Current methods to identify sites of RNA interaction with the genome are limited to the study of a single RNA at a time. Here we describe a protocol for ChAR-seq, a strategy to identify all chromatin-associated RNAs and map their DNA contacts genome-wide. In ChAR-seq, proximity ligation ...
Chromatin-associated RNA sequencing (ChAR-seq) maps genome-wide RNA-to-DNA contacts. Jason C. Bell/.../Aaron F. Straight Systematic Mapping of RNA-Chromatin Interactions In Vivo Bharat Sridhar/.../Sheng Zhong Enhancers as non-coding RNA transcription units: recent insights and future perspectives...
Mammalian cells in different states of cytodifferentiation exhibited different RNA-synthesizing and processing patterns that could be used as markers for phenotypic variability. Inherent in these patterns was an RNA class which was differentially extracted from the cellular homogenate by elevating the temper...
RNAi pathways have evolved as important modulators of gene expression that act in the cytoplasm by degrading RNA target molecules via the activity of short (21-30nt) RNAs1-6 RNAi components have been reported to play a role in the nucleus as they are involved in epigenetic regulation and hete...
Using a combination of proximity ligation assay-based techniques and super-resolution microscopy, we found that the number of protein–DNA and RNA–DNA foci undergoes significant reduction during mitosis, suggesting that mitosis may be accompanied by structural re-arrangement or compaction of specific ...
The RNA chaperone protein, CIRP, plays a critical role in upregulating the inflammatory cascade when released from cells as eCIRP in acute inflammatory conditions, including sepsis. Elevated plasma levels of eCIRP have been independently correlated with worse prognosis in human sepsis [20,125]. Intrac...
elegans. Using an RNA interference (RNAi)-based approach, we identified UBXN-3 (ubiquitin regulatory X (UBX) domain-containing protein in nematodes 3) as a crucial factor that coordinates CDC-48-dependent DNA replication events. Embryos with reduced protein levels of both UBXN-3 and CDC-48 ...
To gain some insight into the mechanism of regulation of gene expression by estradiol in chick oviduct, the effect of steroid administration in vivo on the size distribution of nascent RNA transcripts synthesized in isolated 'chromatin' in vitro was analyzed. In 'chromatin' from withdrawn (control...
1. 1. Three endonucleases designated A 1, A 2 and B have been detected in and purified from chromatin of germinating barley. 2. 2. The enzymes are similar in a number of catalytic properties such as optimal activity at near-neutral pH, capacity for hydrolysis of both RNA and DNA, inabil...
Interrelated effects of DNA supercoiling, ppGpp, and low salt on melting within the Escherichia coli ribosomal RNA rrnB P1 promoter (1992). The chromatin- associated protein H-NS interacts with curved DNA to influence DNA topology and gene expression. Cell 71, 255-265.Ohlsen, K.L... Kari,...