Identification of functional elements and regulatory circuits by Drosophila modENCODE

By Sushmita Roy, Jason Ernst, Peter V. Kharchenko, Pouya Kheradpour, N. Negre, M. Eaton, J. Landolin, Christopher, A. Bristow, Lijia Ma and 99 more. 2011

526 citations recorded by the source corpus.

View Paper: https://www.semanticscholar.org/paper/07719ba2a4e20178048a61486fe41a9073649df8

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Citations in the corpus

Global Quantitative Modeling of Chromatin Factor Interactions (2014, methodology): “Chromatin binding profiles of histones and chromatin proteins were measured by the modENCODE project [1].”
ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia (2012, methodology): “For organisms with small genomes, the modENCODE Consortium has used both ChIP-chip and ChIP-seq, as modern arrays can provide high-resolution coverage of small genomes (Gerstein et al. 2010; Roy et al. 2010).”
Genomewide analysis of Drosophila circular RNAs reveals their structural and sequence properties and age-dependent neural accumulation (2014, unknown): “We typically consider miRNAs that are conserved throughout Sophophora to be well conserved and cataloged 2-8 or 6merA seed matches to such miRNAs (Ruby et al., 2007).”
Zelda Binding in the Early Drosophila melanogaster Embryo Marks Regions Subsequently Activated at the Maternal-to-Zygotic Transition (2011, background): “It is worth noting that before zygotic induction Drosophila embryos are undergoing rapid rounds of DNA replication and ORC, the replication initiator, does not bind to specific sequences [38], but rather depends upon access to open chromatin [39].”
Integrative epigenomic mapping defines four main chromatin states in Arabidopsis (2011, background): “…studies have been performed in yeast (Liu et al, 2005), C. elegans (Gerstein et al, 2010; Liu et al, 2011), Drosophila (Kharchenko et al, 2011; Roy et al, 2010; Riddle et al, 2011) and human cells (Wang et al, 2008; Hon et al, 2009; Ernst and Kellis, 2010; Zhou et al, 2011), which all…”
Genome-Wide Quantitative Enhancer Activity Maps Identified by STARR-seq (2013, unknown): “(A) Genomic distribution of putative enhancers predicted by the 9-‐state hidden markov model (HMM; “enhancer state”) (12), and by (B) open chromatin regions marked with H3K4me1 and H3K27ac (‘clas”
Transcription factor binding in human cells occurs in dense clusters formed around cohesin anchor sites. (2013, unknown): “Therefore, clustering of functionally related TFs is expected, and has been observed (e.g., Boyer et al., 2005; Roy et al., 2010; Stanojevic et al., 1991).”
Histone Lysine Methylation Dynamics: Establishment, Regulation, and Biological Impact (2012, unknown): “KDM4AKDM4D remove H3K9me3/H3K9me2, H3K36me3/H3K36me2, and H1.”