High-order chromatin structure and the epigenome in cellular senescenceChandra, TamirNarita, Masashi
High-order three-dimensional (3D) interactions between more than two genomic loci are common in human chromatin, but their role in gene regulation is unclear. Previous high-order 3D chromatin assays either measure distant interactions across the genome or proximal interactions at selected targets. To...
While the general scaffold of chromatin organization is well described, revealing the mechanisms underlying cell-type-specific chromatin structure and the implications to gene expression remains challenging10,11,12,13,14. Chromatin conformation capture technologies, such as Hi-C, are typically time- and...
This may be of particular importance during times of chromatin remodeling in cells undergoing DNA replication and mitosis. HMG1/2 and possibly histone H1 might not only facilitate but maintain such higher order chromatin structures (13, 20, 21, 37, 40, 41). Such promotion activity of HMG1/...
chromatin, as it controls BRD4-L biding to acetylated histones [37,38]. Therefore, the combination of both interactions, BRD4-L-chromatin and BRD4-L-BRD4-L, appears to be essential for the higher-order chromatin organization (Fig.4). Likewise, a synthetic protein [37] representing BRD4-S ...
The order of RNAPII mutants follows that of the clustered pE-MAP (Figure S2 and Data S1). Analysis of the distribution of phenotypes relative to the RNAPII structure suggested that our alleles might be diverse in their functions. GalR and MPA-sensitive mutations were broadly distributed, whereas...
We have deliberately avoided the clustering steps in the IsoSeq3 pipeline in order that small variances around the splice junctions, such as NAGNAG splice junctions can be preserved. The FLNCs were then converted to FASTA format using samtools and mapped to the TAIR10 genome reference using ...
This result suggests that open chromatin structure maintained by the MLL family proteins and long-range chromatin organization by CTCF may contribute to chromosome breaks and may explain why certain translocations are found in the cancers of specific cell types. Prediction of Novel Transcription Units ...
(CL8, CL80, and CL81). In DH1 and related species, 39- to 40-bp Cent-Dc monomers were organized in a higher-order repeat structure (Supplementary Fig. 9).Daucusspecies distantly related to carrot were enriched for the CL80 repeat, which occupied most subtelomeric and pericentromeric ...
The HFF-trained model imputed almost as well as the hESC-trained model for chromatin contacts within 100 kb and 200 kb range (Fig. 2b). In the cross-species experiment, we trained the model on mESC and tested the performance on hESC. In order to stay consistent with cross-...