scholarly journals piRNA clusters need a minimum size to control transposable element invasions

2019 ◽  
Author(s):  
Robert Kofler
Keyword(s):  
Population Genetics ◽  
Transposable Element ◽  
Minimum Size ◽  
Total Size ◽  
Evolutionary Forces ◽  
A Genome ◽  
In Trans ◽  
Element Activity ◽  
Single Insertion

AbstractpiRNA clusters are thought to repress transposable element activity in mammals and invertebrates. Here we show that a simple population genetics model reveals a constraint on the size of piRNA clusters: the total size of the piRNA clusters of an organism ought to exceed 0.2% of a genome. Larger piRNA clusters accounting for up to 3% of the genome may be necessary when populations are small, transposition rates are high and TE insertions recessive. If piRNA clusters are too small the load of deleterious TE insertions accumulating during a TE invasion may drive populations extinct before an effective piRNA based defence against the TE can be established. Our finding is solely based on three well supported assumptions: i) TEs multiply withing genomes, ii) TEs are mostly deleterious and iii) piRNA clusters act as transposons traps, where a single insertion in a cluster silences all TE copies in trans. Interestingly, piRNA clusters of some species meet our minimum size requirements while clusters of other species don’t. Species with small piRNA clusters, such as humans and mice, may experience severe fitness reductions during invasions of novel TEs, possibly even threatening the persistence of some populations. This work also raises the important question of how piRNA clusters evolve. We propose that the size of piRNA clusters may be at an equilibrium between evolutionary forces that act to expand and contract piRNA clusters.

scholarly journals piRNA Clusters Need a Minimum Size to Control Transposable Element Invasions

2020 ◽  
Vol 12 (5) ◽  
pp. 736-749 ◽  
Author(s):  
Robert Kofler
Keyword(s):  
Population Genetics ◽  
Transposable Element ◽  
Minimum Size ◽  
Total Size ◽  
Evolutionary Forces ◽  
A Genome ◽  
In Trans ◽  
Single Insertion

Abstract piRNA clusters are thought to repress transposable element (TE) activity in mammals and invertebrates. Here, we show that a simple population genetics model reveals a constraint on the size of piRNA clusters: The total size of the piRNA clusters of an organism must exceed 0.2% of a genome to repress TE invasions. Moreover, larger piRNA clusters accounting for up to 3% of the genome may be necessary when populations are small, transposition rates are high, and TE insertions are recessive. If piRNA clusters are too small, the load of deleterious TE insertions that accumulate during a TE invasion may drive populations extinct before an effective piRNA-based defense against the TE can be established. Our findings are solely based on three well-supported assumptions: 1) TEs multiply within genomes, 2) TEs are mostly deleterious, and 3) piRNA clusters act as transposon traps, where a single insertion in a cluster silences all TE copies in trans. Interestingly, the piRNA clusters of some species meet our observed minimum size requirements, whereas the clusters of other species do not. Species with small piRNA clusters, such as humans and mice, may experience severe fitness reductions during invasions of novel TEs, which is possibly even threatening the persistence of some populations. This work also raises the important question of how piRNA clusters evolve. We propose that the size of piRNA clusters may be at an equilibrium between evolutionary forces that act to expand and contract piRNA clusters.

scholarly journals R-STIPPLED MAIZE AS A TRANSPOSABLE ELEMENT SYSTEM

Genetics ◽  
1984 ◽  
Vol 107 (3) ◽  
pp. 477-488
Author(s):  
W M Williams ◽  
K V Satyanarayana ◽  
J L Kermicle
Keyword(s):  
Transposable Element ◽  
Pollen Grains ◽  
Linkage Phase ◽  
Element System ◽  
In Trans ◽  
A Site

ABSTRACT The I-R element at the R locus destabilizes kernel pigmentation giving the variegated pattern known as stippled (R-st). In trans linkage phase with R-st the element was shown to act as a modifier of stippled, intensifying seed spotting in parallel with effects of the dominant linked modifier M-st. Presence of I-R in the genome was, therefore, shown to be detectable as a modifier of R-st. When this test was used, new modifiers resembling M-st were often detected following mutations of R-st to the stable allele R-sc. Such mutations evidently occurred by transposition of I-R away from the R locus to a site where it was identifiable as a modifier. M-st may be such a transposed I-R. Analysis of mutations to R-sc during the second (sperm-forming) mitosis in pollen grains showed that some of the transposed I-R elements were linked with R, whereas others assorted independently. Their strengths varied from barely discernible to a level equal to M-st. Overreplication frequently accompanied transposition at the sperm-forming mitosis, leading to transposed I-R elements in both the mutant and nonmutant sperm.

