A new class of retroviral and satellite encoded small RNAs emanates from mammalian centromeres

Carone, Dawn M.; Longo, Mark S.; Ferreri, Gianni C.; Hall, Laura; Harris, M.M.; Shook, Nicole A.; Bulazel, Kira V.; Carone, Benjamin R.; Obergfell, Craig; O’Neill, Michael; O’Neill, Rachel J.

doi:10.1007/s00412-008-0181-5

Cited by 126 publications

(119 citation statements)

References 52 publications

(82 reference statements)

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“…KERV was previously mapped to chromosome 7 in M. eugenii (23), and we cannot confirm the absence of KERV on the M. rufogriseus sex chromosomes if proviral genomes are present in low copy numbers. The KERV signal in M. rufogriseus spans the centromere and extends into the large pericentromeric regions, whereas the KERV signal in M. eugenii is restricted to the small pericentric/ centric regions (9,15). The in situ localization patterns confirm the KERV copy number differences observed between these Macropus species by quantitative PCR and Southern analyses.…”

Section: Vol 85 2011 Amplification Of Kangaroo Endogenous Retrovirusupporting

confidence: 67%

Recent Amplification of the Kangaroo Endogenous Retrovirus, KERV, Limited to the Centromere

Ferreri

Brown

Obergfell

et al. 2011

J Virol

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Mammalian retrotransposons, transposable elements that are processed through an RNA intermediate, are categorized as short interspersed elements (SINEs), long interspersed elements (LINEs), and long terminal repeat (LTR) retroelements, which include endogenous retroviruses. The ability of transposable elements to autonomously amplify led to their initial characterization as selfish or junk DNA; however, it is now known that they may acquire specific cellular functions in a genome and are implicated in host defense mechanisms as well as in genome evolution. Interactions between classes of transposable elements may exert a markedly different and potentially more significant effect on a genome than interactions between members of a single class of transposable elements. We examined the genomic structure and evolution of the kangaroo endogenous retrovirus (KERV) in the marsupial genus Macropus. The complete proviral structure of the kangaroo endogenous retrovirus, phylogenetic relationship among relative retroviruses, and expression of this virus in both Macropus rufogriseus and M. eugenii are presented for the first time. In addition, we show the relative copy number and distribution of the kangaroo endogenous retrovirus in the Macropus genus. Our data indicate that amplification of the kangaroo endogenous retrovirus occurred in a lineage-specific fashion, is restricted to the centromeres, and is not correlated with LINE depletion. Finally, analysis of KERV long terminal repeat sequences using massively parallel sequencing indicates that the recent amplification in M. rufogriseus is likely due to duplications and concerted evolution rather than a high number of independent insertion events.

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Section: Vol 85 2011 Amplification Of Kangaroo Endogenous Retrovirusupporting

confidence: 67%

Recent Amplification of the Kangaroo Endogenous Retrovirus, KERV, Limited to the Centromere

Ferreri

Brown

Obergfell

et al. 2011

J Virol

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“…Centromeric satellite and retroelement transcripts have been identified in a multitude of different organisms, including rice, maize, beetle, tammar wallaby, mouse, and human, and are of various sizes, from 35 to 5,000 nt in length (Topp et al 2004;BouzinbaSegard et al 2006;Lee et al 2006;Yan et al 2006;Pezer and Ugarković 2008;Carone et al 2009;Chueh et al 2009;Ferri et al 2009;Du et al 2010). CT levels, like PCT levels, can change depending on developmental stage and tissue type.…”

Section: Centromeric Transcriptionmentioning

confidence: 99%

“…For instance, in the beetle, more CTs are observed in the pupae stage than adult (Pezer and Ugarković 2008). In both the beetle and tammar wallaby, transcription of centromeric sequences can be seen from both strands (Pezer and Ugarković 2008;Carone et al 2009), implicating nearby bidirectional promoters within or adjacent to the sequences being transcribed (Lee et al 2006;Pezer and Ugarković 2008;Carone et al 2009). Since retroelement sequences contain their own promoters and are found at most centromeres, it is plausible that these promoters are utilized to transcribe retroelement and adjacent satellite sequences ).…”

