reCRAC: A Stringent Method for Precise Mapping of Protein-RNA Interactions in Yeast. [PDF]
Methods Mol BiolRistová M, Shchepachev V, Tollervey D.
europepmc +2 more sources
Directed evolution of enzymes at the crossroads of tradition and innovation
FEBS Open Bio, EarlyView.An iterative cycle of data‐driven enzyme optimization comprising four stages: genetic diversification of a template enzyme, expression of protein variants, high‐throughput evaluation, and machine‐learning‐guided redesign of the next variant library.
Maria Tomkova +2 more
wiley +1 more source
ProRB: a structure-free unified framework for joint prediction and design of protein-RNA interactions. [PDF]
Nucleic Acids ResXue Y +5 more
europepmc +1 more source
Small RNA pathways in mammalian oocytes
FEBS Open Bio, EarlyView.Three distinct small RNA pathways operate in mammalian oocytes: RNAi interference (RNAi), the microRNA (miRNA) pathway, and the PIWI‐associated RNA (piRNA) pathway. These pathways use small RNAs to guide sequence‐specific repression and contribute to oocyte biology by targeting genes and mobile elements or appear insignificant since different ...
Petr Svoboda, Josef Pasulka
wiley +1 more source
Isotope-free mapping of protein-RNA interactions at single-nucleotide resolution by iCLIP3. [PDF]
STAR ProtocDespic V +7 more
europepmc +1 more source
Transcripts enriched in codons that trigger P‐site tRNA‐mediated mRNA decay possess stable mRNA
FEBS Open Bio, EarlyView.PTMD codons were first described by Mendel et al. as mediators of an mRNA decay pathway dependent on the human protein CNOT3, homologous to yeast Not5. Our findings confirm that PTMD codons destabilize transcripts; however, unlike in yeast, the human pathway specifically targets and slightly destabilizes primarily stable mRNAs.
Rodolfo Lopes Carneiro +1 more
wiley +1 more source
Protein-RNA interactions in centromeric chromatin
Chromosome segregation is a complex and tightly regulated process that is necessary for proper cell division. Chromosomes are aligned at the equatorial plate and transported to nascent daughter cells using motor proteins and microtubules. They are attached to the microtubules by a multiprotein complex, the kinetochore.
openaire +1 more source
Systems-level analysis predicts no autotrophy-linked protein-RNA interactions in Clostridium autoethanogenum. [PDF]
Nat CommunRe A +6 more
europepmc +1 more source
Loss of AMBRA1 activates MAPK and angiogenesis signaling pathways in melanoma cells
FEBS Open Bio, EarlyView.Loss of AMBRA1 in melanoma cells activates multiple oncogenic pathways associated with tumor progression. Transcriptomic and protein network analyses revealed that AMBRA1 depletion enhances MAPK/ERK signaling, angiogenesis, TGF‐β/EMT signaling, and Wnt/axon guidance pathways.
Milad Ibrahim +4 more
wiley +1 more source
scRAPID-web: a web server for predicting protein-RNA interactions from single-cell transcriptomics. [PDF]
BMC GenomicsFiorentino J +4 more
europepmc +1 more source