The structure, organization and radiation of Sadhu non-long terminal repeat retroelements in Arabidopsis species

<p>Abstract</p> <p>Background</p> <p><it>Sadhu </it>elements are non-autonomous retroposons first recognized in <it>Arabidopsis thaliana</it>. There is a wide degree of divergence among different elements, suggesting that these sequences are ancient in origin. Here we report the results of several lines of investigation into the genomic organization and evolutionary history of this element family.</p> <p>Results</p> <p>We present a classification scheme for <it>Sadhu </it>elements in <it>A. thaliana</it>, describing derivative elements related to the full-length elements we reported previously. We characterized <it>Sadhu5 </it>elements in a set of <it>A. thaliana </it>strains in order to trace the history of radiation in this subfamily. Sequences surrounding the target sites of different <it>Sadhu </it>insertions are consistent with mobilization by LINE retroelements. Finally, we identified <it>Sadhu </it>elements grouping into distinct subfamilies in two related species, <it>Arabidopsis arenosa </it>and <it>Arabidopsis lyrata</it>.</p> <p>Conclusions</p> <p>Our analyses suggest that the <it>Sadhu </it>retroelement family has undergone target primed reverse transcription-driven retrotransposition during the divergence of different <it>A. thaliana </it>strains. In addition, <it>Sadhu </it>elements can be found at moderate copy number in three distinct <it>Arabidopsis </it>species, indicating that the evolutionary history of these sequences can be traced back at least several millions of years.</p

The NCBI Comparative Genome Viewer (CGV) is an interactive visualization tool for the analysis of whole-genome eukaryotic alignments.

We report a new visualization tool for analysis of whole-genome assembly-assembly alignments, the Comparative Genome Viewer (CGV) (https://ncbi.nlm.nih.gov/genome/cgv/). CGV visualizes pairwise same-species and cross-species alignments provided by National Center for Biotechnology Information (NCBI) using assembly alignment algorithms developed by us and others. Researchers can examine large structural differences spanning chromosomes, such as inversions or translocations. Users can also navigate to regions of interest, where they can detect and analyze smaller-scale deletions and rearrangements within specific chromosome or gene regions. RefSeq or user-provided gene annotation is displayed where available. CGV currently provides approximately 800 alignments from over 350 animal, plant, and fungal species. CGV and related NCBI viewers are undergoing active development to further meet needs of the research community in comparative genome visualization

Consensus coding sequence (CCDS) database: a standardized set of human and mouse protein-coding regions supported by expert curation.

The Consensus Coding Sequence (CCDS) project provides a dataset of protein-coding regions that are identically annotated on the human and mouse reference genome assembly in genome annotations produced independently by NCBI and the Ensembl group at EMBL-EBI. This dataset is the product of an international collaboration that includes NCBI, Ensembl, HUGO Gene Nomenclature Committee, Mouse Genome Informatics and University of California, Santa Cruz. Identically annotated coding regions, which are generated using an automated pipeline and pass multiple quality assurance checks, are assigned a stable and tracked identifier (CCDS ID). Additionally, coordinated manual review by expert curators from the CCDS collaboration helps in maintaining the integrity and high quality of the dataset. The CCDS data are available through an interactive web page (https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi) and an FTP site (ftp://ftp.ncbi.nlm.nih.gov/pub/CCDS/). In this paper, we outline the ongoing work, growth and stability of the CCDS dataset and provide updates on new collaboration members and new features added to the CCDS user interface. We also present expert curation scenarios, with specific examples highlighting the importance of an accurate reference genome assembly and the crucial role played by input from the research community. Nucleic Acids Res 2018 Jan 4; 46(D1):D221-D228

Many LINE1 elements contribute to the transcriptome of human somatic cells

Over 600 LINE 1 elements are shown to be transcribed in humans; 400 of these are full-length elements in the reference genome

Differential Epigenetic Regulation Within an Arabidopsis Retroposon Family

We previously reported a novel family of Arabidopsis thaliana nonautonomous retroposons, Sadhu, showing epigenetic variation in natural populations. Here, we show that transcripts corresponding to Sadhu elements accumulate in a subset of mutants carrying disruptions in genes encoding chromatin modification enzymes, but are not significantly expressed in mutants defective in RNA silencing pathways, indicating that RNA-directed processes are not necessary to maintain transcriptional suppression of this class of retroelements. We focused our analysis on three representative elements showing differential responses to ddm1, met1, and hda6 mutations. These mutations had differing effects on cytosine methylation depending on the element and the sequence context. Curiously, the Sadhu6-1 element with the strongest CpHpG methylation is expressed in a met1 CpG methyltransferase mutant, but is not expressed in ddm1 or cmt3 mutants. Regardless of the mutant background, H3meK9 was found at silenced loci, while H3meK4 was restricted to expressed alleles. We discuss the different modes of regulation within this family and the potential impact of this regulation on the stability of silencing in natural populations

Meiotically stable natural epialleles of Sadhu, a novel arabidopsis retroposon

Epigenetic variation is a potential source of genomic and phenotypic variation among different individuals in a population, and among different varieties within a species. We used a two-tiered approach to identify naturally occurring epigenetic alleles in the flowering plant Arabidopsis: a primary screen for transcript level polymorphisms among three strains (Col, Cvi, Ler), followed by a secondary screen for epigenetic alleles. Here, we describe the identification of stable, meiotically transmissible epigenetic alleles that correspond to one member of a previously uncharacterized non-LTR retroposon family, which we have designated Sadhu. The pericentromeric At2g10410 element is highly expressed in strain Col, but silenced in Ler and 18 other strains surveyed. Transcription of this locus is inversely correlated with cytosine methylation and both the expression and DNA methylation states map in a Mendelian manner to stable cis-acting variation. The silent Ler allele can be converted by the epigenetic modifier mutation ddm1 to a meiotically stable expressing allele with an identical primary nucleotide sequence, demonstrating that the variation responsible for transcript level polymorphism among Arabidopsis strains is epigenetic. We extended our characterization of the Sadhu family members and show that different elements are subject to both genetic and epigenetic variation in natural populations. These findings support the view that an important component of natural variation in retroelements is epigenetic

Analysis of Cytosine Methylation at <i>At2g10410</i> by McrBC Digestion followed by PCR

<div><p>(A) Diagram of the <i>At2g10410</i> locus in Col including nearby repetitive elements and intergenic regions. Arrow indicates start and direction of transcription. The positions of primers used for PCR analysis are indicated as triangles.</p><p>(B) PCR amplification of genomic DNA +/− McrBC digestion. Cyclophilin is shown as an amplification control.</p><p>(C) McrBC PCR of the <i>At2g10410-</i>transcribed region in Col, Ler, and Ler <i>ddm1–2</i> genomic DNA samples. Cyclophilin is shown as an internal amplification control.</p></div