In human genomes, approximately 74.7% of genomes can be transcribed to form primary RNAs while 62.1% of genomes generating RNAs will be processed [1]. In those RNAs, some have the ability to interact with chromatin directly or indirectly, called chromatin-associated RNAs (caRNAs). Many noncodin...
Emerging roles have been uncovered for these chromatin-associated RNAs (caRNAs) in gene regulation and genome organization, yet they remain challenging to interrogate. Here, we present TaDRIM-seq, a technique employing Protein G (PG)-Tn5-targeted DNA elements and in situ proximity ligation to ...
Figure 6. SAF-A Oligomerization Regulates Interphase Chromosome Structure via Chromatin-Associated RNAs (A) Top: Model for chromatin decompaction by SAF-A oligomerization. Bottom: Experimental strategy to test model. Flp-In T-REx 293 cells depleted of endogenous SAF-A (48 hr) and then doxycycline...
by name, CAMPs refer to chromatin made up of nucleosomes containing DNA and histones. However, several nucleic acids and proteins, i.e., mitochondrial DNA, cell-free (cf) RNAs, microRNAs, telomeric repeat-containing
PRO-seq analyses demonstrate that nascent RNAs originating from both promoters and enhancers are significantly decreased in the METTL3-depleted cells. Furthermore, genes targeted by the Integrator complex for premature termination are depleted of METTL3, suggesting a potential antagonistic relationship ...
Genome instability is a feature of cancer cells, transcription being an important source of DNA damage. This is in large part associated with R-loops, which hamper replication, especially at head-on transcription-replication conflicts (TRCs). Here we sho
Many RNAs associate with chromatin, either directly or indirectly. Several technologies for mapping regions where RNAs interact across the genome have been developed to investigate the function of these RNAs. Obtaining information on the proteins involved in these RNA–chromatin interactions is critical ...
associated regulatory RNAs (carRNAs). The m 6 A levels of these carRNAs were markedly decreased in Mettl3 KO mESCs (Fig. 2B). Approximately 15 to 30% of all carRNAs con- tain m 6 A in mESCs, ~60% of which are reg- ulated by METTL3 (fig. S3A). These m 6 Apeaks contain GA...
small RNAsgene expressionepigeneticsRNA-dependent RNA polymerase2 (RDR2)Though the mechanisms governing nuclear organizatiThelma F MadzimaJi HuangKaren M McGinnisEpigenetics: official journal of the DNA Methylation SocietyMadzima TF, Huang J, McGinnis KM. Chromatin structure and gene expression changes ...
Sequence signals and multispecies conservation have enabled precise annotation of protein coding genes and the identification of increasing numbers of noncoding RNAs, regulatory elements, and motifs. Systematic genotyping studies have identified common variants associated with complex diseases and recurrent ...