Drosophila SWR1 and NuA4 complexes are defined by DOMINO isoforms

Histone acetylation and deposition of H2A.Z variant are integral aspects of active transcription. In Drosophila, the single DOMINO chromatin regulator complex is thought to combine both activities via an unknown mechanism. Here we show that alternative isoforms of the DOMINO nucleosome remodeling ATPase, DOM-A and DOM-B, directly specify two distinct multi-subunit complexes. Both complexes are necessary for transcriptional regulation but through different mechanisms. The DOM-B complex incorporates H2A.V (the fly ortholog of H2A.Z) genome-wide in an ATP-dependent manner, like the yeast SWR1 complex. The DOM-A complex, instead, functions as an ATP-independent histone acetyltransferase complex similar to the yeast NuA4, targeting lysine 12 of histone H4. Our work provides an instructive example of how different evolutionary strategies lead to similar functional separation. In yeast and humans, nucleosome remodeling and histone acetyltransferase complexes originate from gene duplication and paralog specification. Drosophila generates the same diversity by alternative splicing of a single gene

The first myriapod genome sequence reveals conservative arthropod gene content and genome organisation in the centipede Strigamia maritima.

Myriapods (e.g., centipedes and millipedes) display a simple homonomous body plan relative to other arthropods. All members of the class are terrestrial, but they attained terrestriality independently of insects. Myriapoda is the only arthropod class not represented by a sequenced genome. We present an analysis of the genome of the centipede Strigamia maritima. It retains a compact genome that has undergone less gene loss and shuffling than previously sequenced arthropods, and many orthologues of genes conserved from the bilaterian ancestor that have been lost in insects. Our analysis locates many genes in conserved macro-synteny contexts, and many small-scale examples of gene clustering. We describe several examples where S. maritima shows different solutions from insects to similar problems. The insect olfactory receptor gene family is absent from S. maritima, and olfaction in air is likely effected by expansion of other receptor gene families. For some genes S. maritima has evolved paralogues to generate coding sequence diversity, where insects use alternate splicing. This is most striking for the Dscam gene, which in Drosophila generates more than 100,000 alternate splice forms, but in S. maritima is encoded by over 100 paralogues. We see an intriguing linkage between the absence of any known photosensory proteins in a blind organism and the additional absence of canonical circadian clock genes. The phylogenetic position of myriapods allows us to identify where in arthropod phylogeny several particular molecular mechanisms and traits emerged. For example, we conclude that juvenile hormone signalling evolved with the emergence of the exoskeleton in the arthropods and that RR-1 containing cuticle proteins evolved in the lineage leading to Mandibulata. We also identify when various gene expansions and losses occurred. The genome of S. maritima offers us a unique glimpse into the ancestral arthropod genome, while also displaying many adaptations to its specific life history.This work was supported by the following grants: NHGRIU54HG003273 to R.A.G; EU Marie Curie ITN #215781 “Evonet” to M.A.; a Wellcome Trust Value in People (VIP) award to C.B. and Wellcome Trust graduate studentship WT089615MA to J.E.G; Marine rhythms of Life” of the University of Vienna, an FWF (http://www.fwf.ac.at/) START award (#AY0041321) and HFSP (http://www.hfsp.org/) research grant (#RGY0082/2010) to KT-­‐R; MFPL Vienna International PostDoctoral Program for Molecular Life Sciences (funded by Austrian Ministry of Science and Research and City of Vienna, Cultural Department -­‐Science and Research to T.K; Direct Grant (4053034) of the Chinese University of Hong Kong to J.H.L.H.; NHGRI HG004164 to G.M.; Danish Research Agency (FNU), Carlsberg Foundation, and Lundbeck Foundation to C.J.P.G.; U.S. National Institutes of Health R01AI55624 to J.H.W.; Royal Society University Research fellowship to F.M.J.; P.D.E. was supported by the BBSRC via the Babraham Institute;This is the final version of the article. It first appeared from PLOS via http://dx.doi.org/10.1371/journal.pbio.100200

