate decay of short-tailed target mRNAs, preventing their accumulation despite promoting deadenylation.

Global analyses of the dynamics of mammalian microRNA metabolism

The paper measures production and degradation rates of miRNAs in different mouse cell types, revealing rapid duplex production, fast Argonaute loading, and cell-type-dependent half-lives.

Early genome activation in Drosophila is extensive with an initial tendency for aborted transcripts and retained introns

The paper identifies early transcripts during Drosophila zygotic genome activation, showing they are short, frequently aborted, and have retained introns.

Excised linear introns regulate growth in yeast

The paper identifies excised introns in yeast that accumulate under stress and affect growth, showing they have functional roles in the TOR signaling network.

Predicting microRNA targeting efficacy in Drosophila

The paper develops a quantitative model to predict microRNA targeting efficacy in Drosophila, outperforming existing models and updating TargetScanFly.

A Network of Noncoding Regulatory RNAs Acts in the Mammalian Brain

The lncRNA Cyrano drives multiple-turnover degradation of miR-7 in mouse brain, which protects the circRNA Cdr1as from miR-7-dependent, partly miR-671-sliced destruction.

kpLogo: positional k-mer analysis reveals hidden specificity in biological sequences

kpLogo detects and visualizes position-specific ultra-short motifs in biological sequences by addressing limitations of existing tools.