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PLoS One
2010 Oct 27;510:e13681. doi: 10.1371/journal.pone.0013681.
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Different Mi-2 complexes for various developmental functions in Caenorhabditis elegans.
Passannante M
,
Marti CO
,
Pfefferli C
,
Moroni PS
,
Kaeser-Pebernard S
,
Puoti A
,
Hunziker P
,
Wicky C
,
Müller F
.
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Biochemical purifications from mammalian cells and Xenopus oocytes revealed that vertebrate Mi-2 proteins reside in multisubunit NuRD (Nucleosome Remodeling and Deacetylase) complexes. Since all NuRD subunits are highly conserved in the genomes of C. elegans and Drosophila, it was suggested that NuRD complexes also exist in invertebrates. Recently, a novel dMec complex, composed of dMi-2 and dMEP-1 was identified in Drosophila. The genome of C. elegans encodes two highly homologous Mi-2 orthologues, LET-418 and CHD-3. Here we demonstrate that these proteins define at least three different protein complexes, two distinct NuRD complexes and one MEC complex. The two canonical NuRD complexes share the same core subunits HDA-1/HDAC, LIN-53/RbAp and LIN-40/MTA, but differ in their Mi-2 orthologues LET-418 or CHD-3. LET-418 but not CHD-3, interacts with the Krüppel-like protein MEP-1 in a distinct complex, the MEC complex. Based on microarrays analyses, we propose that MEC constitutes an important LET-418 containing regulatory complex during C. elegans embryonic and early larval development. It is required for the repression of germline potential in somatic cells and acts when blastomeres are still dividing and differentiating. The two NuRD complexes may not be important for the early development, but may act later during postembryonic development. Altogether, our data suggest a considerable complexity in the composition, the developmental function and the tissue-specificity of the different C. elegans Mi-2 complexes.
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21060680
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Figure 1. Two NuRD complexes and a MEC complex are present in C. elegans.(A) LET-418 interacts with HDA-1 and LIN-53, but not with CHD-3 nor with HDA-2 and HDA-3. Extracts from wild-type mixed-stage worms were precipitated with either α-LET-418 or no antibodies (negative control). Inputs and immunoprecipitates were subjected to Western analysis and immunoblotted with antibodies directed against proteins indicated next to each panel. (B) HDA-1 binds to CHD-3. Extracts from wild-type or chd-3(eh4) mixed-stage worms were precipitated with either α-HDA-1 or no antibodies (negative control). Inputs and immunoprecipitates were subjected to Western analysis and immunoblotted with antibodies directed against CHD-3. (C) LIN-53::GFP interacts with LET-418, HDA-1 and CHD-3. Extracts from lin-53::gfp or lin-53(-) mixed-stage worms were precipitated with either α-GFP or no antibodies (negative control). Inputs and immunoprecipitates were subjected to Western analysis and immunoblotted with antibodies directed against proteins indicated next to each panel. (D) LIN-40::GFP interacts with LET-418, HDA-1 and CHD-3, but not with MEP-1. Extracts from lin-40::gfp or lin-40(+) mixed-stage worms were precipitated with either α-GFP or no antibodies (negative control). Inputs and immunoprecipitates were subjected to Western analysis and immunoblotted with antibodies directed against proteins indicated next to each panel. (E) EGL-27::GFP does not interact with LET-418 nor with HDA-1. Extracts from egl-27::gfp or egl-27(-) mixed-stage worms were precipitated with either α-GFP or no antibodies (negative control). Inputs and immunoprecipitates were subjected to Western analysis and immunoblotted with antibodies directed against proteins indicated next to each panel. The membrane was reprobed with anti-GFP as a positive control. (F) MEP-1 interacts with LET-418 and HDA-1, but not CHD-3 nor with LIN-53. Extracts from wild-type mixed-stage worms were precipitated with either α-MEP-1 or no antibodies (negative control). Inputs and immunoprecipitates were subjected to Western analysis and immunoblotted with antibodies directed against proteins indicated next to each panel. Input: 5% of the immunoprecipitate; IP: 100% of the immunoprecipitate (1 mg of proteins). All co-immunoprecipitation experiments were reproducibly performed at least twice.
Figure 2. The MEC complex negatively regulates lag-2::gfp expression in the gut.The lag-2::gfp transgene is expressed in the gut of let-418(RNAi), mep-1(RNAi) and hda-1(RNAi) L3 larvae. (A) L3 worms carrying lag-2::gfp transgene and fed bacteria containing empty vector (RNAi control) (A) show expression in the Distal Tip Cells (DTC) and in the ventral nerve cord. No ectopic expression is observed. (B, D–E) lag-2::gfp is ectopically expressed in the gut of let-418(RNAi) (B), mep-1(RNAi) (D) and hda-1(RNAi) (E) L3 larvae. (C) No ectopic expression is observed in chd-3(RNAi) L3 larvae. (F) lag-2::gfp is mainly expressed in the epidermis in lin-53(RNAi) L3 larvae. (G) lag-2::gfp is ectopically expressed only in two cells in the most anterior part of the intestine in lin-40(RNAi) L3 larvae. The asterisk marks the DTC.
