Systematic Protein Location Mapping Reveals Five Principal Chromatin Types in Drosophila Cells

Filion, Guillaume J.; Bemmel, Joke G. van; Braunschweig, Ulrich; Talhout, Wendy; Kind, Jop; Ward, Lucas D.; Brugman, Wim; Castro, Inês J. de; Kerkhoven, Ron; Bussemaker, Harmen J.; Steensel, Bas van

doi:10.1016/j.cell.2011.02.046

Cited by 148 publications

(323 citation statements)

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“…Interestingly, these two H3K36me3‐bearing states are also associated with the highest gene expression levels in the barley seedling (Figure S6). These collective data are consistent with the role of H3K36me3 in Arabidopsis acting antagonistically to H3K27me3 in controlling FLC gene expression (Yang et al ., ), in maize of enrichment in genes expressed at the same level between root and shoot tissue (Wang et al ., ), and in Drosophila of being enriched in housekeeping genes (Filion et al ., ; Brown and Bachtrog, ).…”

Section: Discussionmentioning

confidence: 98%

Chromatin state analysis of the barley epigenome reveals a higher‐order structure defined by H3K27me1 and H3K27me3 abundance

et al. 2015

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SummaryCombinations of histones carrying different covalent modifications are a major component of epigenetic variation. We have mapped nine modified histones in the barley seedling epigenome by chromatin immunoprecipitation next‐generation sequencing (ChIP‐seq). The chromosomal distributions of the modifications group them into four different classes, and members of a given class also tend to coincide at the local DNA level, suggesting that global distribution patterns reflect local epigenetic environments. We used this peak sharing to define 10 chromatin states representing local epigenetic environments in the barley genome. Five states map mainly to genes and five to intergenic regions. Two genic states involving H3K36me3 are preferentially associated with constitutive gene expression, while an H3K27me3‐containing genic state is associated with differentially expressed genes. The 10 states display striking distribution patterns that divide barley chromosomes into three distinct global environments. First, telomere‐proximal regions contain high densities of H3K27me3 covering both genes and intergenic DNA, together with very low levels of the repressive H3K27me1 modification. Flanking these are gene‐rich interior regions that are rich in active chromatin states and have greatly decreased levels of H3K27me3 and increasing amounts of H3K27me1 and H3K9me2. Lastly, H3K27me3‐depleted pericentromeric regions contain gene islands with active chromatin states separated by extensive retrotransposon‐rich regions that are associated with abundant H3K27me1 and H3K9me2 modifications. We propose an epigenomic framework for barley whereby intergenic H3K27me3 specifies facultative heterochromatin in the telomere‐proximal regions and H3K27me1 is diagnostic for constitutive heterochromatin elsewhere in the barley genome.

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Section: Discussionmentioning

confidence: 98%

Chromatin state analysis of the barley epigenome reveals a higher‐order structure defined by H3K27me1 and H3K27me3 abundance

et al. 2015

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“…This means that following validation of the successful construction of a Dam‐fusion expression construct, the experimental procedures will be identical for each protein assayed. Recent studies have taken advantage of this fact, enabling increased experimental throughput so that multiple interaction profiles may be generated . Owing to the necessity of creating transgenic cells for DamID, the technique is not applicable for studies in the small minority of model organisms in which transgenesis is not yet possible.…”

Section: Damid Versus Chipmentioning

confidence: 99%

“…In a recent study, DamID was used to profile binding for over 50 different proteins known to be associated with chromatin in Drosophila cultured cells . From these data, it could be seen that chromatin can be broadly categorized into five principle types based on association with different groups of proteins.…”

Section: Using Damid To Investigate Chromatin Statesmentioning

confidence: 99%

Dam it's good! DamID profiling of protein‐DNA interactions

Aughey

Southall

2015

WIREs Developmental Biology

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The interaction of proteins with chromatin is fundamental for several essential cellular processes. During the development of an organism, genes must to be tightly regulated both temporally and spatially. This is achieved through the action of chromatin‐binding proteins such as transcription factors, histone modifiers, nucleosome remodelers, and lamins. Furthermore, protein–DNA interactions are important in the adult, where their perturbation can lead to disruption of homeostasis, metabolic dysregulation, and diseases such as cancer. Understanding the nature of these interactions is of paramount importance in almost all areas of molecular biological research. In recent years, DNA adenine methyltransferase identification (DamID) has emerged as one of the most comprehensive and versatile methods available for profiling protein–DNA interactions on a genomic scale. DamID has been used to map a variety of chromatin‐binding proteins in several model organisms and has the potential for continued adaptation and application in the field of genomic biology. WIREs Dev Biol 2016, 5:25–37. doi: 10.1002/wdev.205For further resources related to this article, please visit the WIREs website.

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“…Extensive profiling of histone modifications have suggested that genomes are segmented in large domains showing overall coherent chromatin characteristics . Interestingly, comparison between chromatin profiles and physical/topological domains revealed a strong overlap between these two subdivisions .…”

Section: Organizing Cell‐type Specific or Constitutive/pre‐establishementioning

confidence: 99%

Gene regulation during development in the light of topologically associating domains

Remeseiro

Hörnblad

Spitz

2015

WIREs Developmental Biology

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During embryonic development, complex transcriptional programs govern the precision of gene expression. Many key developmental genes are regulated via cis-regulatory elements that are located far away in the linear genome. How sequences located hundreds of kilobases away from a promoter can influence its activity has been the subject of numerous speculations, which all underline the importance of the 3D-organization of the genome. The recent advent of chromosome conformation capture techniques has put into focus the subdivision of the genome into topologically associating domains (TADs). TADs may influence regulatory activities on multiple levels. The relative invariance of TAD limits across cell types suggests that they may form fixed structural domains that could facilitate and/or confine long-range regulatory interactions. However, most recent studies suggest that interactions within TADs are more variable and dynamic than initially described. Hence, different models are emerging regarding how TADs shape the complex 3D conformations, and thereafter influence the networks of cis-interactions that govern gene expression during development. For further resources related to this article, please visit the WIREs website.

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Systematic Protein Location Mapping Reveals Five Principal Chromatin Types in Drosophila Cells

Cited by 148 publications

References 0 publications

Chromatin state analysis of the barley epigenome reveals a higher‐order structure defined by H3K27me1 and H3K27me3 abundance

Chromatin state analysis of the barley epigenome reveals a higher‐order structure defined by H3K27me1 and H3K27me3 abundance

Dam it's good! DamID profiling of protein‐DNA interactions

Gene regulation during development in the light of topologically associating domains

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