'Junk DNA' Intelligent Design News Plants

“Junk DNA” important to flower evolution?

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A reader sent this link to a free 2013 paper in Genome Biol Evol wherein we read:

Although once said to be “junk,” or “parasitic,” DNA (Doolittle and Sapienza 1980; Orgel and Crick 1980), a recent large and rapid accumulation of evidence indicates that transposable elements (TEs) have been a significant factor in the evolution of a wide range of eukaryotic taxa (Bennetzen 2000; Kazazian 2004; Biémont and Vieira 2006; Feschotte and Pritham 2007; Bohne et al. 2008; Hua-Van et al. 2011). We have proposed TEs as powerful facilitators of evolution (Oliver and Greene 2009), formalized this proposal into the TE-Thrust hypothesis (Oliver and Greene 2011), and more recently, expanded and strengthened this hypothesis (Oliver and Greene 2012).
More.

But of course it is still junk, you understand. Great minds can’t be wrong.

See also: Junk DNA region implicated in celiac disease

and

Eric H. Davidson (1937–2015), and the function of “junk DNA”

Here’s the abstract:

Transposable elements (TEs) are a dominant feature of most flowering plant genomes. Together with other accepted facilitators of evolution, accumulating data indicate that TEs can explain much about their rapid evolution and diversification. Genome size in angiosperms is highly correlated with TE content and the overwhelming bulk (>80%) of large genomes can be composed of TEs. Among retro-TEs, long terminal repeats (LTRs) are abundant, whereas DNA-TEs, which are often less abundant than retro-TEs, are more active. Much adaptive or evolutionary potential in angiosperms is due to the activity of TEs (active TE-Thrust), resulting in an extraordinary array of genetic changes, including gene modifications, duplications, altered expression patterns, and exaptation to create novel genes, with occasional gene disruption. TEs implicated in the earliest origins of the angiosperms include the exapted Mustang, Sleeper, and Fhy3/Far1 gene families. Passive TE-Thrust can create a high degree of adaptive or evolutionary potential by engendering ectopic recombination events resulting in deletions, duplications, and karyotypic changes. TE activity can also alter epigenetic patterning, including that governing endosperm development, thus promoting reproductive isolation. Continuing evolution of long-lived resprouter angiosperms, together with genetic variation in their multiple meristems, indicates that TEs can facilitate somatic evolution in addition to germ line evolution. Critical to their success, angiosperms have a high frequency of polyploidy and hybridization, with resultant increased TE activity and introgression, and beneficial gene duplication. Together with traditional explanations, the enhanced genomic plasticity facilitated by TE-Thrust, suggests a more complete and satisfactory explanation for Darwin’s “abominable mystery”: the spectacular success of the angiosperms. – Keith R. Oliver*, Jen A. McComb and Wayne K. Greene, Transposable Elements: Powerful Contributors to Angiosperm Evolution and Diversity, Genome Biol Evol (2013) 5 (10): 1886-1901. doi: 10.1093/gbe/evt141

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6 Replies to ““Junk DNA” important to flower evolution?

  1. 1
    Dionisio says:

    Flowering plants have strikingly distinct genomes, although they contain a similar suite of expressed genes. The diversity of genome structures and organization is largely due to variation in transposable elements (TEs) and whole-genome duplication (WGD) events. We review evidence that chromatin modifications and epigenetic regulation are intimately associated with TEs and likely play a role in mediating the effects of WGDs. We hypothesize that the current structure of a genome is the result of various TE bursts and WGDs and it is likely that the silencing mechanisms and the chromatin structure of a genome have been shaped by these events. This suggests that the specific mechanisms targeting chromatin modifications and epigenomic patterns may vary among different species*. Many crop species have likely evolved[?] chromatin-based mechanisms to tolerate silenced TEs near actively expressed genes. These interactions of heterochromatin and euchromatin are likely to have important roles in modulating gene expression and variability within species*.

    Creating Order from Chaos: Epigenome Dynamics in Plants with Complex Genomes.
    Springer NM, Lisch D, Li Q.
    Plant Cell. 2016 Feb;28(2):314-25.
    doi: 10.1105/tpc.15.00911. Epub 2016 Feb 11.

    The Plant Cell Reviews Small RNA and Chromatin Dynamics: From Small Genetic Circuits to Complex Genomes.
    Eckardt NA.
    Plant Cell. 2016 Feb;28(2):269-71.
    doi: 10.1105/tpc.16.00113. Epub 2016 Feb 11.

    (*) duh! of course!
    glad to see research heading there… 🙂

  2. 2
    Dionisio says:

    News, thank you for this OP.

