DNA Transcription

First time, François Jacob and Jacques Monod emit a molecule that can carry genetic material in the form of proteins. Severo Ochoa won the 1959 Nobel Prize in Physiology or Medicine for developing a method for in vitro synthesis of RNA with polynucleotide phosphorylase, useful for decoding the genetic code. RNA synthesis by RNA polymerase was established in vitro by several laboratories in 1965; however, the RNA synthesised by these enzymes has properties that suggest the existence of an additional factor required to terminate transcription correctly. 

Roger D. Kornberg won the 2006 Nobel Prize in Chemistry “for his investigations on the molecular basis of transcription in eukaryotes”.

DNA Transcription 

Transcription is the process of copying a piece of DNA into RNA.  DNA fragments that are transcribed into RNA molecules that can encode proteins are thought to produce messenger RNA (mRNA). Other pieces of DNA that are copied into RNA molecules are called noncoding RNAs (ncRNAs). Averaged across multiple cell types in a given tissue, the number of mRNAs is 10 times greater than the number of ncRNAs (although ncRNAs from single cell types may exceed mRNA in particular). 

 The general predominance of mRNA in cells holds true even though less than 2% of the human genome can be transcribed into mRNA (Human Genome Coding vs Non-coding DNA), while at least 80% Mammal genomic DNA can be actively transcribed (into one or more cell types), with the majority of 80% being considered as ncRNAs. 

Both DNA and RNA are nucleic acids that use nucleotide base pairs as complementary languages. During transcription, a strand of DNA is read by an RNA polymerase, which produces an additional antipolar RNA strand known as the primary transcript.

The piece of DNA is transcribed into an RNA molecule that codes for a protein, that RNA is called messenger RNA (mRNA); mRNA, in turn, serves as a template for protein synthesis by translation. Other DNA fragments can be transcribed into non-coding small RNAs such as microRNAs, transport RNAs (tRNAs), small nucleolar RNAs (snoRNAs), small nuclear RNAs (snRNAs), or RNA molecules known as ribozymes. 3] as well as molecules not larger than coding RNA such as ribosomal RNA (rRNA) and non coding long RNA (ncRNA). In general, RNA helps with protein synthesis, regulation and processing; it therefore plays a fundamental role in performing functions in a cell.

In virology, the term transcription can also be used to refer to mRNA synthesis from an RNA molecule (that is, equivalent to RNA replication). For example, the genome of a negative-sense single-strand RNA virus (ssRNA) can be a template for a positive-sense single-strand RNA (ssRNA +) [needs explanation]. This is because the plus strand contains the sequence information needed to translate the viral proteins needed for viral replication. This process is catalyzed by viral RNA replicase.

DNA Transcription

Steps of Transcription

Transcription can be divided into four  steps: initiation, promoter, elongation, and termination:

Initiation 

When RNA polymerase binds to a specific DNA sequence known as a “promoter,” it forms a “closed complex” with one or more general transcription factors, which is then released from the promoter and used to initiate transcription. The promoter DNA is still fully double-stranded in the “closed complex” even though the complex is closed.

The RNA polymerase then unwinds roughly 14 base pairs of DNA with the assistance of one or more general transcription factors, resulting in the formation of an RNA polymerase-promoter “open complex.” The promoter DNA in the “open complex” is partially unraveled and single-stranded, indicating that it is active. The “transcription bubble” refers to the single-stranded DNA that has been exposed during the transcription process.

The RNA polymerase then selects a transcription start site in the transcription bubble with the assistance of one or more general transcription factors, binds to an initiating NTP and an extending NTP (or a short RNA primer and an extending NTP) that are complementary to the transcription start site sequence, and catalyses bond formation to yield an initial RNA product.

Promoter

After the first bond is created, the RNA polymerase must exit the promoter. During this phase there is a tendency to release the RNA transcript and make shortened transcripts. This is called abortive initiation, and is frequent for both eukaryotes and prokaryotes.

 Abortive initiation continues to proceed until an RNA product of a threshold length of roughly 10 nucleotides is produced, at which point promoter escape occurs and a transcription elongation complex is created.

Mechanistically, promoter escape occurs through DNA scrunching, giving the energy needed to disrupt connections between RNA polymerase holoenzyme and the promoter.

Elongation 

One strand of the DNA, the template strand (or noncoding strand), is employed as a template for RNA production. As transcription occurs, RNA polymerase traverses the template strand and employs base pairing complementarity with the DNA template to make an RNA copy (which elongates throughout the traversal) (which elongates during the traversal). 

Although RNA polymerase traverses the template strand from 3’ → 5’, the coding (non-template) strand and freshly generated RNA can also be utilized as reference points, so transcription can be defined as occurring 5’ → 3’. This forms an RNA molecule from 5’ → 3’, a perfect copy of the coding strand (except that thymines are substituted with uracils, and the nucleotides are constituted of a ribose (5-carbon) sugar where DNA has deoxyribose (one fewer oxygen atom) in its sugar-phosphate backbone).

Termination 

Both Rho-independent termination and Rho-dependent termination are techniques used by bacteria for transcriptional repression in order to terminate transcription. The transcription of RNA is terminated in Rho-independent transcription termination, which occurs when the freshly synthesised RNA molecule forms a G-C-rich hairpin loop, which is followed by a run of Us. 

When the hairpin forms, the mechanical stress breaks the weak rU-dA connections, allowing the DNA–RNA hybrid to occupy the space created by the hairpin. This causes the poly-U transcript to be pulled out of the active site of the RNA polymerase, resulting in transcription being terminated. In the “Rho-dependent” type of termination, a protein factor known as “Rho” destabilised the association between the template and the mRNA, allowing the newly produced mRNA to be released from the elongation complex and into the nucleus.

Though less well understood than transcription termination in bacteria, polyadenylation is a process that involves cleavage of the new transcript followed by the addition of adenines to the new 3’ end of the transcript in a template-independent manner at the new 3’ end of the transcript.

Conclusion 

Transcription is a highly complicated chain of processes that requires the interaction of several proteins and nucleic acids to result in an mRNA strand that can be translated into a protein. The detection of promoter sites and enhancer regions positioned near transcribed genes is crucial to the commencement of transcription.