CAS BI 203 Lecture Notes - Lecture 3: Noncoding Dna, Alternative Splicing, Differential Inclusion
22 May 2018
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Noncoding Sequences in Higher Eukaryotes
- Exons are the parts of the gene that DO get coded into proteins
Three Types:
1. Introns - In between, will get spliced out. Noncoding DNA sequences located WITHIN
genes that are transcribed along with the coding sequences (exons), and removed from
the mRNA after transcription (splicing).
a. Spacer sequences - noncoding DNA between different genes
b. RNA Pol TRANSCRIBES
c. Prokaryotic genes do not have introns but Eukaryotic genes do.
d. Key Experiment - Introns first discovered during studies on adenovirus
(Experiment pp. 156-157)
➢Example 1 of Eukaryotic gene containing introns: Mouse B-globin gene
i. 5’ UTR & 3’ UTR (UnTranslated Region → Has a role in regulating
translation)
ii. Proteins are coded from the adjacent gene and then mRNA.
➢Purpose of Introns:
- Some introns encode RNA, particularly non-coding regulatory RNAs
(microRNAs)(These interfere with gene function).
- Nested genes - One or Two examples in humans (Very rare!)
- There can be a gene “nested” in the intron of another gene. And
so both strands can be transcribed.
- The intron has a complementary pair that has an actual functional
gene on it and that gene can be important so the intron can be
transcribed.
- Regulatory roles in transcription:
- These can be found “prior” to the gene so they would be found in
5’ → transcription site. But sometimes they can be found in
introns.
- Transcription factors can bind to sites in introns and regulate
levels of transcription in genes.
- Allow for “alternative splicing”
- The differential inclusion or excision of exons during splicing,
yielding multiple possible mature mRNAs.
- Some exons can get skipped and the protein is modified to be a
shorter version. Skipping different exons makes different proteins.
- Ex. Mice can only make 4 variations of a specific gene that uwe
researches while humans can make 40 variations. This is why
even though we have practically the same amount of genes as
mice, we use all the variations and become more complex
creatures.
-Something to Think About (STA): If you skip an exon, you should
be aware of how many nucleotides were in that exon. Was it a
multiple of 3? If not, is the rest of the protein going to be the
same? Will it be modified?
- ~5 alternative splices for each human gene.
2. Repetitive Sequences
➢Simple-sequence repeats are >1,000,000 and ~10% fraction of genome
➢Retrotransposons - We have genes that actually LOOK like retroviruses and so
this is how HIV and other viruses can get in. They use reverse transcription to get
in. ~8% of our genome looks like viruses.
➢These are the Two Types:
- Simple-sequence repeats
- Aka satellite DNA - When genomic DNA is purified and
centrifuged, this DNA separates from the rest of the DNA.
- E.g. ACAACT - Can be repeated in tandem(over and over again)
- These can be found on all our chromosomes
- They play a role in chromosome structure not encoding
proteins
- Helps decide 3D structure, area, orientation, etc. (Current
research indicates)
- Transposons:
- Retrotransposons
- LINEs 21%
- SINEs 13%
- Retrovirus-like elements 8%
- DNA transposons 3%
- All exist as single non-tandem sequences dispersed throughout
the genome.
- These are long sequences (not like s-sr). Can be thousands of
nucleotides long.
- Transposons are also found in other places in the genome. On
different chromosomes.
- Transposons b/c transposable elements. Refers to their
movement as it goes to different sites in genomic DNA during
evolution.
- Two fundamental steps for transposition:
1. Duplication of the transposon
2. Insertion at a distinct site in the genome - Get’s inserted
elsewhere in the genome
➢This is true for all transposons
- So how do they differ?
- In size (# of bp) - LINEs are long, SINEs are small,
Retrovirus is very small (50% of our genome is made of
transposons)
- Similarities in sequence
Document Summary
Exons are the parts of the gene that do get coded into proteins. Introns - in between, will get spliced out. Example 1 of eukaryotic gene containing introns : mouse b-globin gene. 5" utr & 3" utr (untranslated region has a role in regulating translation) Proteins are coded from the adjacent gene and then mrna. ii. Some introns encode rna, particularly non-coding regulatory rnas (micrornas)(these interfere with gene function). Nested genes - one or two examples in humans (very rare!) There can be a gene nested in the intron of another gene. The intron has a complementary pair that has an actual functional gene on it and that gene can be important so the intron can be transcribed. These can be found prior to the gene so they would be found in. But sometimes they can be found in introns. Transcription factors can bind to sites in introns and regulate levels of transcription in genes.
