Nucleus and nucleolus | Cell and molecular biology

Nucleus and nucleolus: The nucleus is surrounded by a double nuclear membrane. The outer membrane is continuous with the rough endoplasmic reticulum. Pores are present in the nuclear membrane. One or more darkly staining spherical bodies called the nucleoli are found inside the nucleus. These are the sites at which ribosomes are assembled. DNA associated with histone proteins forms chromatin.

Comparison between euchromatin and heterochromatin

Euchromatin

Contains transcriptionally active DNA
More abundant
Dispersed
Acetylation of histone proteins essential for gene activation

Heterochromatin

Transcriptionally inactive
Less abundant
Condensed
Barr body is made of heterochromatin
Methylation of DNA represses transcription

Transcription: It is the process of transferring the genetic information in DNA to messenger RNA (mRNA). It begins by binding of RNA polymerase II at promoter regions of DNA. It leads to the formation of an initiation complex composed of RNA polymerase II and transcription factors.

TATA box: It is a promoter sequence located upstream of the start site. Transcription is initiated at the TATA box. It binds transcription factors such as TATA binding protein or TBP. CAAT box: It is located within the promoter region, upstream of the start site. It binds transcription factors like NF1. GC box: It is located upstream to the TATA box and binds transcription factors like SP 1 , WT and zinc-finger proteins.

RNA polymerase II synthesizes the mRNA strand as a primary transcript called heterogenous nuclear RNA or hnRNA, which contains both exons (coding sequences) and introns (non-coding sequences).

Post-translational processing of primary RNA transcript

Capping: It is the addition of 7-methylguanosine at the 5’ end of the RNA transcript. Capping protects RNA from degradation by exonucleases, facilitates transport from the nucleus to the cytoplasm, splicing and attachment to 40S ribosome.
Polyadenylation: It is the addition of about 200 adenosine moieties to the 3’ end of the RNA transcript. It protects RNA, facilitates transport from the nucleus and recognition by ribosomes.
Splicing: All introns are removed while exons are joined together by splicing carried out by the spliceosome. It is composed of small nuclear RNAa (snRNA) associated with proteins to form the small nuclear ribonucleoprotein particles or snRNPs. The junction of exons to introns is called a splice site. Antibodies to snRNPs are found in SLE.

Alternative splicing is a physiological process that enables mRNA to direct synthesis of tissue specific protein variants (isoforms) that may have different cellular functions or properties. It occurs by rearranging the pattern of intron and exon elements that are joined by splicing to alter the mRNA coding sequence. Alternate splicing accounts for 25000 human protein-coding genes being able to generate >90,000 different proteins. Aberrant splicing is seen in many diseases including cancers and beta thalassemia.

Regulation of gene expression: Following factors are important:

i) Only euchromatin is accessible to RNA polymerase II and transcription factors. Heterochromatin is not transcriptionally active.

ii) The rate of binding of RNA polymerase is determined by transcription factor binding to TATA, CAAT and GC boxes in the promoter region.

iii) Enhancers are DNA sequences located upstream or downstream from the promoter region. They bind to regulatory elements like transcription factors and increase the rate of transcription.

iv) Silencers are DNA sequences that bind regulatory elements called repressors leading to decrease in transcription. They can be located either near or away from the promoter, including within the intron.

v) Steroids, growth factors and hormones affect transcription directly and indirectly.