Ο ρόλος των παραγόντων NER στην ανάπτυξη και τη φυσιολογία του ποντικού

Inborn mutations in genes of the Nucleotide Excision Repair (NER) pathway are known to be associated with syndromes showing clinical features with severe developmental abnormalities. However, little is known about the functional role of NER factors in mammalian development. Using a new knock-in mouse model expressing the NER structure-specific endonuclease XPF fused with a FTA-tag that gets specifically biotinylated by the bacterial ligase BirA, we performed pull-down experiments followed by mass spectrometry (MS) to isolate and characterize NER-associated protein complexes during postnatal murine development. We identified 140 XPF-bound core proteins that were common between three replicate experiments. By analyzing the MS data and verifying the interactions by co-immunoprecipitation, we were able to characterize a new protein complex that consists of ERCC1-XPF, CTCF, SMC1A, SMC3 and MBD2. Ablation of Ercc1 or exposure to DNA-damage agents causing intra-stand crosslinks (ICLs) triggers the localization of CTCF to heterochromatin regions in the nucleus and the dissociation of CTCF, SMC1A, SMC3 and ATRX from promoters and imprinting control regions (ICRs) of imprinted genes. In line with these findings, we also observe altered histone post-translational modification (PTMs) marks and the recruitment of RNAPII and basal transcription factors on promoters of imprinted genes. As a result Ercc1 depleted mice show aberrant developmental expression of a subset of imprinted genes without the DNA methylation status of their ICRs being affected. This response is cell-autonomous and requires signaling by ATM. We propose that ERCC1-XPF binds CTCF, SMC1A, SMC3 and MBD2 to form a complex required for the developmental silencing of imprinted genes and that persistent DNA damage signaling triggers chromatin changes that affect gene expression programs associated with NER developmental disorders.Έμφυτες μεταλλάξεις σε γονίδια του μονοπατιού επιδιόρθωσης εκτομής νουκλεοτιδίων (NER) είναι γνωστό ότι σχετίζονται με σύνδρομα που φέρουν σοβαρές αναπτυξιακές ανωμαλίες. Ωστόσο, λίγα είναι γνωστά για τον λειτουργικό ρόλο των παραγόντων του NER μονοπατιού στην ανάπτυξη των θηλαστικών. Χρησιμοποιώντας ένα νέο knock-in μοντέλο ποντικού που εκφράζει την XPF ενδονουκλεάση συντηγμένη με ένα FTA-tag το οποίο βιοτινυλιώνεται ειδικά από την βακτηριακή λιγάση ΒirΑ, πραγματοποιήσαμε πειράματα pull-down σε συνδιασμό με πειράματα φασματομετρία μάζας (MS) για να απομονώσουμε και να χαρακτηρίσουμε σύμπλοκα πρωτεϊνών που αλληλεπιδρούν με την XPF κατά τη διάρκεια της μεταγεννητικής ανάπτυξης του ποντικού. Εντοπίσαμε 140 πρωτεΐνες που αλληλεπιδρούν με την XPF οι οποίες ήταν κοινές μεταξύ τριών πανομοιότυπων πειραμάτων. Με την ανάλυση των δεδομένων από τα πειράματα φασματομετρία μάζας και την επαλήθευση των αλληλεπιδράσεων με πειράματα ανοσοκατακρήμνισης, ήμασταν σε θέση να χαρακτηρίσουμε ένα νέο σύμπλοκο πρωτεϊνών που απαρτίζεται από τις ERCC1-XPF, CTCF, SMC1A, SMC3 και MBD2. Απαλοιφή της ERCC1 ή έκθεση σε παράγοντες που προκαλούν ICLs βλάβες στο DNA προκαλούν τον εντοπισμό του CTCF σε ετεροχρωματινικές περιοχές στον πυρήνα και την αποδέσμευση των CTCF, SMC1A, SMC3 και ATRX από υποκινητές και ρυθμιστικές περιοχές ICR των αποτυπωμένων γονιδίων. Σύμφωνα με τα ευρήματα αυτά, παρατηρούμε επίσης αλλαγή των μετα-μεταφραστικών τροποποιήσεων (PTMs) των ιστονών και την στρατολόγηση της RNAPII και βασικών μεταγραφικών παραγόντων σε υποκινητές και ρυθμιστικές περιοχές ICR των αποτυπωμένων γονιδίων. Ως αποτέλεσμα τα Ercc1-/- ποντίκια εμφανίζουν ανώμαλη έκφραση ενός υποσυνόλου αποτυπωμένων γονιδίων χωρίς να παρατηρείται διαταραχή στο πρότυπο μεθυλίωσης του DNA των ρυθμιστικών περιοχών ICRs των αποτυπωμένων γονιδίων. Αυτή η απόκριση είναι8κυτταρικά αυτόνομη και απαιτεί τη σηματοδότηση του παράγοντα ΑΤΜ. Προτείνουμε ότι η ERCC1-XPF δεσμεύει τους CTCF, SMC1A, SMC3 και MBD2 για να σχηματίσει ένα σύμπλοκο που απαιτείται για την αναπτυξιακή αποσιώπηση αποτυπωμένων γονιδίων και ότι συνεχείς βλάβες στο DNA πυροδότουν αλλαγές στη χρωματίνη επηρεάζοντας με τον τρόπο αυτό προγράμματα γονιδιακής έκφρασης που σχετίζονται με αναπτυξιακές διαταραχές του μονοπατιού NER

