Kamalpreet Singh ©
Basically Results of Various Studies of Genome.
Encyclopedia of DNA elements (ENCODE)
o Goal = Describe the list of Functional elements that compose the human genome.
Combining these elements in the right amounts = information 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
doubts whether the results should be extended to the whole genome.
o Today Encode is based upon 1,640 genome wide data sets from 147 cell types.
o 80% of the genome = elements linked to the biochemical functions
Disproves "Human genome is mostly JUNK DNA"
Space between genes is filled with
Enhancers (regulatory DNA elements)
Promoters (sites at which DNA's transcription into RNA is started)
Many initially ignored areas that encode RNA transcripts that are not
translated into proteins ; Regulatory roles perhaps.
Results also showed that DNA variations linked with certain diseases lie inside
or very close to non-coding functional DNA elements.
New ways to link genetic variation and disease.
Ultra-deep sequencing of RNAs from many different cell lines and from certain compartments
within the cells lead to the conclusion:
o 75% genome = transcribed at some point in cells
o Genes are highly interconnected with overlapping transcripts that are made from both
Force us to redefine a gene and the minimum unit of heredity.
Chromatin related studies
o Based on DNase I hypersensitivity
Detects genomic regions where enzyme access and cleavage is not hindered by
o Researchers found cell specific patterns of DNase I hypersensitive sites that shows
agreement with experimentally found and theoretically predicted binding sites of
o Also doubled the # of known recognition sequences for DNA-Binding proteins in human
o Found a 50 BP sequence that is found in many promoters.
Gerstein + friends = Theory behind the links of transcription factor networks.
o study attempts to clarify hierarchies of the transcription factor networks and assign
simple functions to genome elements.