scholarly journals Spatially coordinated heterochromatinization of distal short tandem repeats in fragile X syndrome

2021 ◽  
Author(s):  
Linda Zhou ◽  
Chunmin Ge ◽  
Thomas Malachowski ◽  
Ji Hun Kim ◽  
Keerthivasan Raanin Chandradoss ◽  
...  
Keyword(s):  
Fragile X Syndrome ◽  
Short Tandem Repeats ◽  
Tandem Repeats ◽  
Fragile X ◽  
Repeat Expansion ◽  
Genome Wide ◽  
A Genome ◽  
In Trans ◽  
Surveillance Mechanism ◽  
Short Tandem

AbstractShort tandem repeat (STR) instability is causally linked to pathologic transcriptional silencing in a subset of repeat expansion disorders. In fragile X syndrome (FXS), instability of a single CGG STR tract is thought to repress FMR1 via local DNA methylation. Here, we report the acquisition of more than ten Megabase-sized H3K9me3 domains in FXS, including a 5-8 Megabase block around FMR1. Distal H3K9me3 domains encompass synaptic genes with STR instability, and spatially co-localize in trans concurrently with FMR1 CGG expansion and the dissolution of TADs. CRISPR engineering of mutation-length FMR1 CGG to normal-length preserves heterochromatin, whereas cut-out to pre-mutation-length attenuates a subset of H3K9me3 domains. Overexpression of a pre-mutation-length CGG de-represses both FMR1 and distal heterochromatinized genes, indicating that long-range H3K9me3-mediated silencing is exquisitely sensitive to STR length. Together, our data uncover a genome-wide surveillance mechanism by which STR tracts spatially communicate over vast distances to heterochromatinize the pathologically unstable genome in FXS.One-Sentence SummaryHeterochromatinization of distal synaptic genes with repeat instability in fragile X is reversible by overexpression of a pre-mutation length CGG tract.

scholarly journals The impact of transposable element activity on therapeutically relevant human stem cells

Mobile DNA ◽  
2019 ◽  
Vol 10 (1) ◽  
Author(s):  
Gerald G. Schumann ◽  
Nina V. Fuchs ◽  
Pablo Tristán-Ramos ◽  
Attila Sebe ◽  
Zoltán Ivics ◽  
...  
Keyword(s):  
Stem Cells ◽  
Transposable Element ◽  
Human Stem Cells ◽  
Element Activity ◽  
The Impact

On the evolution and population genetics of hybrid-dysgenesis-causing transposable elements in Drosophila

1986 ◽  
Vol 312 (1154) ◽  
pp. 205-215 ◽  
Keyword(s):  
Population Genetics ◽  
Natural Selection ◽  
Transposable Elements ◽  
Transposable Element ◽  
Natural Populations ◽  
Element Composition ◽  
Hybrid Dysgenesis ◽  
Evolutionary Significance ◽  
Genetic Elements ◽  
Transposable Genetic Elements

Much has been learned about transposable genetic elements in Drosophila , but questions still remain, especially concerning their evolutionary significance. Three such questions are considered here, (i) Has the behaviour of transposable elements been most influenced by natural selection at the level of the organism, the population, or the elements themselves? (ii) How did the elements originate in the genome of the species? (iii) Why are laboratory stocks different from natural populations with respect to their transposable element composition? No final answers to these questions are yet available, but by focusing on the two families of hybrid dysgenesis-causing elements, the P and I factors, we can draw some tentative conclusions.

scholarly journals Genome-wide analysis and characterization of F-box gene family in Gossypium hirsutum L

BMC Genomics ◽  
2019 ◽  
Vol 20 (1) ◽  
Author(s):  
Shulin Zhang ◽  
Zailong Tian ◽  
Haipeng Li ◽  
Yutao Guo ◽  
Yanqi Zhang ◽  
...  
Keyword(s):  
Signal Transduction ◽  
Gossypium Hirsutum ◽  
Gene Family ◽  
Plant Species ◽  
26S Proteasome ◽  
Genome Wide Analysis ◽  
Evolutionary Forces ◽  
Genome Wide ◽  
A Genome ◽  
F Box Protein

