Eukaryotic genetics

Template strand

positive strand of DNA that is used to generate RNA

Coding strand(Non template strand)

negative strand of DNA that has the same sequence as RNA except swapping T for U

TSS

This is called the transcription start site which is defined as the +1 nucleotide

Transcriptional unit

sequence of nucleotides in DNA that codes for a single RNA molecule along with the regulatory sequences upstream and downstream

UTR

mRNA contains a coding region and untranslated regions which vary depending on gene activity and can be important for the secondary structure of mRNA as well as polyadenylation

Pribnow box

the -10 consensus sequence in prokaryotes that acts as one of the promoters

Consensus sequence

the “average” sequence if the DNA sequence matches it it will have a higher binding affinity to the sigma subunit of RNA pol in prokaryotes

Writers

Add certain functional groups to DNA to modify it

Erasers

remove certain functional groups off DNA to modify it

Remodelling complex

protein machinery that uses ATP to help move and slide DNA and eject it along the nucelosome

RNA pol 1

responsible for expression of rRNA

RNA pol 2

responsible for expression of mRNA, snRNA, miRNAS

RNA pol 3

responsible for expression rRNA, tRNA, snRNA

General transcription machinery

Refers to RNAP and a set of GTF functioning with RNAP 1,2, or 3 for expression of all genes transcribed by a particular RNAP

General transcription factors

composed of multiple subunits which may be shared and required for multiple RNAP’s

Core promoter element

short DNA sequence located right around the TSS that helps position and assemble the basic transcription machinery so RNA polymerase starts in the right place

Scaffolds

bridge the transcription factors and the general transcription machinery

Chromatin modification complexes

Chemically modifying histones through for example methylation or acetylation to make the promoter region either more or less accessible

Chromatin remodelling complex

Structurally modifying the histones in an ATP dependent manner

Heterochromatin

Is the state of DNA when it is compact and less accessible to transcription machinery often causing gene repression

Transcription factor

The same as GTF except for that they are sequence specific often called “transcriptional activators”

Proximal regulatory elements

Located near the core promoter on a DNA strand

Distal regulatory elements

Further away from the core promoter but still influence transcription through DNA looping e.g. enhancers

Inducible gene

A gene that is typically low or off at baseline but can be strongly turned on in response to a specific signal

TAFs

TBP-associated factors play a role in connecting the regulatory inputs to the core machinery AND core promoter recognition. they are a part of the TFIID

Housekeeping gene

Expressed in most cell types most of the time because it encodes products needed for basic cellular function

Enhancer

Are distal regulatory elements that aren’t physically part of the promoter but bring together regulatory proteins into contact with the GTM

Enhancesome

A multi protein complex that binds the enhancer

NMD(Nonsense-mediated mRNA decay)

Eliminates mRNA transcripts that contain premature stop codons which could lead to truncated and deleterious proteins

Haplosufficient

Having one copy of the dominant allele is necessary for the normal phenotype