[PDF] Top 20 Chromatin accessibility: a window into the genome

... MNase-seq data Nucleosome or translational positioning indicates the position of a population of nucleosomes in relation to DNA, and considers a specific reference nu- cleosome point like its start, dyad or end [143]. ... See full document

... probing chromatin accessibility in frozen whole tissue ...of chromatin with Benzonase and Cyanase are remarkably similar and the identified accessible regions correlate with low nucleosomal ... See full document

... Our biophysical perspective on genomic information facilitates the characterization of the dynamic impact of the environment on genome variation. We have translated SNP haplotype data into entropic measures of NIC ... See full document

... cross-cell-type accessibility patterns ...of chromatin accessibility is predictive of functional activity within a specific cell type, and suggests more generally that DHSs with stereotyped cellular ... See full document

... To better understand the relation between model per- formance and HiChIP interaction count, we reran the HiChIP models using different PET cut-offs. As depicted in Additional file 1: Figure S16a, model performance ... See full document

... Previously published [7, 8, 94] RNA-seq datasets were used to calculate early to late whole-embryo gene ex- pression profiles (DDBJ accession DRA003460 for mouse [M. musculus], chicken [G. gallus], softshell turtle ... See full document

... perform genome-wide binding analysis on an in vivo chroma- tin ...closed chromatin indicating that competi- tion with nucleosomes may play a key role in determin- ing Hox target ...of chromatin in ... See full document

... sible chromatin with sequencing (ATAC-seq) to profile the chromatin landscapes of primary human EnSCs in their undifferentiated state and upon ...the accessibility of the genome and map open ... See full document

... in accessibility during mito- sis is more pronounced among peaks than hotspots – a di↵erence that is visible across a wide range of interphase accessibility ...interphase accessibility during ... See full document

... In summary, our genome-wide analysis identifies the comple- ment of opsin genes in B. lanceolatum, confirms expression of all but one genes and documents their stage and/or tissue specificity. Studies of opsin ... See full document

... Additional file 8: Table S2. CNV and gene expression data in context of regions with DA and equivalent accessibility. Single copy probe locations of regions with DA (in bold) and equivalent accessibility ... See full document

... of chromatin structure: outside the flower and at the earliest stages of floral meristem development, these genes are repressed by Polycomb group (PcG) protein com- plexes that act in concert with earlier acting ... See full document

... open chromatin changes specifically to bona-fide sites of transcription initiation, we performed ‘Start-seq’, which precisely determines transcription initiation events by capturing nascent RNAs associated with ... See full document

... This work developed a custom script called DDTS for the e ffi cient and accurate identification of DHSs across the Arabidopsis genome using sequencing data obtained from nanogram quan- tities of DNA isolated from ... See full document

... the genome such as promoters and DNase sensitive hotspots (53), is critical during normal cell ...on chromatin accessibility within metaphase chromosomes, and how it changes with respect to ... See full document

... causing chromatin discordance mainly via the disruption of ...open chromatin suggested selection pressures against C:G > A: T ...pair chromatin differences identified cases in which only twin ... See full document

... of histone H2A and its variants by RT-PCR. However, these transcripts were expressed at similar levels before and after fertilization (see Fig. S8A in the supplementary material). Furthermore, in immunoblotting analyses ... See full document

... spatial chromatin structure requires more elaborate TADs to achieve more precise gene regulation and avoid disordered transcription during cell ...3D genome structure (from large nuclear compartments and ... See full document

... of chromatin modifications (chromatin states)? One scenario that is easy to envision is when histone modifications are produced via looping interactions of a protein complex an- chored at a fixed ... See full document

... Our most intriguing finding among the proteomic data is, however, the interaction of SETD5 with the HDAC-containing complex NCoR. This suggests that SETD5 might be necessary for the recruitment of this ... See full document