The first myriapod genome sequence reveals conservative arthropod gene content and genome organisation in the centipede Strigamia maritima.

Myriapods (e.g., centipedes and millipedes) display a simple homonomous body plan relative to other arthropods. All members of the class are terrestrial, but they attained terrestriality independently of insects. Myriapoda is the only arthropod class not represented by a sequenced genome. We present an analysis of the genome of the centipede Strigamia maritima. It retains a compact genome that has undergone less gene loss and shuffling than previously sequenced arthropods, and many orthologues of genes conserved from the bilaterian ancestor that have been lost in insects. Our analysis locates many genes in conserved macro-synteny contexts, and many small-scale examples of gene clustering. We describe several examples where S. maritima shows different solutions from insects to similar problems. The insect olfactory receptor gene family is absent from S. maritima, and olfaction in air is likely effected by expansion of other receptor gene families. For some genes S. maritima has evolved paralogues to generate coding sequence diversity, where insects use alternate splicing. This is most striking for the Dscam gene, which in Drosophila generates more than 100,000 alternate splice forms, but in S. maritima is encoded by over 100 paralogues. We see an intriguing linkage between the absence of any known photosensory proteins in a blind organism and the additional absence of canonical circadian clock genes. The phylogenetic position of myriapods allows us to identify where in arthropod phylogeny several particular molecular mechanisms and traits emerged. For example, we conclude that juvenile hormone signalling evolved with the emergence of the exoskeleton in the arthropods and that RR-1 containing cuticle proteins evolved in the lineage leading to Mandibulata. We also identify when various gene expansions and losses occurred. The genome of S. maritima offers us a unique glimpse into the ancestral arthropod genome, while also displaying many adaptations to its specific life history

Ancestral protein kinases are extensively lost during arthropod evolution.

<p><i>S. maritima</i> is an exception and retains the largest number of ancestral kinases. Numbers of kinase subfamilies in selected species are shown in parentheses after species names. The gains, losses, and inferred content of common ancestors are listed on internal branches. Kinases found in at least two species from human, <i>C. elegans</i> and <i>Nematostella vectenesis</i> were used as an outgroup.</p

Expansion of chemosensory receptor families.

<p>(A) Phylogenetic relationships among <i>S. maritima</i> (Smar), <i>I. scapularis</i> (Isca), <i>D. pulex</i> (Dpul), and a few insect GRs that encode for sugar, fructose, and carbon dioxide receptors (Dmel, <i>D. melanogaster</i>, and Amel, <i>A. mellifera</i>). (B) Phylogenetic relationships among <i>S. maritima</i>, <i>I. scapularis</i>, and a few <i>D. melanogaster</i> IRs and IgluR genes (the suffix at the end of the protein names indicates: i, incomplete and p, pseudogene).</p

Presence and absence of immunity genes in different arthropods.

<p>Counts of immune genes are shown for <i>S. maritima</i>, <i>D. pulex</i><a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.1002005#pbio.1002005-McTaggart1" target="_blank">[131]</a>, <i>A. mellifera</i><a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.1002005#pbio.1002005-Evans1" target="_blank">[86]</a>, <i>T. castaneum</i>, <i>Anopheles gambiae</i>, and <i>D. melanogaster</i><a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.1002005#pbio.1002005-Dasmahapatra1" target="_blank">[132]</a>. ∼, identity of the gene is uncertain; -, not investigated.</p

Dscam diversity caused either by gene and/or exon duplication in different Metazoa.

<p>^aOnly canonical Dscam paralogues were considered. ^bIn <i>D. melanogaster</i> and <i>D. pulex</i> the paralogue Dscam-L2 has two Ig7 alternative coding exons. ^cPotential number of Dscam isoforms, circulating in one individual, produced by mutually exclusive alternative splicing of duplicated exons.</p