RNA and the Transcriptome Summary

RNA Precursors: Many RNAs are initially synthesized as precursors, also known as primary transcripts or pre-RNAs.
Processing: These precursors undergo processing to yield functional RNA molecules.
Splicing:
- Splicing is a key process where exons (coding regions) are separated from introns (non-coding regions).
- Introns are commonly found in protein-coding genes (PCGs) but are less common in ribosomal RNA (rRNA) and transfer RNA (tRNA).
- Splicing takes place in the nucleus.
- Unspliced pre-mRNA forms the heterogenous nuclear RNA (hnRNA) within the nuclear fraction.
End-Modifications:
- In addition to splicing, RNA undergoes end-modifications.
- These include the addition of a 5'-cap and a 3'-poly(A) tail.
- The 3'-poly(A) tail addition is facilitated by a template-independent RNA polymerase called poly(A) polymerase.

The structure of a typical eukaryotic gene includes the following elements:

5' UTR (Untranslated Region): A region at the 5' end of the mRNA that is not translated into protein but plays a role in translation regulation.
Exons: Coding regions of the gene that are transcribed and ultimately translated into protein.
Introns: Non-coding regions of the gene that are transcribed but removed by splicing before translation.
3' UTR (Untranslated Region): A region at the 3' end of the mRNA that is not translated into protein but affects mRNA stability and translation.
Codons: Triplet sequences of nucleotides within the exons that specify particular amino acids during translation.
Promoter: A region of DNA, such as the TATA box, CAAT box, and GC box, usually found upstream of a gene, that initiates transcription.
Regulatory Elements: DNA sequences, such as enhancers and silencers, that control the rate of gene transcription.
Transcription Initiation Site: The point where RNA polymerase begins transcribing the DNA sequence.
5' Splice Site (GT): The location on the pre-mRNA where splicing occurs to remove an intron.
3' Splice Site (AG): The location on the pre-mRNA where splicing occurs to remove an intron.
Translation Initiation Site: The point on the mRNA where translation begins.
Translation Termination Site: The point on the mRNA where translation ends.
Polyadenylation Site: The sequence on the pre-mRNA that signals the addition of the poly(A) tail.

rRNA and tRNA Processing:
- rRNAs and tRNAs undergo chemical modifications such as methylation, deamination, thio-substitution, base isomerization, and double-bond saturation.
RNA Editing:
- RNA editing involves changes in the mRNA sequence.
- These changes can alter the amino acid sequence of the resulting protein.
Functions of RNA Processing:
- Helps initiate translation.
- Protects RNA from degradation.

Early Definition (circa 1997):
- The transcriptome was initially defined as the "mRNA component" of a cell.
- Studies aimed to identify as many mRNAs as possible to understand overall gene expression patterns in tissues and how these patterns change (e.g., cancer vs. non-cancer cells).
Current Definition:
- The transcriptome now refers to "all the different RNAs" in a cell.
- This definition acknowledges the role of non-coding RNAs (ncRNAs) in cells.
MicroRNAs (miRNAs):
- Small non-coding RNAs (sncRNAs) called microRNAs (miRNAs) regulate gene expression.
- miRNAs degrade mRNAs whose products are no longer needed.
- In humans, approximately 1000 miRNAs have been identified, each targeting single or small groups of mRNAs.

Definition of Proteome: The entire set of proteins expressed by a cell or organism at a certain time.
Proteome in Mammalian Liver Hepatocytes:
- Contains 10,000 – 20,000 different proteins and $8 \times 10^9$ individual molecules, equating to 0.5 ng of protein (18 – 20% of total cell weight).
- Copy numbers of individual proteins vary enormously, from <20,000 molecules per cell (rare) to 100 million copies for common types.
- More than 50,000 copies per cell is considered relatively abundant; about 2,000 proteins fall into this category.
Comparing Proteomes from Different Mammalian Cells:
- Very few differences among common proteins, which are termed housekeeping proteins (HKPs).
- HKPs perform general biochemical activities in cells; proteins for specialized functions are often rare (except for hemoglobin (Hb) in red blood cells (RBCs)).
The Transcriptome-Proteome Link:
- tRNA: Adaptor molecules that convert DNA to amino acid ‘language’.
- Genetic code: Uses codewords (codons) as part of DNA-protein conversion.