Embrace the Junk
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piRNA clusters and open chromatin structure

Transposable elements (TEs) are major structural components of eukaryotic genomes; however, mobilization of TEs generally has negative effects on the host genome. To counteract this threat, host cells have evolved genetic and epigenetic mechanisms that keep TEs silenced. One such mechanism involves the Piwi-piRNA complex, which represses TEs in animal gonads either by cleaving TE transcripts in the cytoplasm or by directing specific chromatin modifications at TE loci in the nucleus. Most Piwi-interacting RNAs (piRNAs) are derived from genomic piRNA clusters. There has been remarkable progress in our understanding of the mechanisms underlying piRNA biogenesis. However, little is known about how a specific locus in the genome is converted into a piRNA-producing site. In this review, we will discuss a possible link between chromatin boundaries and piRNA cluster formation.
Guilherme Dias's insight:

The once called "transposon graveyards" may actually be the nurseries of piRNAs. This suggests that the scrambled pattern of truncated transposons and tandem repeats present in hetero/euchromatin boundaries could reflect a complex level of organization rather than just a disordered soup of repetitive DNA.

Nice!

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Comparative Genomic Paleontology across Plant Kingdom Reveals the Dynamics of TE-Driven Genome Evolution

Comparative Genomic Paleontology across Plant Kingdom Reveals the Dynamics of TE-Driven Genome Evolution | Embrace the Junk | Scoop.it

Long terminal repeat-retrotransposons (LTR-RTs) are the most abundant class of transposable elements (TEs) in plants. They strongly impact the structure, function, and evolution of their host genome, and, in particular, their role in genome size variation has been clearly established. However, the dynamics of the process through which LTR-RTs have differentially shaped plant genomes is still poorly understood because of a lack of comparative studies. Using a new robust and automated family classification procedure, we exhaustively characterized the LTR-RTs in eight plant genomes for which a high-quality sequence is available (i.e., Arabidopsis thaliana, A. lyrata, grapevine, soybean, rice, Brachypodium dystachion, sorghum, and maize). This allowed us to perform a comparative genome-wide study of the retrotranspositional landscape in these eight plant lineages from both monocots and dicots. We show that retrotransposition has recurrently occurred in all plant genomes investigated, regardless their size, and through bursts, rather than a continuous process. Moreover, in each genome, only one or few LTR-RT families have been active in the recent past, and the difference in genome size among the species studied could thus mostly be accounted for by the extent of the latest transpositional burst(s). Following these bursts, LTR-RTs are efficiently eliminated from their host genomes through recombination and deletion, but we show that the removal rate is not lineage specific. These new findings lead us to propose a new model of TE-driven genome evolution in plants.


Via Francis Martin
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The Drosophila Colorfull Chromatin

The Drosophila Colorfull Chromatin | Embrace the Junk | Scoop.it
Guilherme Dias's insight:

We don't know exactly what makes heterochromatin different from euchromatin. Well, this paper shows that we actually don't know the beginning of it.

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The ctenophore genome and the evolutionary origins of neural systems : Nature : Nature Publishing Group

The ctenophore genome and the evolutionary origins of neural systems : Nature : Nature Publishing Group | Embrace the Junk | Scoop.it
Guilherme Dias's insight:

A genome estimated in 160-180 Mb. ~800x sequencing coverage. 'Only' 145 Mb of bases in scaffolds of at least 2kb.

You can't just throw short reads at your problems and hope they go away.

ps. That aside, the genome characterization is really thorough (except for repetitive DNA of course).

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Virtual Poster: Hybrid Genome Assembly of a Nocturnal Lemur - YouTube

Guilherme Dias's insight:

If we are to understand genome evolution, we ought to understand the evolution of repetitive DNA (aka. a big chunk of most eukaryote's genomes). And if we are to understand repetitive DNA evolution it wouldn't hurt to have it properly assembled in our reference genomes.

In this sense, the hybrid model of genome assembly is the current best option to obtain the most accurate genome assemblies with a non-prohibitive budget.

In the hybrid model the advantages of short reads sequencing are coupled with the great capabilities of ultra-long reads. In this virtual poster the researchers sequenced the Aye-Aye genome with 38x coverage using Illumina's short reads (~100bp). With an additional 0.5x (yes, just 0.5x) coverage  of PacBio ultra-long reads they've managed to decrease in almost 10 fold (!) the number of contigs obtained with the Illumina-only assembly.

So, if PacBio is so awesome why not sequence with ultra-long reads only? Well, they are much more expensive (in a per-base cost comparison) and have a much higher error rate. The Illumina reads are used to correct the PacBio ones and thus generate the most reliable assemblage.

I think that we still don't have that much softwares dedicated to the integration of Illumina and PacBio data, but this is certainly going to change fast. The advantages of the hybrid assembly are just too good to let go.

