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Origins of genomic dark matter discovered


Origins of genomic dark matter discovered.

The Non-Coding Genome – 9 – 12 October 2013

The Non-Coding Genome – 9 – 12 October 2013.

Nature ENCODE : Nature Publishing Group : A landmark in the understanding of the human genome



Cell – COLLECTIONS-RNA-Genome-Stability


Cells must control transposons and foreign genetic elements to maintain genomic stability. This is especially important in gametes, where unchecked transposon activity could affect the next generation. We now know that organisms have pathways in which small RNAs guide proteins to actively silence transposons in the genome. These pathways exist in prokaryotes and eukaryotes, with general mechanisms conserved between the two groups. These include mechanisms for recognizing foreign genetic elements, activating the silencing responses, and maintaining a “memory” of the active transposon event. Small RNAs associated with piwi proteins — known as piRNAs — are critical to these processes.

In 2007, Brennecke et al. proposed that the piRNA pathway could act as a molecular adaptive immune system, capable of sensing and reacting to adaptive transposons by silencing them. We begin this Collection looking back at these findings and then taking a broader view to appreciate how much we have learned about the roles of small RNAs in the maintenance of genomic stability.

Discrete Small RNA-Generating Loci as Master Regulators of Transposon Activity in Drosophila.
Julius Brennecke, Alexei A. Aravin, Alexander Stark, Monica Dus, Manolis Kellis, Ravi Sachidanandam, Gregory J. Hannon

SnapShot: Mouse piRNAs, PIWI Proteins, and the Ping-Pong Cycle
Jogender S. Tushir, Phillip D. Zamore, Zhao Zhang




1st Course on Non-Coding Genome – 2012 | Institut Curie – Enseignement

Description of course:

One of the major goals of this course is to give an overview of potential impact of the non coding part of the genome during the cell life. This covers not only regulatory non-coding RNAs, but also unknown ncRNAs such as those emerging from repetitive sequences, both playing a crucial role in the expression and maintenance of the genomes.The course will describe the biogenesis pathways of different ncRNAs, as well as the mechanisms of gene regulation and genome defence implicating these RNAs. It will cover recent achievements in ncRNA detection, emerging findings of novel ncRNA species in the context of development, cellular differentiation and human diseases.
Organizers: D. Bourc’his, E. Heard, M. Kwapisz, A. Londono, A. Morillon, M. Pinskaya, F. Toledo


Human Genome Untangled in 3-D [Video]: Scientific American



The Human Genome at Ten – Nature


The human genome’s breaking points: large-scale differences between human genomes – EMBL

A detailed analysis of data from 185 human genomes sequenced in the course of the 1000 Genomes Project, by scientists at the European Molecular Biology Laboratory (EMBL) in Heidelberg, Germany, in collaboration with researchers at the Wellcome Trust Sanger Institute in Cambridge, UK, as well as the University of Washington and Harvard Medical School, both in the USA, has identified the genetic sequence of an unprecedented 28 000 structural variants (SVs) – large portions of the human genome which differ from one person to another. The work, published today in Nature, could help find the genetic causes of some diseases and also begins to explain why certain parts of the human genome change more than others.

Source Article

Mills et al. Mapping copy number variation by population-scale genome sequencing. Nature, 3 February 2011. DOI:10.1038/nature09708.


Mapping copy number variation by population-scale genome sequencing




Early Reports From the ‘Dark Matter’ of the Genome | Wired Science


Evolutionary dynamics of transposable elements in a small RNA world


Figure 2. Evolutionary games in the germline. (a) In D. melanogaster, fifteen nurse cells contribute maternal resources to the developing egg, but are fated for apoptosis. (b) In A. thaliana, multiple haploid nuclei contribute to the female gametophyte, but only the egg cell passes genetic material to the next generation. In both plants and animals, flanking somatic tissues also promote gametogenesis but are excluded from subsequent generations. In D.melanogaster (a) piRNAs are derived from somatic cells and in nurse cells within a structure called the nuage. An ancestral gene duplication has yielded specialization of the piRNA machinery within the developing egg chamber. piRNAs produced by Aubergine function solely within the germline where as piRNAs produced by Piwi function in somatic follicle cells as well. These somatic piRNAs are specialized to defend against retrovirus-like TEs that proliferate in the soma and spread into the germline. In flowering plants (b)multiple companion nuclei including somatic nuclei, nuclei fated to the endosperm and nuclei within the pollen tube also contribute TE-derived siRNAs. Red arrows indicate the potential paths of TE evolutionary escape from tissues that will not enter the next generation toward those tissues that do. AC, antipodal cells; NC, nurse cells; PN, polar nuclei; PTN, pollen tube nucleus; SC, synergid cells; SN, somatic nucleus; Sperm.E, sperm fertilizing the central cell, thus establishing the endoderm. 

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