Comprehensive analysis of the chromatin landscape in Drosophila

By Peter V. Kharchenko, Artyom A. Alekseyenko, Y. Schwartz, Aki Minoda, N. C. Riddle, Jason Ernst, P. Sabo, E. Larschan, A. Gorchakov, Tingting Gu and 20 more. Nature, 2010

905 citations recorded by the source corpus.

Chromatin is composed of DNA and a variety of modified histones and non-histone proteins, which have an impact on cell differentiation, gene regulation and other key cellular processes. Here we present a genome-wide chromatin landscape for Drosophila melanogaster based on eighteen histone modifications, summarized by nine prevalent combinatorial patterns. Integrative analysis with other data (non-histone chromatin proteins, DNase I hypersensitivity, GRO-Seq reads produced by engaged polymerase, short/long RNA products) reveals discrete characteristics of chromosomes, genes, regulatory elements and other functional domains. We find that active genes display distinct chromatin signatures that are correlated with disparate gene lengths, exon patterns, regulatory functions and genomic contexts. We also demonstrate a diversity of signatures among Polycomb targets that include a subset with paused polymerase. This systematic profiling and integrative analysis of chromatin signatures provides insights into how genomic elements are regulated, and will serve as a resource for future experimental investigations of genome structure and function.

Subfields: Molecular Biology, Plant Science

View Paper: https://www.semanticscholar.org/paper/d3680aaa222a12be6962d616f0697df5b7b3d5fc

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Citations in the corpus

Establishment of regions of genomic activity during the Drosophila maternal to zygotic transition (2014, background): “Flanking nucleosomes were enriched with H3K4me1, H3K27ac, and H3K18ac, marks previously shown to be enriched at active enhancers (Heintzman et al., 2007; Wang et al., 2008; Creyghton et al., 2010; Kharchenko et al., 2011; Rada-Iglesias et al., 2011) and depleted for H3K4me3 and H3K36me3.”
Integrative annotation of chromatin elements from ENCODE data (2012, neutral): “A variety of segmentation models have been described subsequently, employing HMMs with flat (9,10) or hierarchical (11) structures, or generalizing the HMM to a hierarchical change-point model (12).”
Genome Regulation by Polycomb and Trithorax: 70 Years and Counting. (2017, neutral): “Genome-wide mapping of a large set of DNA-binding proteins and histone marks revealed that the genome can be partitioned into epigenetic domains characterized by a specific combination of active or repressive chromatin marks (Filion et al., 2010; Kharchenko et al., 2011; Thurman et al., 2012) (Figur”
Genome-Wide Quantitative Enhancer Activity Maps Identified by STARR-seq (2013, neutral): “(B) Correlation of STARR-‐seq enrichment and luciferase signal for regions in the ‘enhancer state’ from the 9-‐state HMM based on chromatin features (12) with (blue) and without (red) STARR-‐seq signal.”
Heterogeneous substitution systems revisited (2016, neutral): “Global data traffic is projected to grow at an annual rate of 30% from 2018 to 2024 [1].”
Occupying chromatin: Polycomb mechanisms for getting to genomic targets, stopping transcriptional traffic, and staying put (2013, background): “Indeed, new technologies have yielded genome-widemaps of regulatory factors and nucleosomes at previously unachieved levels of comprehensiveness and resolution (Filion et al., 2010; Henikoff et al., 2011; Kharchenko et al., 2011).”
Regulation of nucleosome dynamics by histone modifications (2013, neutral): “3 enrichment, tagged histone incorporation and CATCH-IT are generally highly enriched for histone modifications associated with active transcription, such as acetylation and H3K4 methylation 11,83,85,86 , and nucleosomal histone H3.”
Histone Lysine Methylation Dynamics: Establishment, Regulation, and Biological Impact (2012, neutral): “For instance, worm and fly genes that are expressed in heterochromatic regions have higher levels of H3K9me2/H3K9me3 in their coding regions, while euchromatic genes lack this modification (Kharchenko et al., 2011; Liu et al., 2011; Riddle et al., 2011).”
Three-dimensional folding and functional organization principles of the Drosophila genome. (2012, background): “Previous extensive profiling of histone modifications and binding of chromatin proteins has promoted the view of the fly genome as a set of epigenetic domains, correlated with the regulation of the underlying loci (Filion et al., 2010; Kharchenko et al., 2011).”
Global Quantitative Modeling of Chromatin Factor Interactions (2014, methodology): “ChIP profile is visualized as the space-filling Hilbert curve as in [11], therefore adjacent genomic locations are also close to each other in this 2D representation.”