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The Case for Junk DNA

The Case for Junk DNA | Embrace the Junk | Scoop.it
PLOS Genetics is an open-access

Via Gabriel Wallau
Guilherme Dias's insight:

A really good contribution in the topic of 'Junk DNA'. I'm curious, however, of why there was no mention to the nucleotypic and nucleoskeletal hypotheses (they imply a relationship between genome size and cellular features of adaptative significance).

T. Ryan Gregory, who has contributed a great amount of data and comprehensive analyses of animal genome sizes, has really seemed attached to a nucleotypic and/or nucleoskeletal explanation of genome size on earlier papers. In this paper i kinda feel some "inevitable complexity" argument, much more like Mychael Lynch's.

So far I share the views of Michael Lynch and others who believe that junk DNA is nothing but the result of passive accumulation of extra DNA through non-adaptative processes and that very large genomes with much junk illustrate the inability of cells to get rid of this extra DNA. The reduced population sizes of most eukaryotic species also result in a low efficiency of natural selection and thus, prevent the evolution of streamlined, 100% functional DNA genomes.

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Noncoding origins of anthropoid traits and a new null model of transposon functionalization

Noncoding origins of anthropoid traits and a new null model of transposon functionalization | Embrace the Junk | Scoop.it
An international, peer-reviewed genome sciences journal featuring outstanding original research that offers novel insights into the biology of all organisms

Via Gabriel Wallau
Guilherme Dias's insight:

Elegant indeed!

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Gabriel Wallau's curator insight, July 22, 2014 7:13 PM

Little is known about novel genetic elements that drove the emergence of anthropoid primates. We exploited the sequencing of the marmoset genome to identify 23,849 anthropoid-specific constrained (ASC) regions, and confirmed their robust functional signatures. 99.7% of ASC basepairs were noncoding, suggesting that novel anthropoid functional elements were overwhelmingly cis-regulatory. ASCs were highly enriched in loci associated with fetal brain development, motor coordination, neurotransmission and vision, thus providing a large set of candidate elements for exploring the molecular basis of hallmark primate traits. We validated ASC192 as a primate-specific enhancer in proliferative zones of the developing brain. Unexpectedly, transposable elements (TEs) contributed to >56% of ASCs, and almost all TE families showed functional potential similar to that of non-repetitive DNA. Three L1PA repeat-derived ASCs displayed coherent eye-enhancer function, thus demonstrating that the 'gene-battery' model of TE functionalization applies to enhancers in vivo. Our study provides fundamental insights into genome evolution and the origins of anthropoid phenotypes, and supports an elegantly simple new null model of TE exaptation.

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Animal Genome Size Database:: Home

Animal Genome Size Database:: Home | Embrace the Junk | Scoop.it
Guilherme Dias's insight:

Always good to point out Dr. Ryan Gregory's great compilation of genome size data. Free and accessible to everyone.

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Centromere identity from the DNA point of view

Centromere identity from the DNA point of view | Embrace the Junk | Scoop.it
Guilherme Dias's insight:

A very nice review on centromeres, focusing on the DNA sequence that underlies them.

I like this sentence the most: "It has become evident that centromeres can be established literally on any DNA sequence (...)".

Just so that you know.

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Mind the Gap: Upgrading Genomes with Pacific Biosciences RS Long-Read Sequencing Technology

Mind the Gap: Upgrading Genomes with Pacific Biosciences RS Long-Read Sequencing Technology | Embrace the Junk | Scoop.it
Guilherme Dias's insight:

Talking of genome assembly...

Most gaps in reference genomes are generated because of the inability of genome assemblers to deal with repetitive regions such as segmental duplications, transposable elements and tandem repeats.

But there are good news (not that new actually). Adam C. English and collaborators from the Baylor College of Medicine developed an algorithm called PBJelly that automates the gap closing process by employing PacBio long reads.

Actually, even if the long reads don't span the gap entirely, they can be used to shorten it. The researchers closed 69% and shortened 12% of the remaining gaps in the Drosophila pseudoobscura genome release 2.0.

What about that?

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Stretching the Rules: Monocentric Chromosomes with Multiple Centromere Domains

Stretching the Rules: Monocentric Chromosomes with Multiple Centromere Domains | Embrace the Junk | Scoop.it
PLOS Genetics is an open-access
Guilherme Dias's insight:

I really don't think this paper has received all the attention it deserves.

Neumann et al. trully advanced our understanding of what a centromere looks like. And it looks amazing!
They found that Pisum sativum centromeres are actually composed of multiple CENH3 domains (up to 5 per chromosome). They've named these chromosomes "meta-polycentric" and i think the new nomenclature fits perfectly.

The researchers verified that the meta-centromeres (meaning the primary constriction) can span up to 107 Mbp of sequence and are composed of an impressive array of 13 distinct satellite DNA families.

Just like all great research it generates important questions, to name a few:

1-Are these meta-polycentric chromosomes an exclusivity of the Pea? Or plants?

2-Are all CENH3 domains necessary for a faithful segregation?

ps. The fluorescence images are just impressive. (Mendel would be proud)

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