Landscape of the human genome

Question 1

Genome - general

Answer 1

• 3.2 billion bases
• 4.8% unknown
• 0.14% unplaced
• 21,000 genes

Question 2

Genome subdivided

Answer 2

genes and gene-related sequences

• genes
• gene-related sequences
  
  • pseudogenes
  • gene fragments
  • introns, UTRs

intergenic DNA

• interspersed repeats
  
  • LINEs
  • SINEs
  • LTRs
  • DNA transposons
• other intergenic regions
  
  • microsatellites
  • etc

Question 3

Genes and gene-related

Answer 3

genes = 1%

gene-related = 36%

Question 4

Gene-related

Answer 4

• introns
• UTR
• promoters
• RNA genes
• pseudogenes
• gene fragments

Question 5

tRNA genes

Answer 5

• 100 genes in multiple chromosomes
• some in large clusters

Question 6

Ribozymes

Answer 6

• cleave other RNAs
• enzymes made of RNA
• single strand = interacts with DNA, binds RNA

Question 7

Ribonucleoproteins

Answer 7

• ribozymes that form complexes with proteins
• process nucleic acids
• ribosomes, splicosomes, telomersase

Question 8

Many RNA genes are involved in

Answer 8

antisense regulation of mRNA

• encoded in same segment of DNA as mRNA
• if read off in opposite direction can bind to mRNA made from same region of DNA (reverse complement)
• binds to argonaute = chops mRNA

Question 9

micro RNA
miRNA

Answer 9

• 22nt
• hairpin cleaved out
• exported from nucleus, cut in 2, double stranded
• regulation of gene expression in post-transcription
  
  • siRNA
  • RNAi
  • in cytoplasm

Question 10

long regulatory ncRNAs

Answer 10

• regulaiton of gene expression
• anti-sense regulators

Question 11

Antisense regulation

Answer 11

long DS RNA

→ dicer makes siRNA

→ SS RNA binds reverse complement

→ guide argonaute complexes to:

• cleave matching mRNA transcripts
• methylate DNA near newly synthesizing mRNA
  
  • regulates how much mRNA makes protein

Question 12

piwi protein interacting RNA (piRNA)

Answer 12

• from long RNA precursor
• active in germline cells, regulation of transcription expression

Question 13

small nucleolar RNA

(snoRNA)

Answer 13

• maturation of rRNA
  
  • site specific methylation
  • uridine → pseudouridine

Question 14

RNA interference

Answer 14

mature mRNA in cytoplasm

→ DS precursors of siRNA and miRNA bind dicer

→ made into short segments

→ short DS RNA binds argonaute

1 strand remains bound to argonaute (guide strand) to make RISC

• siRNA = perfect complement to target mRNA
• miRNA imprecise = targets hundreds

→ argonaute cleaves mRNA, degraded

Question 15

Pseudogenes and gene fragments

Answer 15

• partial gene sequences that don’t code viable proteins
• mutated copies of functional genes
• just exons
• gene followed by pseudogene that looks like it with inverted copy → transcribed to hairpin loop that’s chopped by dicer → 21nt siRNAs that cause cleavage of other mRNA transcripts

Question 16

LINEs

Answer 16

encode 2 proteins

• ORF1p = RNA binding and nucleic acid chaperone
  
  • kept safe
• ORF2p = reverse transcriptase and endonuclease
  
  • DNA, into genome

Question 17

SINEs

Answer 17

• ALU elements
• inverted repeates on right and left arms = RNA folds back on itself

Question 18

LTRs

Answer 18

• retrovirus, human endogenous retroviral sequences (HERVs)
• 6-11 kbp (long) → protease, reverse transcriptase to move around, reshuffle
• 1.5-3 kbp (short) → fewer/no genes

Question 19

DNA transposons

Answer 19

• cut and paste
• large autonomous transposons
  
  • encode transposase
• small non-autonomous transposons
  
  • min inverted repeat transposable elements
  • encode miRNAs
  • no transposase

Question 20

Microsatellites

Answer 20

• simple sequence repeats
• length evolves (replication slippage)
  
  • affects gene expression
• pop gen to see differences between closely related individuals because evolve so quickly

Question 21

Mitochondrial genome

Answer 21

• 66% protein-coding genes
• thousands of copies in every cell
• shorter and more gene-rich than nuclear genome
• 2 places for replication to start → transcribe in both directions
• own tRNA
• some genes overlap = 2 genes encoded by the same bit of DNA
• more than 1 ORF, all functional

Question 22

ENCODE

Answer 22

• claims 80.4% of genome with biological function
• 147 types of tissue

methods

• RNA seq
• CAGE
• RNA-PET
• ChIP-seq
• DNase-seq
• FAIRE-seq
• RRBS

Question 23

RNA-seq

Answer 23

isolate RNA sequences, sequence

Question 24

CAGE

cap analysis gene expression

Answer 24

• captures methylated cap at 5’ end of RNA
• sequence adjacent tags → transcriptional start sites

Question 25

RNA-PET

Answer 25

• paired end tags
• captures RNA with 5’ methyl cap and poly(A) tail
• = full length RNA, sequence end tags

Question 26

ChIP-seq

Answer 26

• regions of crosslinked chromatin
• selected with specific antibody
• sequence regions most often bound by the protein (in chromatin)

Question 27

DNas-seq

Answer 27

• DNaseI cuts DNA where accessible
• sequence cut regions to show open chromatin

Question 28

FAIRE-seq

Answer 28

• freeze and pull out DNA with bound protein to see what part of DNA binds protein

Question 29

RRBS

Answer 29

• methylation affects function
• unmethylated = C → U
  
  • U where unmethylated C
  • methylation protects C from becoming U
• see methylation sites