Molecular recognition of histone lysine methylation by the Polycomb group repressor dSfmbt

Grimm, Clemens; Matos, Raquel; Ly‐Hartig, Nga; Steuerwald, Ulrich; Lindner, Doris; Rybin, Vladimir; Müller, Jürg; Müller, Christoph

doi:10.1038/emboj.2009.147

Cited by 81 publications

(119 citation statements)

References 34 publications

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“…In contrast, Context Mirror predicts the PHO/SFMBT interaction (Alfieri et al, 2013) and the well-characterized interactions between these two subunits of the PhoRC complex and those of PRC1: PHO/PC (Mohd-Sarip et al, 2002), PHO/PH-P (Mohd- Sarip et al, 2002) and SFMBT/SCM (Grimm et al, 2009). The bioinformatic method also predicts the well-established interactions between subunits of the PRC1 complex, that is, PH-P/PC (Strutt and Paro, 1997), PH-P/PSC (Kyba and Brock, 1998), PH-P/SCM (Peterson et al, 1997), PC/PSC (Kyba and Brock, 1998), PC/SCE and PSC/SCE (Gorfinkel et al, 2004).…”

Section: Discussionmentioning

confidence: 90%

Adaptive selection and coevolution at the proteins of the Polycomb repressive complexes in Drosophila

et al. 2015

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JM Calvo-Martín, P Librado, M Aguadé, M Papaceit and C Segarra Polycomb group (PcG) proteins are important epigenetic regulatory proteins that modulate the chromatin state through posttranslational histone modifications. These interacting proteins form multimeric complexes that repress gene expression. Thus, PcG proteins are expected to evolve coordinately, which might be reflected in their phylogenetic trees by concordant episodes of positive selection and by a correlation in evolutionary rates. In order to detect these signals of coevolution, the molecular evolution of 17 genes encoding the subunits of five Polycomb repressive complexes has been analyzed in the Drosophila genus. The observed distribution of divergence differs substantially among and along proteins. Indeed, CAF1 is uniformly conserved, whereas only the established protein domains are conserved in other proteins, such as PHO, PHOL, PSC, PH-P and ASX. Moreover, regions with a low divergence not yet described as protein domains are present, for instance, in SFMBT and SU(Z)12. Maximum likelihood methods indicate an acceleration in the nonsynonymous substitution rate at the lineage ancestral to the obscura group species in most genes encoding subunits of the Pcl-PRC2 complex and in genes Sfmbt, Psc and Kdm2. These methods also allow inferring the action of positive selection in this lineage at genes E(z) and Sfmbt. Finally, the protein interaction network predicted from the complete proteomes of 12 Drosophila species using a coevolutionary approach shows two tight PcG clusters. These clusters include well-established binary interactions among PcG proteins as well as new putative interactions.

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Section: Discussionmentioning

confidence: 90%

Adaptive selection and coevolution at the proteins of the Polycomb repressive complexes in Drosophila

et al. 2015

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“…This small-scale differentiation facilitates effective identification of candidate genes influenced by spatially varying selection. Figure 4 shows one example in which a 1-kb windows in the top 2.5% F ST tail localizes to Sfmbt, a chromatin-binding protein involved in gene regulation (Grimm et al 2009). A genome browser displaying 1-kb windows and their associated F ST estimates is available at http:/ / altair.dartmouth.edu/ucsc/index.html.…”

Section: à16mentioning

confidence: 99%

Genomic Differentiation Between Temperate and Tropical Australian Populations ofDrosophila melanogaster

et al. 2011

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Determining the genetic basis of environmental adaptation is a central problem of evolutionary biology. This issue has been fruitfully addressed by examining genetic differentiation between populations that are recently separated and/or experience high rates of gene flow. A good example of this approach is the decades-long investigation of selection acting along latitudinal clines in Drosophila melanogaster. Here we use next-generation genome sequencing to reexamine the well-studied Australian D. melanogaster cline. We find evidence for extensive differentiation between temperate and tropical populations, with regulatory regions and unannotated regions showing particularly high levels of differentiation. Although the physical genomic scale of geographic differentiation is small-on the order of gene sized-we observed several larger highly differentiated regions. The region spanned by the cosmopolitan inversion polymorphism In(3R)P shows higher levels of differentiation, consistent with the major difference in allele frequencies of Standard and In(3R)P karyotypes in temperate vs. tropical Australian populations. Our analysis reveals evidence for spatially varying selection on a number of key biological processes, suggesting fundamental biological differences between flies from these two geographic regions.

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“…41 In vitro studies using isolated MBT domains and histone peptides have demonstrated a general preference for binding to mono-or di-methylated, over un-or tri-methylated peptides. 27,[42][43][44][45][46][47][48][49] An exception to this general rule is provided by the Caenorhabditis elegans protein LIN-61, which displays specificity toward di-and tri-methylated H3K9 histone peptides. 50 A recent study investigating the MBT domains of all 9 human family members has found that some MBT domains (L3MBTL1, L3MBTL3) recognize mono-and/or di-methyl-lysine in a promiscuous, non-sequence-specific fashion, whereas others (SCML2, L3MBTL4, MBTD1, L3MBTL2) specifically bind to only a few selected histone sequences.…”

Section: -23mentioning

confidence: 99%

Chromatin regulation: How complex does it get?

Meier¹,

Brehm

2014

Epigenetics

100

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Molecular recognition of histone lysine methylation by the Polycomb group repressor dSfmbt

Cited by 81 publications

References 34 publications

Adaptive selection and coevolution at the proteins of the Polycomb repressive complexes in Drosophila

Adaptive selection and coevolution at the proteins of the Polycomb repressive complexes in Drosophila

Genomic Differentiation Between Temperate and Tropical Australian Populations ofDrosophila melanogaster

Chromatin regulation: How complex does it get?

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