Linder B et al. (2004), The SNF2 domain protein family in higher verteb...

XB-ART-4096

Gene 2004 Feb 04;326:59-66. doi: 10.1016/j.gene.2003.09.053.

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The SNF2 domain protein family in higher vertebrates displays dynamic expression patterns in Xenopus laevis embryos.

Linder B , Cabot RA , Schwickert T , Rupp RA .

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All eukaryotes share a common nuclear infrastructure, in which DNA is packaged into nucleosomal chromatin. Its functional states, in particular the accessibility of the chromatin fiber to trans-acting factors, are determined by two classes of evolutionarily conserved enzymes, i.e. histone modifying enzymes and ATP-driven nucleosome remodeling machines. Browsing the annotated human genome database, we establish here a family of SNF2-like nuclear ATPases, which are the core enzymatic subunits of chromatin remodeling protein complexes. Homologues of those human genes are also to a large extent found in the Xenopus laevis genome, indicating a high degree of sequence conservation of this family among vertebrates. Expression analyses of the ATPase family of proteins reveal stage- and tissue-specific domains of peak RNA expression during early frog embryogenesis. These dynamic expression profiles suggest specific functional requirements for individual members of this family throughout early stages of vertebrate development.

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Species referenced: Xenopus laevis
Genes referenced: atrx btaf1 chd1 chd2 chd3 chd4 chd5 chd6 chd7 chd8 crebbp ep400 foxe1 hells hltf ino80 rad54l rad54l2 smarca2 smarca4 smarca5 smarcad1 smarcal1 srcap tbp ttf2

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	Fig. 1. Overview of the human SNF2-domain family of ATPases. The cartoons of SNF2-domain members represent in each case the longest single database entry currently available (not drawn to scale), showing characteristic domains and their relative position within the open reading frames. Partial cDNA entries are indicated with p.s., all other entries contain putative full-length sequences.
	Fig. 2. Sequence similarity tree of the human SNF2-domain containing proteins. The amino acid sequences comprising of the SNF2-domains of the human SNF2-like ATPases indicated above were aligned using the ClustalW alignment program in the MegAlign module of the DNA STAR software package (version 4.0). Two main branches can be distinguished due to sequence similarity.
	Fig. 3. Expression patterns of Xenopus SNF2-domain proteins. (A) Top left shows a cartoon of a Xenopus embryo at the tailbud stage. Relevant tissues are marked by arrows: b.a.: branchial arches, otic v.: otic vesicle, vbi: ventral blood islands. All other pictures show representative photographs of mRNA whole mount hybridisations of Xenopus tailbud embryos (St. 28-35 according to Nieuwkoop and Faber (1967)) according to the subgroups of Table 1. Peak expression domains are in detail discussed in the text. Anterior is to the left and dorsal side up. (B) Expression pattern of xBrm. Slightly oblique transversal sections of a tailbud stage embryo stained for xBrm mRNA. Panel a: section of the head region with Brm expression in the neural tube (nt), cranial neural crest (nc), lens (l) and the head mesoderm (hm) and to a lower extend in th retina (r), but not in heart (h). Panel b shows a blow up of the eye with specific staining in the proliferative ciliary marginal zone (cmz) and lens; Brm is not expressed in differentiated retinal cells (nr). Panel c shows a section of the anterior trunk with peak expression domains in the pronephric anlage (pa) and to a lesser extent in the spinal chord (sc). Panel d shows a section in the mid-trunk region, strong staining in somites (so) and notochord (no) is visible but not in the spinal chord.
	atrx (alpha thalassemia/mental retardation syndrome X-linked) gene expression in Xenopus laevis embryo, assayed via in situ hybridization, NF stage 28, lateral view, anterior left, dorsal up.
	btaf1 (B-TFIID TATA-box binding protein associated factor 1) gene expression in Xenopus laevis embryo, assayed via in situ hybridization, NF stage 28, lateral view, anterior left, dorsal up.
	chd1 (chromodomain helicase DNA binding protein 1) gene expression in Xenopus laevis embryo, assayed via in situ hybridization, NF stage 28, lateral view, anterior left, dorsal up.
	chd2 (chromodomain helicase DNA binding protein 2) gene expression in Xenopus laevis embryo, assayed via in situ hybridization, NF stage 28, lateral view, anterior left, dorsal up.
	chd3 (chromodomain helicase DNA binding protein 3) gene expression in Xenopus laevis embryo, assayed via in situ hybridization, NF stage 28, lateral view, anterior left, dorsal up.
	chd4 (chromodomain helicase DNA binding protein 4) gene expression in Xenopus laevis embryo, assayed via in situ hybridization, NF stage 28, lateral view, anterior left, dorsal up.
	chd6 (chromodomain helicase DNA binding protein 6) gene expression in Xenopus laevis embryo, assayed via in situ hybridization, NF stage 28, lateral view, anterior left, dorsal up.
	chd7 (chromodomain helicase DNA binding protein 7) gene expression in Xenopus laevis embryo, assayed via in situ hybridization, NF stage 28, lateral view, anterior left, dorsal up.
	chd8 (chromodomain helicase DNA binding protein 8) gene expression in Xenopus laevis embryo, assayed via in situ hybridization, NF stage 28, lateral view, anterior left, dorsal up.
	ep400 (E1A binding protein p400) gene expression in Xenopus laevis embryo, assayed via in situ hybridization, NF stage 28, lateral view, anterior left, dorsal up.
	hltf (helicase-like transcription factor) gene expression in Xenopus laevis embryo, assayed via in situ hybridization, NF stage 28, lateral view, anterior left, dorsal up.
	ino80 (INO80 complex ATPase subunit) gene expression in Xenopus laevis embryo, assayed via in situ hybridization, NF stage 28, lateral view, anterior left, dorsal up.
	rad54l (RAD54-like) gene expression in Xenopus laevis embryo, assayed via in situ hybridization, NF stage 28, lateral view, anterior left, dorsal up.
	rad54l2 (RAD54-like 2) gene expression in Xenopus laevis embryo, assayed via in situ hybridization, NF stage 28, lateral view, anterior left, dorsal up.
	smarca2 (SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 2 ) gene expression in Xenopus laevis embryo, assayed via in situ hybridization, NF stage 28, lateral view, anterior left, dorsal up.
	smarca5 (SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 5) gene expression in Xenopus laevis embryo, assayed via in situ hybridization, NF stage 35, lateral view, anterior left, dorsal up.
	smarcad1 (SWI/SNF-related, matrix-associated actin-dependent regulator of chromatin, subfamily a, containing DEAD/H box 1) gene expression in Xenopus laevis embryo, assayed via in situ hybridization, NF stage 28, lateral view, anterior left, dorsal up.
	smarcal1 (SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a-like 1) gene expression in Xenopus laevis embryo, assayed via in situ hybridization, NF stage 28, lateral view, anterior left, dorsal up.
	srcap (Snf2-related CREBBP activator protein) gene expression in Xenopus laevis embryo, assayed via in situ hybridization, NF stage 28, lateral view, anterior left, dorsal up.
	ttf2 (transcription termination factor, RNA polymerase II) gene expression in Xenopus laevis embryo, assayed via in situ hybridization, NF stage 28, lateral view, anterior left, dorsal up.