transcription (genetics) - Eukaryotic transcription, Measuring and detecting transcription, History, Terminology, Reverse transcription

The making of a complementary RNA copy of a gene in the DNA. Transcription requires the DNA or chromatin to be in an open configuration, allowing the binding of specific proteins (transcription factors) to the promoter of the gene being transcribed. Transcription is carried out by enzymes known as RNA polymerases.

Transcription is the process through which a DNA sequence is enzymatically copied by an RNA polymerase to produce a complementary RNA. Or, in other words, the transfer of genetic information from DNA into RNA.

Like DNA replication, transcription proceeds in the 5' → 3' direction (ie the old polymer is read in the 3' → 5' direction and the new, complementary fragments are generated in the 5' → 3' direction).

Initiation

The following steps occur, in order, for transcription initiation:

RNA polymerase (RNAP) recognizes and specifically binds to the promoter region on DNA. The RNA polymerase transcribes the DNA, but produces about 10 abortive (short, non-productive) transcripts which are unable to leave the RNA polymerase because the exit channel is blocked by the σ-factor. Promoter strength is in many (but not all) cases, a matter of how tightly RNA polymerase and its associated accessory proteins bind to their respective DNA sequences.

Termination

Two termination mechanisms are well known:

Intrinsic termination (also called Rho-independent termination) involves terminator sequences within the RNA that signal the RNA polymerase to stop. The inverted repeat forms a stable stem loop structure in the RNA, which causes the RNA to dissociate from the DNA template. The DNA on the template strand between the +1 site and the terminator is transcribed into RNA, which is then translated into protein.

Eukaryotic transcription

Eukaryotes have evolved much more complex transcriptional regulatory mechanisms than prokaryotes. DNA is also present in mitochondria in the cytoplasm and mitochondria utilize a specialized RNA polymerase for transcription. This allows for the temporal regulation of gene expression through the sequestration of the RNA in the nucleus, and allows for selective transport of RNAs to the cytoplasm, where the ribosomes reside.

Adding to this complexity, eukaryotes have three nuclear RNA polymerases, each with distinct roles and properties:

RNA Polymerase I is located in the nucleolus and transcribes ribosomal RNA (rRNA). RNA Polymerase II is localized to the nucleus, and transcribes messenger RNA (mRNA) and most small nuclear RNAs (snRNAs). RNA Polymerase III is localized to the nucleus (and possibly the nucleolar-nucleoplasm interface), and transcribes transfer RNA (tRNA) and other small RNAs (including the small 5S rRNA).

These three RNA polymerases are commonly referred to as Pol I, Pol II and Pol III (and less often Pol A, Pol B, and Pol C, respectively).

Further complexity is added by the multitude of transcription factors and signaling pathways that may interact in combination to mediate cell-type and developmental transcriptional regulation.

The basal eukaryotic transcription complex includes the RNA polymerase and additional proteins that are necessary for correct initiation and elongation.

Primary (initial) mRNA transcripts in eukaryotic cells are synthesized as larger precursor RNAs that are processed by splicing out introns (non-coding sequences) and ligating exons (non-contiguous coding sequences) into the mature mRNA.

Gene expression in eukaryotes is also controlled by complex interactions between cis-acting elements within the regulatory regions of the DNA, and trans-acting factors that include transcription factors and the basal transcription complex.

Initiation

The core promoter of protein-encoding genes also contains binding sites for the basal transcription complex and RNA polymerase II, and is normally within about 50 bases upstream of the transcription initiation site. The core promoter for Pol II often contains a TATA box, the highly conserved DNA recognition sequence for the TATA box binding protein, TBP, whose binding initiates transcription complex assembly at the promoter.

Some genes also have enhancer elements that can be thousands of bases upstream or downstream of the transcription initiation site.

Transcription process

For the pathway and process of construction of the transcription complex please see the individual polymerases: RNA polymerase I RNA polymerase II RNA polymerase III

Measuring and detecting transcription

Transcription can be measured and detected in a variety of ways:

Northern blot RNase protection assay RT-PCR In vitro transcription In situ hybridization DNA microarrays

History

Roger D.

RNA synthesis by RNA polymerase had been established in vitro by several laboratories by 1965; however, the RNA synthesized by these enzymes had properties that suggested the existence of an additional factor needed to terminate transcription correctly.

Terminology

Activator, is a DNA-binding protein that regulates one or more genes by increasing the rate of transcription Repressor, is a DNA-binding protein that regulates one or more genes by decreasing the rate of transcription

Reverse transcription

Some viruses(such as HIV, the cause of AIDS), have the ability to transcribe RNA into DNA in order to infect a cell's genome.