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207 Articles Notes.pdf

26 Pages

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Nicole Myers

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Kamalpreet Singh Encode Explained Basically Results of Various Studies of GenomeEncyclopedia of DNA elements ENCODEo GoalDescribe the list of Functional elements that compose the human genome Combining these elements in the right amountsinformation needed to make up all types of cells body organs and basically an entire person o Initially focused on just 1 of the genome and results hinted that list of human genes was incompletedoubts whether the results should be extended to the whole genomeo Today Encode is based upon 1640 genome wide data sets from 147 cell types Interesting Findingo 80 of the genomeelements linked to the biochemical functions Disproves Human genome is mostly JUNK DNA Space between genes is filled with Enhancers regulatory DNA elementsPromoters sites at which DNAs transcription into RNA is startedMany initially ignored areas that encode RNA transcripts that are not translated into proteinsRegulatory roles perhaps Results also showed that DNA variations linked with certain diseases lie inside or very close to noncoding functional DNA elements New ways to link genetic variation and disease Ultradeep sequencing of RNAs from many different cell lines and from certain compartments within the cells lead to the conclusion o 75 genometranscribed at some point in cells o Genes are highly interconnected with overlapping transcripts that are made from both DNA strandsForce us to redefine a gene and the minimum unit of heredity Chromatin related studieso Based on DNase I hypersensitivityDetects genomic regions where enzyme access and cleavage is not hindered by chromatin proteins o Researchers found cell specific patterns of DNase I hypersensitive sites that shows agreement with experimentally found and theoretically predicted binding sites of transcription factorso Also doubled theof known recognition sequences for DNABinding proteins in human genome o Found a 50 BP sequence that is found in many promoters GersteinfriendsTheory behind the links of transcription factor networks o study attempts to clarify hierarchies of the transcription factor networks and assign simple functions to genome elementsKamalpreet SinghENCODE also aims to map more than 1000 long range signals that help communication between the various elements of DNA in each cell typeo Findings disprove the fact that regulation of a gene is dominated by its closeness to the nearest regulatory elements Future Challenges for ENCODEo Looking at the Dynamic aspects of gene regulationRight now we only really consider one event at a time The combined effect may be different from what we think o Figure out how the individual genomic componentscombine to create gene networks and biochemical pathways that do complex functions Cellcell communication that let organs and tissues to develop o Use the Vast data stillincreasingfrom genomesequencing projects to understand a range of human phenotypes traitsfrom normal developmental processes such as ageing to diseases such asAlzheimersTo Solve Future challengesInvest LOTS of time in studying simple organismsFigure 1
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