EU-RNA-seq for in vivo labeling and high throughput sequencing of nascent transcripts.
AuthorsPalozola KC,Donahue G,Zaret KS
JournalSTAR protocols
PubMed ID34485932
The protocol allows for labeling nascent RNA without isolating nuclei. The cell-permeable uridine analog, 5-ethynyluridine (EU), is added to media to allow in vivo labeling of nascent transcripts. Cells are lysed, total RNA is collected, and biotin is conjugated to EU-labeled RNAs. Custom biotin RNAs are added and biotinylated RNAs ... More
METTL14 is a chromatin regulator independent of its RNA N6-methyladenosine methyltransferase activity.
METTL3 and METTL14 are two components that form the core heterodimer of the main RNA m6A methyltransferase complex (MTC) that installs m6A. Surprisingly, depletion of METTL3 or METTL14 displayed distinct effects on stemness maintenance of mouse embryonic stem cell (mESC). While comparable global hypo-methylation in RNA m6A was observed in ... More
Exploring RNA transcription and turnover in vivo by using click chemistry.
AuthorsJao CY, Salic A,
JournalProc Natl Acad Sci U S A
PubMed ID18840688
We describe a chemical method to detect RNA synthesis in cells, based on the biosynthetic incorporation of the uridine analog 5-ethynyluridine (EU) into newly transcribed RNA, on average once every 35 uridine residues in total RNA. EU-labeled cellular RNA is detected quickly and with high sensitivity by using a copper ... More
Camptothecin (CPT), a topoisomerase (Top) I-targeting drug that stabilizes Top1-DNA covalent adducts, can induce S-phase-specific cytotoxicity due to the arrest of progressing replication forks. However, CPT-induced non-S-phase cytotoxicity is less well characterized. In this study, we have identified topoisomerase IIß (Top2ß) as a specific determinant for CPT sensitivity, but not ... More
Click chemistry and bioorthogonal reactions: unprecedented selectivity in the labeling of biological molecules.
AuthorsBest MD,
JournalBiochemistry
PubMed ID19485420
In recent years, a number of bioorthogonal reactions have been developed, exemplified by click chemistry, that enable the efficient formation of a specific product, even within a highly complex chemical environment. While the exquisite selectivity and reliability of these transformations have led to their broad application in diverse research areas, ... More
N6-Deoxyadenosine Methylation in Mammalian Mitochondrial DNA.
Authors
JournalMol Cell
PubMed ID32183942
Dynamics and Spatial Genomics of the Nascent Transcriptome by Intron seqFISH.
Authors
JournalCell
PubMed ID29887381
A distinct role for recombination repair factors in an early cellular response to transcription-replication conflicts.
Authors
JournalNucleic Acids Res
PubMed ID32329774
Transcription-mediated organization of the replication initiation program across large genes sets common fragile sites genome-wide.
Authors
JournalNat Commun
PubMed ID31836700
Neuronal ribosomes exhibit dynamic and context-dependent exchange of ribosomal proteins.
Authors
JournalNat Commun
PubMed ID34675203
Mitochondrial Potentiation Ameliorates Age-Related Heterogeneity in Hematopoietic Stem Cell Function.
Authors
JournalCell Stem Cell
PubMed ID33086034
Impaired function of rDNA transcription initiation machinery leads to derepression of ribosomal genes with insertions of R2 retrotransposon.
Authors
JournalNucleic Acids Res
PubMed ID35037046
Canonical WNT signaling-dependent gating of MYC requires a noncanonical CTCF function at a distal binding site.
Authors
JournalNat Commun
PubMed ID35017527
Ribosome biogenesis during cell cycle arrest fuels EMT in development and disease.