David P. Bartel
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View article: mRNA 3′ UTRs direct microRNA degradation to participate in imprinted gene networks and regulate growth
mRNA 3′ UTRs direct microRNA degradation to participate in imprinted gene networks and regulate growth Open
MicroRNAs direct downregulation of target mRNAs. Sometimes, however, this regulatory paradigm inverts, and a target RNA triggers the degradation of a microRNA. This target-directed microRNA degradation (TDMD) requires ZSWIM8. Zswim8 −/− mi…
View article: Functional microRNA targeting without seed pairing
Functional microRNA targeting without seed pairing Open
MicroRNAs (miRNAs) associate with Argonaute (AGO) proteins to serve as guides, directing binding to partially complementary sites in mRNAs, ultimately causing post-transcriptional repression. Complementarity to the miRNA seed (miRNA nucleo…
View article: mRNA poly(A)-tail length is a battleground for coronavirus–host competition
mRNA poly(A)-tail length is a battleground for coronavirus–host competition Open
Most eukaryotic mRNAs contain a poly(A) tail, which in post-embryonic cells enhances their stability. Many cytoplasmic RNA viruses also harbor poly(A) tails on their genomic RNA and mRNAs. Here, we report that coronavirus infection causes …
View article: Lysosomal RNA profiling reveals targeting of specific types of RNAs for degradation
Lysosomal RNA profiling reveals targeting of specific types of RNAs for degradation Open
Autophagy targets a wide variety of substrates for degradation within lysosomes 1 . While lysosomes are known to possess RNase activity 2 , the role of lysosomal RNA degradation in post-transcriptional gene regulation is not well understoo…
View article: PAL-AI reveals genetic determinants that control poly(A)-tail length during oocyte maturation, with relevance to human fertility
PAL-AI reveals genetic determinants that control poly(A)-tail length during oocyte maturation, with relevance to human fertility Open
View article: Global inhibition of deadenylation stabilizes the transcriptome in mitotic cells
Global inhibition of deadenylation stabilizes the transcriptome in mitotic cells Open
In the presence of cell division errors, mammalian cells can pause in mitosis for tens of hours with little to no transcription, while still requiring continued translation for viability. These unique aspects of mitosis require substantial…
View article: 5′ untranslated regions tune <i>Toxoplasma</i> translation
5′ untranslated regions tune <i>Toxoplasma</i> translation Open
Some of the longest 5′ untranslated regions (UTRs) documented in eukaryotes belong to parasites of the phylum Apicomplexa. Translational regulation plays prominent roles in the development of these parasites, including the agents of toxopl…
View article: Derepression of a single microRNA target causes female infertility in mice
Derepression of a single microRNA target causes female infertility in mice Open
The miR-200a and miR-200b families control mouse ovulation and are essential for female fertility. The ZEB1 transcription factor is a conserved target of both families and has been implicated as a key player in female fertility at multiple…
View article: Functional microRNA targeting without seed pairing
Functional microRNA targeting without seed pairing Open
MicroRNAs (miRNAs) associate with Argonaute (AGO) proteins to serve as guides, directing binding to partially complementary sites in mRNAs, ultimately causing post-transcriptional repression. Complementarity to the miRNA seed region (miRNA…
View article: The structural basis for RNA slicing by human Argonaute2
The structural basis for RNA slicing by human Argonaute2 Open
View article: PAL-AI reveals genetic determinants that control poly(A)-tail length during oocyte maturation, with relevance to human fertility
PAL-AI reveals genetic determinants that control poly(A)-tail length during oocyte maturation, with relevance to human fertility Open
In oocytes of mammals and other animals, gene regulation is mediated primarily through changes in poly(A)-tail length 1–9 . Here, we introduce PAL-AI, an integrated neural network machine-learning model that accurately predicts tail-length…
View article: Nuclear release of eIF1 restricts start-codon selection during mitosis
Nuclear release of eIF1 restricts start-codon selection during mitosis Open
View article: Widespread destabilization of <i>Caenorhabditis elegans</i> microRNAs by the E3 ubiquitin ligase EBAX-1
Widespread destabilization of <i>Caenorhabditis elegans</i> microRNAs by the E3 ubiquitin ligase EBAX-1 Open
MicroRNAs (miRNAs) associate with Argonaute (AGO) proteins to form complexes that direct mRNA repression. miRNAs are also the subject of regulation. For example, some miRNAs are destabilized through a pathway in which pairing to specialize…
View article: The G3BP stress-granule proteins reinforce the integrated-stress-response translation program
The G3BP stress-granule proteins reinforce the integrated-stress-response translation program Open
When mammalian cells are exposed to stress, they coordinate the condensation of stress granules (SGs) through the action of proteins G3BP1 and G3BP2 (G3BPs) and, simultaneously, undergo a massive reduction in translation. Although SGs and …
View article: The structural basis for RNA slicing by human Argonaute2
The structural basis for RNA slicing by human Argonaute2 Open
SUMMARY Argonaute (AGO) proteins associate with guide RNAs to form complexes that slice transcripts that pair to the guide. This slicing drives post-transcriptional gene-silencing pathways that are essential for many eukaryotes and the bas…
View article: The guide-RNA sequence dictates the slicing kinetics and conformational dynamics of the Argonaute silencing complex
The guide-RNA sequence dictates the slicing kinetics and conformational dynamics of the Argonaute silencing complex Open
View article: Widespread destabilization of<i>C. elegans</i>microRNAs by the E3 ubiquitin ligase EBAX-1
Widespread destabilization of<i>C. elegans</i>microRNAs by the E3 ubiquitin ligase EBAX-1 Open
