Transcription

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Transcription is the process when a particular segment of DNA is copied into RNA by the enzyme RNA polymerase. The RNA polymerase binds to a region of DNA called the promoter, and transcription is initiated. The RNA polymerase adds complementary RNA nucleotides to a template DNA strand; thus the RNA molecule is identical to the coding DNA strand, except that the DNA base thymine is replaced with uracil. Several chemical modifications are made to the nascent RNA molecule; a cap and a tail are added to the 5' and 3' ends, respectively.

The transcription start site (TSS) are the nucleotides that are the first to be transcribed from DNA into RNA. Transcription produces a complementary RNA strand called a primary transcript.

Molecular basis of eukaryotic transcription

http://www.nobelprize.org/nobel_prizes/chemistry/laureates/2006/advanced-chemistryprize2006.pdf

How RNA Polymerase Binds to DNA

Briefly, RNA polymerases combine with DNA binding factors to form the holoenzyme. The DNA binding factors ind to promoters and that's how RNA polymerases are directed to where to start transcription. There are known as http://en.wikipedia.org/wiki/Sigma_factor in bacteria. In eukaryotes there are about a dozen general initiation factors.

http://sandwalk.blogspot.jp/2008/09/how-rna-polymerase-binds-to-dna.html

Capping

Re-capping the message - http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2743798/

Splicing

Pause locally, splice globally - http://www.ncbi.nlm.nih.gov/pubmed/21530266 (transcription and splicing are functionally coupled)

Pervasive transcription

Multiple lines of evidence were used to conclude that the mammalian genome is pervasively transcribed (i.e., most of the genome is associated with at least one primary transcript) [1]. This review [2] discusses the ramifications of genome-wide transcription with respect to genomic organisation.

  1. Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project http://www.nature.com/nature/journal/v447/n7146/full/nature05874.html
  2. Genome-wide transcription and the implications for genomic organization http://www.nature.com/nrg/journal/v8/n6/full/nrg2083.html

Transcriptional noise

Transcriptional noise and the fidelity of initiation by RNA polymerase II - http://www.nature.com/nsmb/journal/v14/n2/abs/nsmb0207-103.html

Ripples from neighbouring transcription - http://www.ncbi.nlm.nih.gov/pubmed/19160492

Illegitimate transcription

Illegitimate transcription: transcription of any gene in any cell type - http://www.ncbi.nlm.nih.gov/pmc/articles/PMC286968/

Blog posts

Transcription initiation http://sandwalk.blogspot.ca/2013/09/transcription-initiation-sites-do-you.html and http://sandwalk.blogspot.jp/2014/07/transcription-initiation-sites-do-you.html (Two blog posts on this retracted paper http://www.nature.com/nature/journal/v502/n7469/full/nature12535.html). See also http://www.nature.com/nature/journal/v511/n7510/full/nature13587.html

http://sandwalk.blogspot.jp/2007/08/theme-transcription.html

When presenting genome-wide transcription data, remember to present the abundance of RNA, i.e. the expression level, and consider alternative explanations for transcription, such as spurious transcription: http://sandwalk.blogspot.jp/2009/04/how-to-evaluate-genome-level.html