Distribution of intrachromosomal telomeric sequences (ITS) on Macaca fascicularis (Primates) chromosomes and their implication for chromosome evolution

Ruiz‐Herrera, Aurora; García, Francisca; Azzalin, Claus M.; Giulotto, Elena; Egozcue, J.; Ponsà, M.; Garcı́a, M.

doi:10.1007/s00439-002-0730-6

Cited by 65 publications

(80 citation statements)

References 61 publications

(71 reference statements)

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“…7D). Several high-copy-number repeat elements (up to 800 copies per haploid genome) are located near the telomeres but also along other regions in the largest Toxoplasma chromosomes (25,32,33).…”

Section: Identification Of a New Family Of Hmtase Related To Humanmentioning

confidence: 99%

SET8-Mediated Methylations of Histone H4 Lysine 20 Mark Silent Heterochromatic Domains in Apicomplexan Genomes

Sautel

Cannella

Bastien

et al. 2007

Molecular and Cellular Biology

119

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Posttranslational histone modifications modulate chromatin-templated processes in various biological systems. H4K20 methylation is considered to have an evolutionarily ancient role in DNA repair and genome integrity, while its function in heterochromatin function and gene expression is thought to have arisen later during evolution. Here, we identify and characterize H4K20 methylases of the Set8 family in Plasmodium and Toxoplasma, two medically important members of the protozoan phylum Apicomplexa. Remarkably, parasite Set8-related proteins display H4K20 mono-, di-, and trimethylase activities, in striking contrast to the monomethylase-restricted human Set8. Structurally, few residues forming the substrate-specific channel dictate enzyme methylation multiplicity. These enzymes are cell cycle regulated and focally enriched at pericentric and telomeric heterochromatin in both parasites. Collectively, our findings provide new insights into the evolution of Set8-mediated biochemical pathways, suggesting that the heterochromatic function of the marker is not restricted to metazoans. Thus, these lower eukaryotes have developed a diverse panel of biological stages through their high capacity to differentiate, and epigenetics only begins to emerge as a strong determinant of their biology.The fundamental unit of chromatin, termed the nucleosome, is subject to a dizzying array of posttranslational modifications, which work alone or in combination to constitute a histone code that regulates chromatin structure and function (18). Among these modifications, lysine methylations index chromatin regions, facilitating epigenetic organization of eukaryotic genomes. In contrast to other histone-modifying enzymes, histone lysine (K) methyltransferases (HKMTs) are enzymes devoted to the methylation of highly specific lysine residues which either promote gene activation (H3K4, H3K79, and H3K36) or generate a repressed chromatin state (H3K9, H3K27, and H4K20). With just one exception (Dot1p), these enzymes belong to the SET family. The SET domain, which initially took its name from the Drosophila genes Su(var)3-9, enhancer of zeste, and trithorax, is crucial for the catalytic activity of HKMTs (3, 9, 24). While lysine methylation mainly occurs on histone H3 tails, the only lysine residue of histone H4 shown to be methylated in vivo is lysine 20. Methylation of H4K20 is involved in a diverse array of nuclear processes, including gene silencing (12, 26), pericentric heterochromatin formation (37), mitotic regulation in metazoans (20, 21), and DNA damage checkpoint control in the cell cycle of Schizosaccharomyces pombe (35).A number of different SET proteins have been identified as being able to methylate H4K20, including metazoan Set8 (also named Pr-Set7) (12, 26), Drosophila ASH1 (2), murine NSD1 (30), mammalian SUV4-20H1/2 (37), and its S. pombe ortholog SET9 (35). The modification is evidently absent in several simple eukaryotes, such as Saccharomyces cerevisiae and the ciliated protozoan Tetrahymena thermophila (26). H4K20 methylati...

