ENCODE

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ENCODE (composed of ENC yclopedia O f D NA E lements, Encyclopedia of DNA Elements ) is a research project that was initiated in September 2003 by the US National Human Genome Research Institute (NHGRI). The aim of the project is to identify and characterize all functional elements of the human genome as well as the transcriptome . ENCODE is thus the follow-up project of the Human Genome Project , which the sequencing had the human genome to the target and which is closed since of 2003. Another aim of ENCODE is the development and implementation of high throughput methods for identifying the functional elements.

ENCODE is carried out by a research consortium that includes around 30 working groups at various institutes. The project will be carried out in three phases: a pilot phase, which aims to analyze 1% (30 megabases ) of the genome and evaluate the research methods, and a technological phase, in which the data throughput is increased and the costs of acquiring the data are reduced and a production phase in which the remaining 99% of the genome is to be analyzed. All data generated in the course of the ENCODE project are made available to the general public in a publicly accessible database. As a first result, ENCODE was able to confirm in 2007 that around half of all RNAs produced by a cell are neither mRNA nor ribosomal RNA or other RNA end products, but other RNAs for which it is not known whether and which function they fulfill.

The results of ENCODE are controversial, methodological errors were criticized and contradictions to evolutionary biological ideas are supposed to exist.

Pilot phase

In the pilot phase, initially 30 megabases of DNA sequence of the human genome, which comprises around 1%, were selected and analyzed using established methods. 50% of this sample was selected specifically and 50% at random. The transcriptome, i.e. all transcribed sequences, was mapped, as well as transcription starting points, promoters , enhancers , repressors or silencers , exons , origins of replication , replication termination sites, binding sites of transcription factors, methylation sites , DNase-I hypersensitive regions, chromatin modifications and regions, the are highly conserved, but have so far no known function, identified. Genetic variations within these highly conserved areas are also documented. The methods used include sequencing, microarrays , chromatin immunoprecipitation (ChIP) and quantitative PCR .

Technological development phase

The further technical development of the methods takes place at the same time as the pilot phase. New laboratory techniques and computer programs are to be developed.

Production phase

In the last productive phase, the remaining 99% of the sequence of the human genome should be mapped analogously to the first percent and functional elements identified, and this as inexpensively and reliably as possible. Further functional elements that were not yet taken into account in the pilot phase, such as telomeres and centromeres , will then be characterized.

Results

As a result, ENCODE showed that considerably more DNA is active in the human genome than assumed. While 2% of the DNA protein-coding genes are attributed and so far regarded as active, according to ENCODE about 80% of the DNA is active. According to ENCODE, 76% of the genome is transcribed into RNA. There are 2.9 million regulatory elements in the genome. Different genome segments are active depending on the cell type. However, these results are not accepted by all scientists, but are rather doubted due to methodological questions.

costs

Initially, eight working groups were funded with a total of 12 million US dollars in the pilot phase. Since then, other groups have been added that deal, for example, with the coordination of the databases. In total, the pilot cost $ 55 million, and the production phase, which ended in 2012, was another 130 million.

Web links

Individual evidence

  1. ↑ a b The ENCODE (ENCyclopedia Of DNA Elements) Project . The ENCODE Project Consortium. In: Science , 22 October 2004, Vol. 306. no. 5696, pp. 636-640, doi: 10.1126 / science.1105136 .
  2. ↑ genome.ucsc.edu
  3. ↑ ENCODE Project Data Release Policy . genome.gov
  4. ^ A b D. Graur et al .: On the immortality of television sets: “function” in the human genome according to the evolution-free gospel of ENCODE . In: Genome Biol Evol. , February 20, 2013, PMID 23431001 (English)
  5. ↑ genome.gov
  6. ↑ The ENCODE project: 80% of the genome are active ( German ) wissensschau.de. Retrieved March 6, 2013.
  7. ^ Brendan Maher: ENCODE: The human encyclopaedia. In: Nature . 489, 2012, pp. 46-48, doi: 10.1038 / 489046a .