Sex comb on midleg (Scm) is a functional link between PcG-repressive complexes in<i>Drosophila</i>

Kang, Hyuckjoon; McElroy, Kyle A.; Jung, Youngsook L.; Alekseyenko, Artyom A.; Zee, Barry M.; Park, Peter J.; Kuroda, Mitzi I.

doi:10.1101/gad.260562.115

Cited by 75 publications

(99 citation statements)

References 106 publications

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“…The same binding site is recognized by the GAF and Psq protein pair, despite that they have different types of DNA-binding domains [124] ( Table 1). The binding site of the Zeste protein is also recognized by the Fs(1)h (female sterile (1) homeotic) protein, which has been characterized as a TrxG factor [154] and, at the same time, purifies with the PRC1 complex when tagged with the Pc protein [155,156]. The recruitment of Fs(1)h to PREs and its implication in PcG function are yet to be verified.…”

Section: Role Of Protein Binding Sites In Repressionmentioning

confidence: 99%

Drosophila DNA-Binding Proteins in Polycomb Repression

2018

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Abstract:The formation of individual gene expression patterns in different cell types is required during differentiation and development of multicellular organisms. Polycomb group (PcG) proteins are key epigenetic regulators responsible for gene repression, and dysregulation of their activities leads to developmental abnormalities and diseases. PcG proteins were first identified in Drosophila, which still remains the most convenient system for studying PcG-dependent repression. In the Drosophila genome, these proteins bind to DNA regions called Polycomb response elements (PREs). A major role in the recruitment of PcG proteins to PREs is played by DNA-binding factors, several of which have been characterized in detail. However, current knowledge is insufficient for comprehensively describing the mechanism of this process. In this review, we summarize and discuss the available data on the role of DNA-binding proteins in PcG recruitment to chromatin.

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Section: Role Of Protein Binding Sites In Repressionmentioning

confidence: 99%

Drosophila DNA-Binding Proteins in Polycomb Repression

2018

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“…Using parallel TAP-tagged purification approaches, it was shown that SCM is the only protein, which is enriched in both PRC1 and PRC2 type complexes. It seems that the SAM domain containing SCM protein can offer the functional link between Polycomb repressive complexes [141].…”

Section: Discovery Of Polycomb Repressive Complexesmentioning

confidence: 99%

From Flies to Mice: The Emerging Role of Non-Canonical PRC1 Members in Mammalian Development

2018

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Originally two types of Polycomb Repressive Complexes (PRCs) were described, canonical PRC1 (cPRC1) and PRC2. Recently, a versatile set of complexes were identified and brought up several dilemmas in PRC mediated repression. These new class of complexes were named as non-canonical PRC1s (ncPRC1s). Both cPRC1s and ncPRC1s contain Ring finger protein (RING1, RNF2) and Polycomb group ring finger catalytic (PCGF) core, but in ncPRCs, RING and YY1 binding protein (RYBP), or YY1 associated factor 2 (YAF2), replaces the Chromobox (CBX) and Polyhomeotic (PHC) subunits found in cPRC1s. Additionally, ncPRC1 subunits can associate with versatile accessory proteins, which determine their functional specificity. Homozygous null mutations of the ncPRC members in mice are often lethal or cause infertility, which underlines their essential functions in mammalian development. In this review, we summarize the mouse knockout phenotypes of subunits of the six major ncPRCs. We highlight several aspects of their discovery from fly to mice and emerging role in target recognition, embryogenesis and cell-fate decision making. We gathered data from stem cell mediated in vitro differentiation assays and genetically engineered mouse models. Accumulating evidence suggests that ncPRC1s play profound role in mammalian embryogenesis by regulating gene expression during lineage specification of pluripotent stem cells.

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“…BioTAP-XL has successfully identified key interactors of the male-specific lethal (MSL) dosage compensation and heterochromatin protein (HP1a) complexes in Drosophila (5) and revealed novel components of the Polycomb Repressive Complex 2 in human tissue culture cells (6) and fruit flies (7). Despite the aforementioned advantages, BioTAP-XL suffers from several limitations.…”

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confidence: 99%

Streamlined discovery of cross-linked chromatin complexes and associated histone modifications by mass spectrometry

Zee

Alekseyenko

McElroy

et al. 2016

Proc. Natl. Acad. Sci. U.S.A.

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Posttranslational modifications (PTMs) are key contributors to chromatin function. The ability to comprehensively link specific histone PTMs with specific chromatin factors would be an important advance in understanding the functions and genomic targeting mechanisms of those factors. We recently introduced a cross-linked affinity technique, BioTAP-XL, to identify chromatin-bound protein interactions that can be difficult to capture with native affinity techniques. However, BioTAP-XL was not strictly compatible with similarly comprehensive analyses of associated histone PTMs. Here we advance BioTAP-XL by demonstrating the ability to quantify histone PTMs linked to specific chromatin factors in parallel with the ability to identify nonhistone binding partners. Furthermore we demonstrate that the initially published quantity of starting material can be scaled down orders of magnitude without loss in proteomic sensitivity. We also integrate hydrophilic interaction chromatography to mitigate detergent carryover and improve liquid chromatography-mass spectrometric performance. In summary, we greatly extend the practicality of BioTAP-XL to enable comprehensive identification of protein complexes and their local chromatin environment.chromatin complexes | affinity pulldown | liquid chromatography-mass spectrometry | BioTAP-XL | histone modifications C hromatin encompasses the subset of proteins and RNAs in complex with DNA to form the chromosomes within eukaryotic nuclei. As the primary protein constituents of chromatin, histones organize genomic DNA into nucleosomes and display an extensive array of posttranslational modifications (PTMs) (1). It is increasingly evident that specific histone PTMs are selectively recognized by specific nonhistone proteins that are themselves regulators of many nuclear events such as epigenetic silencing (2, 3). Consequently, defects in these chromatin components often manifest in a number of human diseases (4).As specific interactions between modified histones and nonhistone proteins help distinguish complexes participating in distinct processes, the identification of protein and modification-dependent interactions provides key insights into chromatin biology. Various chromatography and pulldown methods have been developed to identify binding partners. In a typical native pulldown experiment, nuclei from hypotonically lysed cells are digested with micrococcal nuclease (MNase). Extracted chromatin is subjected to immunoprecipitation to isolate the desired complexes. If using a tag such as FLAG, complexes are then competitively eluted and identified. Several drawbacks to native pulldowns as described here are that MNase leaves behind a substantial insoluble nuclear pellet and degrades associating RNAs, that salt extraction of the digested nucleosomes risks dissociation of the tagged bait from its interacting partners, and that most tags do not have sufficient affinity for their respective antibody to permit highly stringent washes. The result is often an incomplete picture of the chromatin...

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Sex comb on midleg (Scm) is a functional link between PcG-repressive complexes inDrosophila

Cited by 75 publications

References 106 publications

Drosophila DNA-Binding Proteins in Polycomb Repression

Drosophila DNA-Binding Proteins in Polycomb Repression

From Flies to Mice: The Emerging Role of Non-Canonical PRC1 Members in Mammalian Development

Streamlined discovery of cross-linked chromatin complexes and associated histone modifications by mass spectrometry

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