sign in sign up
<<
Home , Messenger RNA

More than a Messenger: The Secret of RNA

Radhika Mathur Matt Schwartz Ilana Kelsey

Biological & Biomedical Sciences Harvard University

1 Roadmap for the evening

1. Introduction to RNA and its Messenger Roles

2. Non-Messenger Roles of RNA

3. RNA and Healthcare

2 1. Introduction to RNA and its Messenger Roles

3 DNA: The Source of Information • Inherited genetic material present in every of the body

DNA

Nucleus

Cytoplasm

4 DNA: The Source of Information • DNA stores information in segments called .

Gene B

Gene A

• The sequence of each gene contains the information required to form a single .

Protein B Protein A 5 : Functional of the Cell

• Present within the cell, on the cell surface, and outside of cells

• Highly diverse in structure and function

• What are some of these functions?

–

– Membrane channels

– Transporters

– Hormones

– Antibodies

6 How is information contained in genes? • DNA consisting of 4 ‘bases’: , Cytosine, Thymine, and Guanine • A and T are complementary, C and G are complementary • The is a sequence of ~3 billion bases of DNA

7 How is the information on genes accessed?

Gene A

DNA

8 How is the information on genes accessed?

Gene A

Sequence of Gene A: TGACCG

Protein A 9 How is the information on genes accessed?

Gene A

Messenger RNA

10 DNA RNA

• 4 distinct bases • 4 distinct bases

• Length ~3 billion bases • Length ~1000 bases

• Double stranded • Single stranded

• Confined to the nucleus • Travels outside the nucleus

• High stability • Low stability

11

• Process by which information contained on a gene is copied to a matching strand of Messenger RNA.

DNA

RNA

12 Transcription U G A C C A A A C A C A G

A C C U G A C A A C A G

13

• Process by the instructions on Messenger RNA are used to create protein.

RNA

Protein

14 Translating the Genetic

G A C C A C U A A G A C

• Reads 3 bases at a time • AAC Asparagine • AGA Arginine • CUG Leucine • ACC Threonine

15 Transcription & Translation U G A C C A A A C A C A G

G A C C U C A A A C A G

16 The Messenger Role of RNA

DNA Transcription

RNA

Translation

Protein

“The Central Dogma of Molecular ”

17 Questions?

18 The Messenger Role of RNA

DNA

RNA

Protein

19 Is Messenger RNA just an intermediate? U G A C C A A A A C C A G C C U G A A C A A C A G A C U G U G G A U A G U C A C U A U C G A C A A U U

20 Images from Shuttersotck (Nazlizart) and Meregalli et al, (2011) DOI: 10.5772/24013. Is Messenger RNA just an intermediate? U G A C C A A A G A C C A • The function of a cell is dependent upon the proteins it contains.

MUSCLE CELLS PANCREATIC CELLS

Myosin

• Every cell contains the genes required to create every protein. 21

Messenger RNA allows cells to specialize

MUSCLE CELLS PANCREATIC CELLS

Insulin Gene

Insulin Gene

C U G G A C C G A U U C Myosin G A Gene C A A A C A G U A G U

Myosin Gene

22 Messenger in Development

23 Messenger RNAs in Development

• Cells differentiate by transcribing messenger RNAs from lineage-specific genes

C U A C C A G A C U C U A G A A G A C A A U U A C

U G G A C U G A U A G U C

• Transcription factors regulate which messenger RNAs are transcribed

+ MyoD

A C C U G A C A A C A G

24 Summary

• RNA plays a critical messenger role by carrying information from DNA outside of the nucleus, where it is used to create protein.

• Genes are transcribed to messenger RNAs, which are then translated to proteins.

• The messenger RNAs that are transcribed in a cell determine which proteins are created and how the cell functions.

• Transcription of lineage-specific genes allows cells to differentiate, and is essential for the development of multicellular .

25 Roadmap for the evening

1. Introduction to RNA and its Messenger Roles

2. Non-Messenger Roles of RNA

3. RNA and Healthcare

26 2. Non-Messenger Roles of RNA

27 Citation goes here, do not copy/paste URLs if possible! RNA: The Messenger

DNA

RNA

Protein

28 Human Genome is 3 Billion Bases

• What portion of the genome encodes proteins?

• How much of the genome is transcribed?

29 (National Human Genome Research Institute) RNA: More Than A Messenger

DNA

RNA 76%

Protein 3%

30 76% What is the other 73%?

