Gene Structure and Chromatin Flashcards
3 components defining a gene (in eukaryotes)
1) transcribed section of DNA molecule and its
2) CIS regulatory elements
3) this section of DNA sequence contributes to a phenotypic trait (influences structure/function of organism)
what does the translated or “protein coding” portion of the gene consist of? how long is it?
average 1200 bp; consists of exons (some exons have UTRs also)
what does the transcribed part of the gene include? average size?
all exons and introns; 27,000 bp
what do exons contain?
protein-coding regions and untranslated sequences (5’ and 3’ UTRs)
what do introns contain?
start with splice donor sites and end with splice acceptor sites
two consequences of alternative splicing
1) can cause some exons to be removed with introns
2) can cause some introns to be used as exons
are CREs (cis-regulatory elements) transcribed?
no
where is the promoter located?
right next to transcriptional start (beginning of exon 1); where the pre-initiation complex forms
how many promoters per gene?
one
characteristics of promoters
binding site for RNA pol, binding site for “general” transcription factors, often have TATA boxes, around 100-1000 bp
where are enhancers located?
often far (100 kbp) from transcriptional start and first exon; can be in introns of same gene, in adjacent gene or downstream
purpose of enhancers
needed for expression in specific tissues/ cell types at specific time
how many enhancers per gene?
several
characteristics of enhancers
bind cell-type specific transcription factors, have transcription factor binding sites (TBSs), around 100-1000 bp long
role of shadow enhancers
redundant, back-up enhancer (functionally equivalent to enhancers)
role of silencers
prevent transcription in particular cell types; bound by “repressing” transcription factors
4 CREs
promoters, enhancers, shadow enhancers, silencers
why are CREs hard to find?
TBSs are short and “degenerate” (their sequences are not very strict), and the rules in which they are ordered and spaced are unknown, located up to 500,000 bp away from promoter
approximate size of an average eukaryotic “gene” (including space between CREs and exons)
100,000-1,000,000 bp
given the average size of a eukaryotic gene and the fact that we have 3.1 billion bp, how do we have so many different “genes”?
1) genes can overlap; all or parts of adjacent genes can be present between Exons and CREs
2) genes can be on either strand, with transcription oriented in different directions
3) genes can share enhancers
define nuclear genome
all DNA in your nucleus
in eukaryotic cells, the nuclear genome is made of..
individual, linear, double stranded DNA molecules called chromosomes
genes are sequences on…
chromosomes
how long are human chromosomes
57-250 million bp long
how many genes do human chromosomes have?
200-2000 genes each
what does the word “chromosome” technically refer to?
DNA molecules with their associated proteins
what are chromosomes made of?
chromatin (any sequence of DNA + associated proteins)
what are the proteins associated with DNA called?
histones
basic unit of chromatin
nucleosome
define nucleosome
147 bp of DNA wrapped around 8 histone proteins (histone octamer)
what happens to nucleosomes during transcription?
RNA polymerase pushes off histones then nucleosome reforms behind it
open, loosely wrapped and actively transcribed chromatin
euchromatin
tightly wrapped, generally inactive and untranscribed
heterochromatin
location of euchromatin
unwrapped and free in nucleus
location of heterochromatin
attached to nuclear envelope (membrane)
