Flanking genes of an essential gene give information about the evolution of metazoa

Zimek, Alexander; Weber, Klaus

doi:10.1016/j.ejcb.2010.10.005

Cited by 9 publications

(6 citation statements)

References 22 publications

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“…Because these proteins, especially the components of PRC2, are bound by many lncRNAs, we speculated that not all of the low-scoring hits were functionally irrelevant. A popular method to roughly determine whether a DNA sequence is functional is to evaluate its conserved context [45-47]. We examined the hits of all of the queries in human, chimpanzee, mouse, rat and platypus.…”

Section: Resultsmentioning

confidence: 99%

The sequence, structure and evolutionary features of HOTAIR in mammals

2011

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BackgroundAn increasing number of long noncoding RNAs (lncRNAs) have been identified recently. Different from all the others that function in cis to regulate local gene expression, the newly identified HOTAIR is located between HoxC11 and HoxC12 in the human genome and regulates HoxD expression in multiple tissues. Like the well-characterised lncRNA Xist, HOTAIR binds to polycomb proteins to methylate histones at multiple HoxD loci, but unlike Xist, many details of its structure and function, as well as the trans regulation, remain unclear. Moreover, HOTAIR is involved in the aberrant regulation of gene expression in cancer.ResultsTo identify conserved domains in HOTAIR and study the phylogenetic distribution of this lncRNA, we searched the genomes of 10 mammalian and 3 non-mammalian vertebrates for matches to its 6 exons and the two conserved domains within the 1800 bp exon6 using Infernal. There was just one high-scoring hit for each mammal, but many low-scoring hits were found in both mammals and non-mammalian vertebrates. These hits and their flanking genes in four placental mammals and platypus were examined to determine whether HOTAIR contained elements shared by other lncRNAs. Several of the hits were within unknown transcripts or ncRNAs, many were within introns of, or antisense to, protein-coding genes, and conservation of the flanking genes was observed only between human and chimpanzee. Phylogenetic analysis revealed discrete evolutionary dynamics for orthologous sequences of HOTAIR exons. Exon1 at the 5' end and a domain in exon6 near the 3' end, which contain domains that bind to multiple proteins, have evolved faster in primates than in other mammals. Structures were predicted for exon1, two domains of exon6 and the full HOTAIR sequence. The sequence and structure of two fragments, in exon1 and the domain B of exon6 respectively, were identified to robustly occur in predicted structures of exon1, domain B of exon6 and the full HOTAIR in mammals.ConclusionsHOTAIR exists in mammals, has poorly conserved sequences and considerably conserved structures, and has evolved faster than nearby HoxC genes. Exons of HOTAIR show distinct evolutionary features, and a 239 bp domain in the 1804 bp exon6 is especially conserved. These features, together with the absence of some exons and sequences in mouse, rat and kangaroo, suggest ab initio generation of HOTAIR in marsupials. Structure prediction identifies two fragments in the 5' end exon1 and the 3' end domain B of exon6, with sequence and structure invariably occurring in various predicted structures of exon1, the domain B of exon6 and the full HOTAIR.

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Section: Resultsmentioning

confidence: 99%

The sequence, structure and evolutionary features of HOTAIR in mammals

2011

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“…2). Whereas the nuclear localization signal in bilateral metazoa involves 4 consecutive basic residues, the lamins from the two species of the radiata currently known show only 3 basic residues in the sequences KRSR (Hydra) and KRAR (Nematostella) (Zimek and Weber, 2011). The deduced protein sequence of 760 amino acids corresponds to a size of 85.4 kDa and shows a length like in protostomic metazoa (Zimek and Weber, 2008).…”

Section: Identification Of a Cytoplasmic Nematostella If Proteinmentioning

confidence: 97%

“…Because of the closeness of these values it is currently impossible to decide which mammalian IF protein is the obvious counterpart of Nematostella IF cytovec. Attempts to get information via flanking genes as previously done for lamin genes (Zimek and Weber, 2011) were not possible because of the gaps in the genome of Nematostella. We note however that in the primitive bilateral animal, the nematode C. elegans, there is firm in vivo and in vitro evidence for a keratin-like obligatory heteropolymer system, but no indication for an additional homopolymer system (Karabinos et al, 2003).…”

Section: Identification Of a Cytoplasmic Nematostella If Proteinmentioning

confidence: 99%

Genes encoding cytoplasmic intermediate filament proteins of vertebrates revisited: Identification of a cytoplasmic intermediate filament protein in the sea anemone Nematostella

Zimek

Thiering

Weber

et al. 2012

European Journal of Cell Biology

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The cytoskeleton is crucial in determining cell architecture, division, motility, transport processes and in local control of signal transduction. Relatives of actin and tubulin are expressed in all phyla, underlining the fundamental importance of conserved cytoskeletal functions. Intermediate filament proteins have evolved in parallel with tissue diversity in the animal kingdom, likely from the demand to adapt one class of cytoskeletal proteins to cell type-restricted functions. Up to now, the evolutionary origin of cytoplasmic intermediate filament proteins remains unknown. Using a known gene encoding a cytoplasmic intermediate filament protein from the hemichordate Saccoglossus kowalevskii, we have identified the first corresponding gene in the sea anemone Nematostella, tentatively named cytovec. Our data reveal a relationship of cytovec with Hydra vulgaris nematocilins A and B that also lack a CAAX box. In light of additional recent findings, our data show that cytoplasmic intermediate filament genes are present in the common ancestor of Cnidaria and Bilateria.

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“…LMNB1 encodes lamin B1, and LMNB2 encodes lamins B2 and B3. An evolutionary study of lamins suggested that all metazoan cells have at least one B-type lamin, and LMNB1 is the most ancient and conserved form of the lamin gene [43].…”

Section: The Nuclear Laminamentioning

confidence: 99%

Role of the Nuclear Lamina in Age-Associated Nuclear Reorganization and Inflammation

Kristiani

Kim

2020

Cells

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Aging is characterized by the gradual loss of tissue function and integrity. Activation of inflammatory responses accelerates the deterioration of cells and tissues. Many studies have shown that alteration of the components of the nuclear lamina is associated with inflammation, both in vivo and in vitro. However, the mechanism by which the nuclear lamina regulates inflammation is largely unknown. Recent studies have suggested that the nuclear lamina regulates both organization of the three-dimensional chromatin structure at the nuclear periphery and global gene expression, such as the expression of inflammatory response genes. Here, we discuss the current updates in the research on nuclear lamina alteration, activation of inflammation, and nuclear reorganization in models of cellular senescence and organismal aging.

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Flanking genes of an essential gene give information about the evolution of metazoa

Cited by 9 publications

References 22 publications

The sequence, structure and evolutionary features of HOTAIR in mammals

The sequence, structure and evolutionary features of HOTAIR in mammals

Genes encoding cytoplasmic intermediate filament proteins of vertebrates revisited: Identification of a cytoplasmic intermediate filament protein in the sea anemone Nematostella

Role of the Nuclear Lamina in Age-Associated Nuclear Reorganization and Inflammation

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