Tag: transcription

Difficult to disentangle the effects of promoter and ribosome binding site on gene expression level just with a Ribo-seq dataset

December 10, 2023

Most Ribo-seq datasets would correlate a gene with an expression level. Thus, there may be a possibility of using such dataset to find correlations between promoter and an expression level. However, this approach faces the challenge of inability to disentangle the effects of ribosome binding site (translation), and promoter (transcription) on the gene expression level … More Difficult to disentangle the effects of promoter and ribosome binding site on gene expression level just with a Ribo-seq dataset

Protein degradation is one of two switches that control gene expression

November 27, 2021

At any point in time, not all genes in the genome are expressed. The first step of expression would involve transcription of the pertinent gene. Once the gene has been transcribed and translated, the enzyme or protein would remain active in the cell. So, how does a cell shutdown the activity of an enzyme or … More Protein degradation is one of two switches that control gene expression

RNA viruses evolve more rapidly than DNA viruses

November 20, 2020

Viruses can generally be classified as DNA and RNA viruses, which differ in their genetic makeup. During infection, DNA viruses inject DNA into the host cells, which is transcribed to mRNA for downstream protein translation. On the other hand, RNA viruses inject RNA into host cells, which must be reverse-transcribed into DNA, prior to transcription … More RNA viruses evolve more rapidly than DNA viruses

Lack of universal method for activating silent biosynthetic gene cluster

August 24, 2020

Many species of filamentous bacteria and fungi are prolific producers of natural products useful for a variety of medicinal applications such as serving as antibiotics, immunosuppressants etc. However, mining microbial sources for novel natural products from secondary metabolism has reached a roadblock presented by our inability to profile bioactive molecules from unexpressed biosynthetic gene clusters. … More Lack of universal method for activating silent biosynthetic gene cluster

Transcriptional pausing by RNA polymerase II

April 1, 2020

RNA polymerase transcribes DNA into messenger RNA for downstream translation to synthesise protein. A recent study has described the transcriptional pausing of RNA polymerase II after transcription of 60 nucleotides based on data from high resolution cryo-electron microscopy structural images of the transcriptional complex. The papers are as listed below. Transcriptional speed bumps revealed in … More Transcriptional pausing by RNA polymerase II

Cryo-electron microscopy enables the profiling of molecular interactions between macromolecular complexes acting on DNA

December 18, 2019

DNA is a long molecule encoding genetic information. In its full length, it could not be encapsulated within the cell. Hence, proteins such as histone are important players in spooling and condensing DNA into structures known as nucleosomes that facilitate the packaging of long DNA molecules into structures small enough to fit inside individual cells. … More Cryo-electron microscopy enables the profiling of molecular interactions between macromolecular complexes acting on DNA

Much of a yeast promoter may be redundant

December 14, 2019

Promoters in yeast are typically longer than those in bacterial species. Hence, in synthetic biology applications, plasmids constructed for use in yeast would contain long stretches of promoter together with the target gene. Given that each gene in yeast requires a dedicated promoter unlike the case in bacterial species where a single promoter could help … More Much of a yeast promoter may be redundant

Cell free transcription/translation system provides a clean genetic background for testing genetic circuits in synthetic biology

August 12, 2019

Whole cells have been workhorses in biocatalysis, particularly in providing a conducive environment for enzyme function as well as providing for cofactor regeneration. However, heterologous overexpression of genes within an endogenous genetic context may encounter problems associated with cross-talks between the heterologous and endogenous systems. The problem is not significant if the goal is in … More Cell free transcription/translation system provides a clean genetic background for testing genetic circuits in synthetic biology

Phase separation of transcriptional activation complex in cells

August 2, 2018

DNA transcription is a complex choreographed exercise where myriad transcription factors, accessory proteins and RNA polymerase assemble on defined sites close to the transcriptional start site for the generation of a messenger RNA (mRNA) from DNA. While it was conventionally viewed as distinct molecules mediating the process, recent studies have observed, through various microscopy techniques, … More Phase separation of transcriptional activation complex in cells

Bacterial immune system utilized for genome editing

August 27, 2017

Feature article in Nature, Vol. 541, Issue 7637, pp. 280-282, “CRISPR’s Mysteries”   Summary of article: Used by bacterial and archaeal species for immune surveillance and defence of the cell against viruses, the single cell organism’s immune system, clustered regularly interspaced short palindromic repeats (CRISPR) system has increasingly find use in alternate scenarios, the most … More Bacterial immune system utilized for genome editing