    RNA Polymerase II (Pol II) regulatory cascades involving transcription factors (TFs) and their targets orchestrate the genetic circuitry of every eukaryotic organism. In order to understand how these cascades function, they can be dissected into small genetic networks, each containing just a few Pol II transcribed genes, that generate specific signal-processing outcomes.

    Small RNA regulatory circuits involve direct regulation of a small RNA by a TF and/or direct regulation of a TF by a small RNA and have been shown to play unique roles in many organisms.

    Here, we will focus on small RNA regulatory circuits containing Pol II transcribed microRNAs (miRNAs). While the role of miRNA-containing regulatory circuits as modular building blocks for the function of complex networks has long been on the forefront of studies in the animal kingdom, plant studies are poised to take a lead role in this area because of their advantages in probing transcriptional and posttranscriptional control of Pol II genes. The relative simplicity of tissue- and cell-type organization, miRNA targeting, and genomic structure make the Arabidopsis thaliana plant model uniquely amenable for small RNA regulatory circuit studies in a multicellular organism. In this Review, we cover analysis, tools, and validation methods for probing the component interactions in miRNA-containing regulatory circuits. We then review the important roles that plant miRNAs are playing in these circuits and summarize methods for the identification of small genetic circuits that strongly influence plant function. We conclude by noting areas of opportunity where new plant studies are imminently needed.

    Small Genetic Circuits and MicroRNAs: Big Players in Polymerase II Transcriptional Control in Plants.
    Megraw M, Cumbie JS, Ivanchenko MG, Filichkin SA.
    Plant Cell. 2016 Feb;28(2):286-303.
    doi: 10.1105/tpc.15.00852. Epub 2016 Feb 11.

    gpuccio, any comments on this thread?
    Doesn’t it say some of the things you have mentioned before?

  3. 3
    Dionisio says:

    Transposable elements (TEs) are mobile units of DNA that comprise large portions of plant genomes. Besides creating mutations via transposition and contributing to genome size, TEs play key roles in chromosome architecture and gene regulation. TE activity is repressed by overlapping mechanisms of chromatin condensation, epigenetic transcriptional silencing, and targeting by small interfering RNAs. The specific regulation of different TEs, as well as their different roles in chromosome architecture and gene regulation, is specified by where on the chromosome the TE is located*: near a gene, within a gene, in a pericentromere/TE island, or at the centromere core. In this Review, we investigate the silencing mechanisms responsible for inhibiting TE activity for each of these chromosomal contexts, emphasizing that chromosomal location is the first rule dictating the specific regulation of each TE.

    The First Rule of Plant Transposable Element Silencing: Location, Location, Location.
    Sigman MJ, Slotkin RK.
    Plant Cell. 2016 Feb;28(2):304-13.
    doi: 10.1105/tpc.15.00869. Epub 2016 Feb 11.

    (*) how is that location determined?

  4. 4
    Dionisio says:

    Genomes of higher eukaryotes, including plants, contain numerous transposable elements (TEs), that are often silenced by epigenetic mechanisms, such as histone modifications and DNA methylation. Although TE silencing adversely affects expression of nearby genes, recent studies reveal the presence of intragenic TEs marked by repressive heterochromatic epigenetic marks within transcribed genes. However, even for the well-studied plant model Arabidopsis?thaliana, the abundance of intragenic TEs, how they are epigenetically regulated, and their potential impacts on host gene expression, remain unexplored.

    […] understanding of the functional relevance of intronic TEs requires further analyses,…

    Whether intragenic TEs within the set of genes become adaptive, however, remains unclear.

    Analyses of plants with larger genomes could provide further insights into the functional relevance and contribution of intragenic TEs to genome evolution.

    Epigenetic regulation of intragenic transposable elements impacts gene transcription in Arabidopsis ?thaliana
    Tu N. Le, Yuji Miyazaki, Shohei Takuno, and Hidetoshi Saze
    doi: 10.1093/nar/gkv258
    Nucleic Acids Res. 43(8): 3911–3921.
    http://nar.oxfordjournals.org/content/43/8/3911

  5. 5
    gpuccio says:

    Dionisio:

    “gpuccio, any comments on this thread?
    Doesn’t it say some of the things you have mentioned before?”

    Definitely! 🙂

    I have just posted about this in the other thread:

    http://www.uncommondescent.com.....ent-607347

    Post #143.

    I am very happy that my good friends, the transposons, are so fashionable in this moment. They are true rockstars! 🙂

  6. 6
    Dionisio says:

    gpuccio

    Yes, those transposons are popping up all over many research papers.

    Any comments on the “location” issue @3?
    How is it determined and setup/established?

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