Section: Centromeric Transcriptionmentioning

confidence: 99%

“…The function of the RNA may also be dependent on the type of repeat element being transcribed. For example, there are different subtypes of centromeric retroelements in rice and wallaby, and some of these subtypes are processed into small RNAs while others remain as long transcripts (Neumann et al 2007;Carone et al 2009;Ferreri et al 2011). Interestingly, some of these retroelement transcripts are also alternatively spliced resulting in the production of slightly different transcripts (Neumann et al 2007).…”

Section: Centromeric Transcriptionmentioning

confidence: 99%

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Pericentric and centromeric transcription: a perfect balance required

2012

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The pericentromere and centromere regions of the genome have previously been considered tightly compacted and transcriptionally inert. However, there is mounting evidence that these regions not only actively produce transcripts but that these pericentric and centromeric transcripts are also vital to maintaining genome stability and proper cell division. In this review, we define the pericentromere and centromere of eukaryotic chromosomes in terms of their histone modifications and their nascent transcripts. In addition, we present the currently known roles these transcripts play in heterochromatin formation, development, and differentiation, as well as their interaction with centromeric proteins, and ultimately centromere function. Recent work has added considerable complexity to the theoretical framework defining the innate requirement for pericentric and centromeric transcription. It is clear that maintaining a fine balance of transcriptional output is critical, as deviations from this balance result in centromere disfunction and genomic instability.

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“…Similarly, neocentromere formation can cause silencing of the underlying transgene in C. albicans (Ketel et al, 2009). Transcripts derived from centromeric repetitive DNA were reported in a number of plant and animal species (Topp et al, 2004;May et al, 2005;Wong et al, 2007;Carone et al, 2009). However, the transcription of centromeric DNA is likely associated with H3 nucleosomes within the centromeric cores.…”

Section: Transcription and Centromere Functionmentioning

confidence: 99%

Euchromatic Subdomains in Rice Centromeres Are Associated with Genes and Transcription

Kikuchi

Yan

et al. 2011

The Plant Cell

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The presence of the centromere-specific histone H3 variant, CENH3, defines centromeric (CEN) chromatin, but poorly understood epigenetic mechanisms determine its establishment and maintenance. CEN chromatin is embedded within pericentromeric heterochromatin in most higher eukaryotes, but, interestingly, it can show euchromatic characteristics; for example, the euchromatic histone modification mark dimethylated H3 Lys 4 (H3K4me2) is uniquely associated with animal centromeres. To examine the histone marks and chromatin properties of plant centromeres, we developed a genomic tiling array for four fully sequenced rice (Oryza sativa) centromeres and used chromatin immunoprecipitation-chip to study the patterns of four euchromatic histone modification marks: H3K4me2, trimethylated H3 Lys 4, trimethylated H3 Lys 36, and acetylated H3 Lys 4, 9. The vast majority of the four histone marks were associated with genes located in the H3 subdomains within the centromere cores. We demonstrate that H3K4me2 is not a ubiquitous component of rice CEN chromatin, and the euchromatic characteristics of rice CEN chromatin are hallmarks of the transcribed sequences embedded in the centromeric H3 subdomains. We propose that the transcribed sequences located in rice centromeres may provide a barrier preventing loading of CENH3 into the H3 subdomains. The separation of CENH3 and H3 subdomains in the centromere core may be favorable for the formation of three-dimensional centromere structure and for rice centromere function.

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A new class of retroviral and satellite encoded small RNAs emanates from mammalian centromeres

Cited by 126 publications

References 52 publications

Recent Amplification of the Kangaroo Endogenous Retrovirus, KERV, Limited to the Centromere

Recent Amplification of the Kangaroo Endogenous Retrovirus, KERV, Limited to the Centromere

Pericentric and centromeric transcription: a perfect balance required

Euchromatic Subdomains in Rice Centromeres Are Associated with Genes and Transcription

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