Eukaryotic Transcription, RNA Processing, and Non-Coding RNAs

Vocabulary practice flashcards covering eukaryotic transcription initiation, RNA polymerases, preinitiation complex formation, co-transcriptional RNA processing (capping, splicing, polyadenylation), the spliceosome mechanism, and small non-coding RNAs (miRNA, siRNA, and RNA interference).

Gene Spacing (Bacteria vs. Humans)

The relative distance between genes in a genome; bacteria have approximately $1\,\text{gene}$ per $1400\,\text{bp}$, whereas humans have roughly $1\,\text{gene}$ per $100{,}000\,\text{bp}$.

Primary Transcript (pre-mRNA)

The newly synthesized, unprocessed eukaryotic RNA molecule that must undergo modifications before exiting the nucleus.

Mature mRNA

The fully processed RNA transcript that has undergone 5' capping, splicing, and polyadenylation, making it competent for export from the nucleus to the cytoplasm.

RNA Polymerase I

The eukaryotic enzyme that transcribes ribosomal RNA (rRNA) genes, excluding the $5\text{S}\text{ rRNA}$.

RNA Polymerase II

The eukaryotic enzyme that transcribes all protein-encoding genes to yield mRNA, as well as transcribing some small nuclear RNAs (snRNAs).

RNA Polymerase III

The eukaryotic enzyme that transcribes small functional RNA genes, such as transfer RNAs (tRNAs), $5\text{S}\text{ rRNA}$, and some snRNAs.

General Transcription Factors (GTFs)

A group of accessory proteins that assemble at the promoter before or after RNA polymerase II binds, required for RNA polymerase II to initiate RNA synthesis.

Preinitiation Complex (PIC)

The macromolecular assembly at the gene promoter formed by General Transcription Factors (GTFs) together with the RNA polymerase II core.

TATA Box

A conserved promoter sequence located roughly $30\,\text{bp}$ upstream of the transcription start site that serves as the binding site for the TATA-binding protein (TBP).

TATA-Binding Protein (TBP)

A general transcription factor subunit (part of TFIID) that binds directly to the TATA box and recruits other GTFs and the RNA polymerase II core to form the PIC.

Carboxyl-Terminal Domain (CTD)

The flexible tail domain of RNA polymerase II that is phosphorylated by a GTF to permit transcription elongation and coordinates co-transcriptional RNA processing enzymes.

5' Cap

A methylated 7-methylguanosine residue added to the 5' end of a nascent pre-mRNA transcript via a 5'-to-5' triphosphate bridge after the first $25\,\text{nt}$ are synthesized.

Exons

The protein-coding segments of eukaryotic genes that are retained and ligated together during splicing to create a sequence colinear with the encoded protein.

Introns

Non-coding intervening sequences within eukaryotic genes that interrupt exons and are excised from pre-mRNA during RNA splicing.

Alternative Splicing

A regulatory mechanism whereby variations in the inclusion and exclusion of exons or splice sites in a primary transcript generate multiple distinct mRNA isoforms and protein variants.

Polyadenylation

The endonucleolytic cleavage of pre-mRNA downstream of an AAUAAA or AUUAAA consensus sequence followed by the template-independent addition of a $150\text{--}200$ adenine nucleotide poly(A) tail to the 3' end.

Spliceosome

A large macromolecular ribonucleoprotein machine composed of 5 snRNP subunits and greater than 100 proteins that assembles stepwise on pre-mRNAs to excise introns.

snRNPs (Small Nuclear Ribonucleoproteins)

RNA-protein complexes (including U1, U2, U4, U5, and U6) that recognize key splicing signals in pre-mRNA and catalyze the removal of introns.

GU–AG Rule

The conserved rule of pre-mRNA splicing stating that introns typically begin with the dinucleotide GU at the 5' splice site and terminate with AG at the 3' splice site.

Branch Point

A conserved intronic sequence located $15\text{--}45\,\text{nt}$ upstream of the 3' splice site containing a crucial adenosine residue whose 2'-hydroxyl group attacks the 5' splice site.

Transesterification

The two-step chemical mechanism of splicing: first, the 2'-OH of the branch point adenosine attacks the 5' splice site; second, the 3'-OH of the 5' exon attacks the 3' splice site, yielding linked exons and an excised lariat intron.

Long Non-Coding RNA (lncRNA)

A class of regulatory non-coding RNA transcripts that are equal to or greater than $200\,\text{nucleotides}$ in length ($\ge 200\,\text{nt}$).

Small Non-Coding RNA (small ncRNA)

A class of regulatory non-coding RNA molecules that are less than $200\,\text{nucleotides}$ in length ($< 200\,\text{nt}$), including microRNAs, siRNAs, snoRNAs, snRNAs, and piRNAs.

microRNA (miRNA)

Endogenous, genome-encoded small non-coding RNAs of $19\text{--}22\,\text{nucleotides}$ that regulate gene expression primarily via post-transcriptional gene silencing.

Small Interfering RNA (siRNA)

Short double-stranded regulatory RNAs (roughly $20\text{--}25\,\text{nt}$) predominantly derived from exogenous triggers (such as viruses, transposons, or transgenes) that target specific RNAs for degradation.

RNA Interference (RNAi)

A biological process discovered in 1998 by Andrew Z. Fire and Craig C. Mello where exogenous double-stranded RNA triggers sequence-specific gene silencing.

Dicer

An RNase III-family endonuclease that excises small RNA duplexes (~$20\text{--}25\,\text{nt}$) from long double-stranded or precursor hairpin RNAs.

Argonaute (Ago) Proteins

Core effector proteins that bind processed small RNAs (miRNAs/siRNAs) to guide sequence-specific gene silencing, translational repression, RNA degradation, or heterochromatin formation.