Figure 3. LET-418 and MEP-1 regulate common target genes.A strong correlation is observed between the genes deregulated in let-418(RNAi) and mep-1(RNAi) L1 larvae. The fold change of each of the common genes was plotted on the graph (X-axis: fold change of let-418(RNAi) genes, Y-axis: fold change of the mep-1(RNAi)). Each circle represents a single gene. A standard correlation factor of R = 0.98 was calculated according to the linear regression.
Figure 4. LET-418 and MEP-1 regulate germline and early embryonic genes.Pie charts show repartition and functional annotation of the common deregulated genes (A) and the early genes (B) according to gene ontology (GO) annotations. The GO terms are indicated on the right of each pie chart. (A) The pie chart shows the repartition of the 914 common deregulated genes compared to the list of 4699 germline genes. The common genes are divided into four groups: upregulated germline (rose slice) and non germline (gray slice) genes; and downregulated germline (pink slice) and non germline (blue slice) genes. (B) The pie chart shows the repartition of the 228 early genes compared to the common upregulated genes and to the list of 4699 germline genes. 49 common upregulated genes are also early genes. They are subdivided in germline (pink slice) and non germline (rose slice) genes. The remaining early genes, that are not targets of MEC, are subdivided in germline (blue slice) and non germline (gray slice) genes.
Figure 5. CHD-3 acts as a component of the NuRD complex to regulate fbxa-103.Fold change of fbxa-103 mRNA was analyzed by qRT-PCR in diverse RNAi-treated L1 larvae, as indicated on the right of the panel. fbxa-103 is upregulated in chd-3(RNAi) and lin-53(RNAi) but not in let-418(RNAi) nor in mep-1(RNAi) L1 larvae.
Figure 6. let-418 and chd-3 transcriptional reporters have different expression patterns.(A-B) Young adults animals carrying both a transcriptional let-418p::Venus (first lane) and a transcriptional chd-3p::DsRed2 (second lane) reporter genes were analyzed by confocal microscopy. The third lane is the merged picture from both let-418p::Venus and chd-3p::DsRed2 reporters. Expression is shown (A) in the head and (B) in the vulva and somatic gonad. v: vulva (ventral view); g: somatic gonad; vn: ventral nerve cord.
Figure 7. Summary figure of the complexes and their proposed roles.The two C. elegans Mi-2 proteins are members of at least three different complexes, two distinct NuRD complexes and a MEC complex.
Figure 8. Phylogenetic comparison of the C. elegans, Drosophila and human Mi-2 orthologues.The regions of the different Mi-2 proteins corresponding to residues 320 to 1076 of the CeLET-418 sequence were used to construct the phylogenetic tree. Numbers refer to bootstrap values supporting particular groupings.
Ahringer,
NuRD and SIN3 histone deacetylase complexes in development.
2000, Pubmed
Ahringer,
NuRD and SIN3 histone deacetylase complexes in development.
2000,
Pubmed
Al-Shahrour,
BABELOMICS: a systems biology perspective in the functional annotation of genome-scale experiments.
2006,
Pubmed
Andersen,
C. elegans ISWI and NURF301 antagonize an Rb-like pathway in the determination of multiple cell fates.
2006,
Pubmed
Ballestar,
A Drosophila MBD family member is a transcriptional corepressor associated with specific genes.
2001,
Pubmed
Belfiore,
The MEP-1 zinc-finger protein acts with MOG DEAH box proteins to control gene expression via the fem-3 3' untranslated region in Caenorhabditis elegans.
2002,
Pubmed
Berezikov,
Homologous gene targeting in Caenorhabditis elegans by biolistic transformation.
2004,
Pubmed
Bettinger,
Stage-specific accumulation of the terminal differentiation factor LIN-29 during Caenorhabditis elegans development.
1996,
Pubmed
Bouazoune,
ATP-dependent chromatin remodeling complexes in Drosophila.
2006,
Pubmed
Bowen,
Mi-2/NuRD: multiple complexes for many purposes.
2004,
Pubmed
Brehm,
dMi-2 and ISWI chromatin remodelling factors have distinct nucleosome binding and mobilization properties.
2000,
Pubmed
Brenner,
The genetics of Caenorhabditis elegans.
1974,
Pubmed
Chen,
C. elegans Rb, NuRD, and Ras regulate lin-39-mediated cell fusion during vulval fate specification.
2001,
Pubmed
Chen,
Role of C. elegans lin-40 MTA in vulval fate specification and morphogenesis.
2001,
Pubmed
Chuang,
Sex-specific assembly of a dosage compensation complex on the nematode X chromosome.
1996,
Pubmed
Couteau,
HTP-1 coordinates synaptonemal complex assembly with homolog alignment during meiosis in C. elegans.
2005,
Pubmed
Denslow,
The human Mi-2/NuRD complex and gene regulation.
2007,
Pubmed
Dufourcq,
Functional requirement for histone deacetylase 1 in Caenorhabditis elegans gonadogenesis.