MicroRNAs (miRNAs) associate with Argonaute (AGO) proteins to form complexes that direct mRNA repression. miRNAs are also the subject of regulation. For example, some miRNAs are destabilized through a pathway in which pairing to specialize…
View article: Nuclear release of eIF1 globally increases stringency of start-codon selection to preserve mitotic arrest physiology
Nuclear release of eIF1 globally increases stringency of start-codon selection to preserve mitotic arrest physiology Open
Regulated start-codon selection has the potential to reshape the proteome through the differential production of uORFs, canonical proteins, and alternative translational isoforms. However, conditions under which start-codon selection is al…
View article: Control of poly(A)-tail length and translation in vertebrate oocytes and early embryos
Control of poly(A)-tail length and translation in vertebrate oocytes and early embryos Open
During oocyte maturation and early embryogenesis, changes in mRNA poly(A)-tail lengths strongly influence translation, but how these tail-length changes are orchestrated has been unclear. Here, we performed tail-length and translational pr…
View article: Control of poly(A)-tail length and translation in vertebrate oocytes and early embryos
Control of poly(A)-tail length and translation in vertebrate oocytes and early embryos Open
SUMMARY During oocyte maturation and early embryogenesis, changes in mRNA poly(A)-tail lengths strongly influence translation, but how these tail-length changes are orchestrated has been unclear. Here, we performed tail-length and translat…
View article: The guide RNA sequence dictates the slicing kinetics and conformational dynamics of the Argonaute silencing complex
The guide RNA sequence dictates the slicing kinetics and conformational dynamics of the Argonaute silencing complex Open
SUMMARY The RNA-induced silencing complex (RISC), which powers RNA interference (RNAi), consists of a guide RNA and an Argonaute protein that slices target RNAs complementary to the guide. We find that for different guide-RNA sequences, sl…
View article: ZSWIM8 destabilizes many murine microRNAs and is required for proper embryonic growth and development
ZSWIM8 destabilizes many murine microRNAs and is required for proper embryonic growth and development Open
MicroRNAs (miRNAs) pair to sites in mRNAs to direct the degradation of these RNA transcripts. Conversely, certain RNA transcripts can direct the degradation of particular miRNAs. This target-directed miRNA degradation (TDMD) requires the Z…
View article: The widespread influence of ZSWIM8 on microRNAs during mouse embryonic development
The widespread influence of ZSWIM8 on microRNAs during mouse embryonic development Open
MicroRNAs (miRNAs) pair to sites in mRNAs to direct the degradation of these RNA transcripts. Conversely, certain RNA transcripts can direct the degradation of particular miRNAs. This target-directed miRNA degradation (TDMD) requires the Z…
View article: A statistical approach for identifying primary substrates of ZSWIM8-mediated microRNA degradation in small-RNA sequencing data
A statistical approach for identifying primary substrates of ZSWIM8-mediated microRNA degradation in small-RNA sequencing data Open
Background One strategy for identifying targets of a regulatory factor is to perturb the factor and use high-throughput RNA sequencing to examine the consequences. However, distinguishing direct targets from secondary effects and experimen…
View article: Endogenous transcripts direct microRNA degradation in Drosophila, and this targeted degradation is required for proper embryonic development
Endogenous transcripts direct microRNA degradation in Drosophila, and this targeted degradation is required for proper embryonic development Open
MicroRNAs (miRNAs) typically direct degradation of their mRNA targets. However, some targets have unusual miRNA-binding sites that direct degradation of cognate miRNAs. Although this target-directed miRNA degradation (TDMD) is thought to s…
View article: The Parkinson’s disease protein alpha-synuclein is a modulator of processing bodies and mRNA stability
The Parkinson’s disease protein alpha-synuclein is a modulator of processing bodies and mRNA stability Open
View article: The interplay between translational efficiency, poly(A) tails, microRNAs, and neuronal activation
The interplay between translational efficiency, poly(A) tails, microRNAs, and neuronal activation Open
Neurons provide a rich setting for studying post-transcriptional control. Here, we investigate the landscape of translational control in neurons and search for mRNA features that explain differences in translational efficiency (TE), consid…
View article: MicroRNA 3′-compensatory pairing occurs through two binding modes, with affinity shaped by nucleotide identity and position
MicroRNA 3′-compensatory pairing occurs through two binding modes, with affinity shaped by nucleotide identity and position Open
MicroRNAs (miRNAs), in association with Argonaute (AGO) proteins, direct repression by pairing to sites within mRNAs. Compared to pairing preferences of the miRNA seed region (nucleotides 2–8), preferences of the miRNA 3′ region are poorly…
View article: Author response: MicroRNA 3′-compensatory pairing occurs through two binding modes, with affinity shaped by nucleotide identity and position
Author response: MicroRNA 3′-compensatory pairing occurs through two binding modes, with affinity shaped by nucleotide identity and position Open
Article Figures and data Abstract Editor's evaluation Introduction Results Discussion Materials and methods Data availability References Decision letter Author response Article and author information Metrics Abstract MicroRNAs (miRNAs), in…
View article: A statistical approach for identifying primary substrates of ZSWIM8-mediated microRNA degradation in small-RNA sequencing data
A statistical approach for identifying primary substrates of ZSWIM8-mediated microRNA degradation in small-RNA sequencing data Open
Background One strategy for identifying targets of a regulatory factor is to perturb the factor and use high-throughput RNA sequencing to examine the consequences. However, distinguishing direct targets from secondary effects and experimen…