AAGAG repeat RNA is an essential component of nuclear matrix in<i><i>Drosophila</i></i>

Pathak, Rashmi U.; Mamillapalli, Anitha; Rangaraj, Nandini; Kumar, Ram P.; Dasari, Vasanthi; Mishra, Krishnaveni; Mishra, Rakesh

doi:10.4161/rna.24326

Cited by 54 publications

(45 citation statements)

References 61 publications

(60 reference statements)

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“…Yet, we find that certain organisms have a capacity to accumulate and tolerate high repeat lengths. We have previously shown that AAGAG repeats get transcribed and are important constituents of nuclear matrix in Drosophila (Pathak, et al 2013). Transcription from a few long non coding loci can trigger a large number of associated loci or cluster them into specific compartments, thereby acting as switches for coordinated genome regulation.…”

Section: Ssrs Have Subgroup-specific Preferences For Longer Ssr Lengthsmentioning

confidence: 99%

“…Hence, this work cannot address whether these elements are a consequence of DNA repair / replication errors or mutational mechanisms. Many factors may be at play including, but not limited to, positive selection for repeat expansion (Li, et al 2004), binding sites for proteins (Hu, et al 2007;Liu, et al 2017), effect on DNA structure and formation of secondary structures affecting transcription (reviewed in (Li, et al 2002)), and relationships with high-order chromatin structure and genomic function Pathak, et al 2013).…”

Section: Ssrs Operate Under Selection Pressurementioning

confidence: 99%

“…A few studies have also highlighted the roles of SSRs in genome organization. AGAT repeats of 40-48nt length are shown to function as enhancer-blockers in both Drosophila and human cells , while transcripts arising from AAGAG repeats have been identified as important constituents of nuclear matrix in Drosophila embryos (Pathak, et al 2013).…”

Section: Introductionmentioning

confidence: 99%

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Patterns of microsatellite distribution reflect the evolution of biological complexity

Surabhi

Avvaru

Sowpati

et al. 2018

Preprint

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Microsatellites, also known as Simple Sequence Repeats (SSRs), are evolutionarily conserved repeat elements distributed non-randomly in all genomes. Many studies have investigated their pattern of occurrence in order to understand their role, but their identification has largely been nonexhaustive and limited to a few related species or model organisms. Here, we identify ~685 million microsatellites from 719 eukaryotes and analyze their evolutionary trends from protists to mammals. We document novel patterns uniquely demarcating closely related species, including in pathogens like Leishmania as well as in higher organisms such as Drosophila, birds, primates, and cereal crops. The distribution of SSRs in coding and non-coding regions reveals taxon-specific variations in their exonic, intronic and intergenic densities. We also show that specific SSRs accumulate at longer lengths in higher organisms indicating an evolutionary selection pressure. In general, we observe greater constraints in the SSR composition of multicellular organisms with complex cell types, while simpler organisms show more diversity. The conserved microsatellite trends and species-specific signatures identified in this study closely mirror phylogenetic relationships and we hypothesize that SSRs are integral components in speciation and the evolution of organismal complexity. The microsatellite dataset generated in this work provides a large number of candidates for functional analysis and unparalleled scope for understanding their roles across the evolutionary landscape.peer-reviewed)

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Section: Ssrs Have Subgroup-specific Preferences For Longer Ssr Lengthsmentioning

confidence: 99%

Section: Ssrs Operate Under Selection Pressurementioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Patterns of microsatellite distribution reflect the evolution of biological complexity

Surabhi

Avvaru

Sowpati

et al. 2018

Preprint

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“…1). Further characterizations and functional analyses were focused on AAGAG(n) RNA (hereafter AAGAG RNA) because it is highly abundant and linked to the nuclear matrix 16 .…”

Section: Introductionmentioning

confidence: 99%

RNA transcribed from heterochromatic simple-tandem repeats are required for male fertility and histone-protamine exchange in Drosophila melanogaster

Ycg

et al. 2019

Preprint

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Long arrays of simple, tandemly repeated DNA sequences (known as satellites) are enriched in centromeres 1 and pericentromeric regions 2 , and contribute to chromosome segregation and other heterochromatin functions 3,4 . Surprisingly, satellite DNAs are expressed in many multicellular eukaryotes, and their aberrant transcription may contribute to carcinogenesis and cellular toxicity 5-7 . Satellite transcription and/or RNAs may also promote centromere and heterochromatin activities 8-12 . However, we lack direct evidence that satellite DNA transcripts are required for normal cell or organismal functions. Here, we show that satellite RNAs derived from AAGAG tandem repeats are transcribed in many cell types throughout Drosophila melanogaster development, enriched in neuronal tissues and testes, localized within heterochromatic regions, and important for viability. Strikingly, we find that AAGAG transcripts are necessary for male fertility and are specifically required for normal histone-protamine exchange and sperm chromatin organization. Since AAGAG RNA-dependent events happen late in spermatogenesis when the transcripts are not detected, we speculate that AAGAG RNA functions in primary spermatocytes to 'prime' post-meiosis steps in sperm maturation. In addition to demonstrating specific essential functions for AAGAG RNAs, comparisons between closely related Drosophila species suggest that satellite repeats and their transcription evolve quickly to generate new functions.

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“…cancer and neurological disorders), [reviewed in (Boland and Goel, 2010, Shokal and Sharma, 2012, Polyzos and McMurray, 2017, Pearson et al, 2005, Richard et al, 2008)]. STR polymorphisms also play a role in gene expression variation (Gymrek et al, 2016), alternative splicing (Hui et al, 2005), chromatin packaging (Kirkpatrick et al, 1999), and nuclear organization (Pathak et al, 2013) [reviewed also in (Bagshaw, 2017)]. In spite of the functional importance of STRs, our understanding of the drivers of their evolution is far from complete [reviewed in (Ellegren, 2004, Richard et al, 2008)], with mononucleotide repeats, the second most common repeat type in the human genome, particularly neglected due to the difficulty of accurately determining their lengths [reviewed in (Ellegren, 2004, Zavodna et al, 2018)).…”

Section: Introductionmentioning

confidence: 99%

Length asymmetry and heterozygosity strongly influences the evolution of poly-A microsatellites at meiotic recombination hotspots

Heissl

Betancourt

Hermann

et al. 2018

Preprint

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Meiotic recombination has strong, but poorly understood, effects on short tandem repeat (STR) instability. Here, we screened thousands of single recombinant products to characterize the transmission and evolution of polymorphic poly-A repeats at a human recombination hotspot. We show that length asymmetry between heterozygous poly-As plays a key role in the recombination outcome and their transmission. A difference of 10 As (9A/19A) elevates the frequency of non-crossovers, complex recombination products, and long conversion tracts. Moreover, asymmetry also influences STR transmission: the shorter allele is transmitted more frequently (deletion bias) at the asymmetric STR (9A/19A), while the longer allele is favored (insertion bias) at the site with a small STR length difference (6A/7A). Finally, potentially due to this opposing insertion/deletion driven evolution, we find that poly-As are enriched at human recombination hotspots predominantly with short poly-As, possibly influencing open chromatin regions that in turn can activate hotspots.

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AAGAG repeat RNA is an essential component of nuclear matrix inDrosophila

Cited by 54 publications

References 61 publications

Patterns of microsatellite distribution reflect the evolution of biological complexity

Patterns of microsatellite distribution reflect the evolution of biological complexity

RNA transcribed from heterochromatic simple-tandem repeats are required for male fertility and histone-protamine exchange in Drosophila melanogaster

Length asymmetry and heterozygosity strongly influences the evolution of poly-A microsatellites at meiotic recombination hotspots

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