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Section: Identification Of a New Family Of Hmtase Related To Humanmentioning

confidence: 99%

SET8-Mediated Methylations of Histone H4 Lysine 20 Mark Silent Heterochromatic Domains in Apicomplexan Genomes

Sautel

Cannella

Bastien

et al. 2007

Molecular and Cellular Biology

119

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“…In Macaca fascicularis, genome many ITS coincide with chromosome fragile sites. (92) ITS may contain slightly diverged TTAGGG repeats but, in the Chinese hamster genome, many of them do not have internal sites for restriction nuclease HindIII and are associated with long (>100 kb) gene-free arrays hybridizing to telomeric probes. (93) The reasons for the apparent instability of ITS are unknown.…”

Section: Global Sine Clustering and Line Depletion In Gc-rich Gene-rimentioning

confidence: 99%

Regulation of mammalian gene expression by retroelements and non‐coding tandem repeats

Tomilin

2008

BioEssays

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Genomes of higher eukaryotes contain abundant non‐coding repeated sequences whose overall biological impact is unclear. They comprise two categories. The first consists of retrotransposon‐derived elements. These are three major families of retroelements (LINEs, SINEs and LTRs). SINEs are clustered in gene‐rich regions and are found in promoters of genes while LINEs are concentrated in gene‐poor regions and are depleted from promoters. The second class consists of non‐coding tandem repeats (satellite DNAs and TTAGGG arrays), which are associated with mammalian centromeres, heterochromatin and telomeres. Terminal TTAGGG arrays are involved in telomere capping and satellite DNAs are located in heterochromatin, which is implicated in transcription silencing by gene repositioning (relocalization). It is unknown whether interstitial TTAGGG sequences, which are present in many vertebrates, have a function. Here, evidence will be presented that retroelements and TTAGGG arrays are involved in regulation of gene expression. Retroelements can provide binding sites for transcription factors and protect promoter CpG islands from repressive chromatin modifications, and may be also involved in nuclear compartmentalization of transcriptionally active and inactive domains. Interstitial telomere‐like sequences can form dynamically maintained three‐dimensional nuclear networks of transcriptionally inactive domains, which may be involved in transcription silencing like classic heterochromatin. BioEssays 30:338–348, 2008. © 2008 Wiley Periodicals, Inc.

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“…Interstitial (TTAGGG)n-like sequence distribution was examined because of its potential role in subtelomeric recombination and telomere healing (Mondello et al 2000;Azzalin et al 2001;Ruiz-Herrera et al 2002), and its hypothesized role as a boundary element for subtelomeric DNA compartments (Flint et al 1997b). All significant RepeatMasker matches to the simple repeats (TTAGGG)n and (CCCTAA)n were counted as telomere-like sequence islands.…”

Section: Sequence Organization Of Subtelomeric Dnamentioning

confidence: 99%

Mapping and Initial Analysis of Human Subtelomeric Sequence Assemblies

Riethman¹,

Ambrosini²,

Castañeda³

et al. 2004

Genome Res.

115

119

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Physical mapping data were combined with public draft and finished sequences to derive subtelomeric sequence assemblies for each of the 41 genetically distinct human telomere regions. Sequence gaps that remain on the reference telomeres are generally small,well-defined,and for the most part,restricted to regions directly adjacent to the terminal (TTAGGG)n tract. Of the 20.66 Mb of subtelomeric DNA analyzed, 3.01 Mb are subtelomeric repeat sequences (Srpt),and an additional 2.11 Mb are segmental duplications. The subtelomeric sequence assemblies are enriched >25-fold in short,internal (TTAGGG)n-like sequences relative to the rest of the genome; a total of 114 (TTAGGG)n-like islands were found,55 within Srpt regions,35 within one-copy regions,11 at one-copy/Srpt or Srpt/segmental duplication boundaries,and 13 at the telomeric ends of assemblies. Transcripts were annotated in each assembly,noting their mapping coordinates relative to their respective telomere and whether they originate in duplicated DNA or single-copy DNA. A total of 697 transcripts were found in 15.53 Mb of one-copy DNA,76 transcripts in 2.11 Mb of segmentally duplicated DNA,and 168 transcripts in 3.01 Mb of Srpt sequence. This overall transcript density is similar (within ∼10%) to that found genome-wide. Zinc finger-containing genes and olfactory receptor genes are duplicated within and between multiple telomere regions

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Distribution of intrachromosomal telomeric sequences (ITS) on Macaca fascicularis (Primates) chromosomes and their implication for chromosome evolution

Cited by 65 publications

References 61 publications

SET8-Mediated Methylations of Histone H4 Lysine 20 Mark Silent Heterochromatic Domains in Apicomplexan Genomes

SET8-Mediated Methylations of Histone H4 Lysine 20 Mark Silent Heterochromatic Domains in Apicomplexan Genomes

Regulation of mammalian gene expression by retroelements and non‐coding tandem repeats

Mapping and Initial Analysis of Human Subtelomeric Sequence Assemblies

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