2002,
Pubmed
Felsenstein,
Phylogenies from molecular sequences: inference and reliability.
1988,
Pubmed
Ge,
Molecular analysis of a major antigenic region of the 240-kD protein of Mi-2 autoantigen.
1995,
Pubmed
Goodyer,
HTP-3 links DSB formation with homolog pairing and crossing over during C. elegans meiosis.
2008,
Pubmed
Gould,
Tandem affinity purification and identification of protein complex components.
2004,
Pubmed
Guerry,
The Mi-2 nucleosome-remodeling protein LET-418 is targeted via LIN-1/ETS to the promoter of lin-39/Hox during vulval development in C. elegans.
2007,
Pubmed
Gutierrez,
Evolution of dnmt-2 and mbd-2-like genes in the free-living nematodes Pristionchus pacificus, Caenorhabditis elegans and Caenorhabditis briggsae.
2004,
Pubmed
Harrison,
Some C. elegans class B synthetic multivulva proteins encode a conserved LIN-35 Rb-containing complex distinct from a NuRD-like complex.
2006,
Pubmed
Harrison,
LIN-61, one of two Caenorhabditis elegans malignant-brain-tumor-repeat-containing proteins, acts with the DRM and NuRD-like protein complexes in vulval development but not in certain other biological processes.
2007,
Pubmed
Hellman,
Improvement of an "In-Gel" digestion procedure for the micropreparation of internal protein fragments for amino acid sequencing.
1995,
Pubmed
Herman,
EGL-27 is similar to a metastasis-associated factor and controls cell polarity and cell migration in C. elegans.
1999,
Pubmed
Ho,
Chromatin remodelling during development.
2010,
Pubmed
Hubbell,
Robust estimators for expression analysis.
2002,
Pubmed
Kiefer,
PHA-4/FoxA cooperates with TAM-1/TRIM to regulate cell fate restriction in the C. elegans foregut.
2007,
Pubmed
Kon,
Developmental roles of the Mi-2/NURD-associated protein p66 in Drosophila.
2005,
Pubmed
,
Xenbase
Kunert,
dMec: a novel Mi-2 chromatin remodelling complex involved in transcriptional repression.
2009,
Pubmed
Lu,
lin-35 and lin-53, two genes that antagonize a C. elegans Ras pathway, encode proteins similar to Rb and its binding protein RbAp48.
1998,
Pubmed
Lynch,
The altered evolutionary trajectories of gene duplicates.
2004,
Pubmed
Marhold,
The Drosophila methyl-DNA binding protein MBD2/3 interacts with the NuRD complex via p55 and MI-2.
2004,
Pubmed
Murawska,
dCHD3, a novel ATP-dependent chromatin remodeler associated with sites of active transcription.
2008,
Pubmed
Nan,
Transcriptional repression by the methyl-CpG-binding protein MeCP2 involves a histone deacetylase complex.
1998,
Pubmed
Poulin,
Chromatin regulation and sumoylation in the inhibition of Ras-induced vulval development in Caenorhabditis elegans.
2005,
Pubmed
Puig,
The tandem affinity purification (TAP) method: a general procedure of protein complex purification.
2001,
Pubmed
Reinke,
Genome-wide germline-enriched and sex-biased expression profiles in Caenorhabditis elegans.
2004,
Pubmed
Rocheleau,
WRM-1 activates the LIT-1 protein kinase to transduce anterior/posterior polarity signals in C. elegans.
1999,
Pubmed
Seelig,
The major dermatomyositis-specific Mi-2 autoantigen is a presumed helicase involved in transcriptional activation.
1995,
Pubmed
Shakhnovich,
Origins and impact of constraints in evolution of gene families.
2006,
Pubmed
Shi,
A CBP/p300 homolog specifies multiple differentiation pathways in Caenorhabditis elegans.
1998,
Pubmed
Siegfried,
POP-1 controls axis formation during early gonadogenesis in C. elegans.
2002,
Pubmed
Solari,
NURD-complex genes antagonise Ras-induced vulval development in Caenorhabditis elegans.
2000,
Pubmed
Sternberg,
Vulval development.
2005,
Pubmed
Thomas,
New genes that interact with lin-35 Rb to negatively regulate the let-60 ras pathway in Caenorhabditis elegans.
2003,
Pubmed
Unhavaithaya,
MEP-1 and a homolog of the NURD complex component Mi-2 act together to maintain germline-soma distinctions in C. elegans.
2002,
Pubmed
Updike,
P granule assembly and function in Caenorhabditis elegans germ cells.
2010,
Pubmed
Wang,
Identification of genes expressed in the hermaphrodite germ line of C. elegans using SAGE.
2009,
Pubmed
Yuzyuk,
The polycomb complex protein mes-2/E(z) promotes the transition from developmental plasticity to differentiation in C. elegans embryos.
2009,
Pubmed
von Zelewsky,
The C. elegans Mi-2 chromatin-remodelling proteins function in vulval cell fate determination.
2000,
Pubmed