Abstract Background F-box proteins are substrate-recognition components of the Skp1-Rbx1-Cul1-F-box protein (SCF) ubiquitin ligases. By selectively targeting the key regulatory proteins or enzymes for ubiquitination and 26S proteasome mediated degradation, F-box proteins play diverse roles in plant growth/development and in the responses of plants to both environmental and endogenous signals. Studies of F-box proteins from the model plant Arabidopsis and from many additional plant species have demonstrated that they belong to a super gene family, and function across almost all aspects of the plant life cycle. However, systematic exploration of F-box family genes in the important fiber crop cotton (Gossypium hirsutum) has not been previously performed. The genome-wide analysis of the cotton F-box gene family is now possible thanks to the completion of several cotton genome sequencing projects. Results In current study, we first conducted a genome-wide investigation of cotton F-box family genes by reference to the published F-box protein sequences from other plant species. 592 F-box protein encoding genes were identified in the Gossypium hirsutume acc.TM-1 genome and, subsequently, we were able to present their gene structures, chromosomal locations, syntenic relationships with their parent species. In addition, duplication modes analysis showed that cotton F-box genes were distributed to 26 chromosomes, with the maximum number of genes being detected on chromosome 5. Although the WGD (whole-genome duplication) mode seems play a dominant role during cotton F-box gene expansion process, other duplication modes including TD (tandem duplication), PD (proximal duplication), and TRD (transposed duplication) also contribute significantly to the evolutionary expansion of cotton F-box genes. Collectively, these bioinformatic analysis suggest possible evolutionary forces underlying F-box gene diversification. Additionally, we also conducted analyses of gene ontology, and expression profiles in silico, allowing identification of F-box gene members potentially involved in hormone signal transduction. Conclusion The results of this study provide first insights into the Gossypium hirsutum F-box gene family, which lays the foundation for future studies of functionality, particularly those involving F-box protein family members that play a role in hormone signal transduction.

scholarly journals Real Time Study of Transposable Element Activity

2017 ◽  
Vol 112 (3) ◽  
pp. 284a
Author(s):  
Neil Hyuneil Kim ◽  
Gloria Lee ◽  
Nicholas A. Sherer ◽  
K. Michael Martini ◽  
Nigel Goldenfeld ◽  
...  
Keyword(s):  
Transposable Element ◽  
Real Time ◽  
Time Study ◽  
Element Activity

scholarly journals Genome sequence resource for the plant pathogen Sclerotinia sclerotiorum WH6 isolated in China

Plant Disease ◽  
2021 ◽  
Author(s):  
Xiong Zhang ◽  
Xiaohui Cheng ◽  
Lijiang Liu ◽  
Shengyi Liu
Keyword(s):  
Sclerotinia Sclerotiorum ◽  
Genome Sequence ◽  
Fungal Pathogen ◽  
Sclerotinia Stem Rot ◽  
High Quality ◽  
Total Size ◽  
Host Interactions ◽  
A Genome ◽  
The World ◽  
High Quality Genome

Sclerotinia sclerotiorum is a notorious fungal pathogen that causes sclerotinia stem rot (SSR) on many important crops in China and worldwide. Here, we present a high- quality genome assembly of S. sclerotiorum strain WH6 using the PacBio SMRT cell platform. The assembled genome has a total size of 38.96 Mbp, with a contig N50 length of 1.90 Mbp, and encodes 10,512 predicted coding genes, including 685 secreted proteins and 65 effector candidates. This is the the first report of a genome sequence from China. The WH6 genome sequence provides a valuable resource for facilitating our understanding of S. sclerotiorum-host interactions and SSR control in China and the world.

scholarly journals Ac induces homologous recombination at the maize P locus.

Genetics ◽  
1991 ◽  
Vol 128 (1) ◽  
pp. 163-173 ◽  
Author(s):  
P Athma ◽  
T Peterson
Keyword(s):  
Homologous Recombination ◽  
Transposable Element ◽  
Direct Repeat ◽  
Null Alleles ◽  
Direct Repeats ◽  
Ac Element ◽  
Repeat Sequences ◽  
P Gene ◽  
In Trans ◽  
P Locus

Abstract The maize P gene conditions red phlobaphene pigmentation to the pericarp and cob. Starting from two unstable P alleles which carry insertions of the transposable element Ac, we have derived 51 P null alleles; 47 of the 51 null alleles have a 17-kb deletion which removes the 4.5-kb Ac element and 12.5 kb of P sequences flanking both sides of Ac. The deletion endpoints lie within two 5.2-kb homologous direct repeats which flank the P gene. A P allele which contains the direct repeats, but does not have an Ac insertion between the direct repeats, shows very little sporophytic or gametophytic instability. The apparent frequency of sporophytic mutations was not increased when Ac was introduced in trans. Southern analysis of DNA prepared from the pericarp tissue demonstrates that the deletions can occur premeiotically, in the somatic cells during development of the pericarp. Evidence is presented that the deletions occurred by homologous recombination between the two direct repeats, and that the presence of an Ac element at the P locus is associated with the recombination/deletion. These results add another aspect to the spectrum of activities of Ac: the destabilization of flanking direct repeat sequences.

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