Noncoding RNA

3% 31 Coding vs Noncoding RNA

• Coding Transcripts: – messenger RNA – made into proteins – 3% of the genome • Noncoding Transcripts: – Not made into proteins – Complex structure and folding – Regulate – 73% of the genome 32 (William G Scott) Noncoding RNA Publications by Year

16000

14000

12000

10000

8000

6000

4000

2000

0 1967 1968 1969 1970 1971 1972 1973 1974 1975 1976 1977 1978 1979 1980 1981 1982 1983 1984 1985 1986 1987 1988 1989 1990 1991 1992 1993 1994 1995 1996 1997 1998 1999 2000 2001 2002 2003 2004 2005 2006 2007 2008 2009 2010 2011 2012 2013 33 RNA Alphabet Soup

DNA snRNA, snoRNA siRNA, piRNA RNA lncRNA tRNA, rRNA microRNA Protein

34 Questions?

35 • ~22 base single-stranded RNAs • Function by base pairing with their target mRNAs • Often have many targets

36 Caenorhabditis elegans

• Model system since 1963, • 1 mm transparent round worms • Free living, eat , 10,000 per petri dish • 3 day live cycle, 2-3 week lifespan, many offspring

37 (Zeynep F Altun, WormClassroom) The First microRNA

• lin-4 microRNA discovered 1993 in roundworm – lin-4 mutant “adults” maintain larval tissues – Don’t develop adult tissues – Continual molting

L1 L2 38 (WormAtlas.org, Adapted from Reinhardt BJ et al., 2000) The First microRNA

• Identified a small 22 base microRNA, lin-4

mutant Type Wild lin-4

22

39 (Adapted from Lee et al., 1993) The Second microRNA • let-7 microRNA discovered 2000 in C. elegans – 7 years later!

L3

L4 Adult

40 (WormAtlas.org, Adapted from Reinhardt BJ et al., 2000) let-7 microRNA

• let-7 found across bilateral , including humans

41 (Adapted from Pasquinelli AE et al., 2000) Human microRNAs

• let-7 also the first discovered human microRNA (2000) – Humans have 18 microRNAs in the let-7 family – Each with 1000-8000 of their own predicted targets

• Recent estimates suggest there are ~4500 human microRNAs (Friedlander et al., 2014)

42 (microRNA.org) Long noncoding RNAs (lncRNA)

DNA

RNA lncRNA

Protein

43 Long noncoding RNAs (lncRNA)

• Do not proteins

• Size Range: 200 – 100,000’s bases

• May activate or repress gene expression

• Fold into complex structures

• Estimates suggest as many as >113,000 lncRNAs in the human genome (LNCipedia.org)

44 (Adapted from Novikova et al., 2014) lncRNA Mechanisms • Activate or Repress Gene Expression – DNA – RNA

– Protein

45 (Adapted from Novikova et al., 2014) lncRNA • Discovered 1992 • Required to silence expression of one of the female X chromosomes

46 (Adapted from Zlir’a and YassineMrabet) Xist lncRNA

47 (Adapted from Reinius et al., 2010) RNA Comparison

mRNA microRNA lncRNA

Coding Potential Protein Noncoding Noncoding

Regulatory Potential Mainly No Yes Yes

Folding Maybe? No Yes

Sequence or Interactions Sequence Sequence Structure

Size Long Short Long

48 Summary • Although only 3% of the genome encodes proteins, ~76% of the genome is transcribed • Much of that transcription represents noncoding RNAs • microRNAs are small (~22 base) noncoding RNAs which silence gene expression • Long noncoding RNAs (>200 – 100’s kb) likely represent multiple distinct classes of ncRNA and activate or repress gene expression by sequence or structural interactions

49 Questions?

50 Roadmap for the evening

1. Introduction to RNA and its Messenger Roles

2. Non-Messenger Roles of RNA

3. RNA and Healthcare

51 3. RNA and Healthcare Outline

• What can cause disease? • How do traditional drugs work? • Depleting too much protein in order to treat disease • Adding protein back in diseases caused by loss of a gene

53 What Can Cause Disease?

• Too much of a protein – Cancer – Viral infections – Huntington’s Disease

54 What Can Cause Disease?

• Not enough of a protein – Cystic fibrosis – Tumor syndromes caused by gene loss – Macular degeneration, vision loss

55 What are drugs, and when do we use them? • Drugs are small molecules that bind to proteins in the cell • Usually used to turn off a protein • Sometimes turn on a protein

56 How do drugs work?

Traditional method Traditionally of drugging with “undruggable” small molecules targets

57 58 USING RNA IN DISEASES CAUSED BY TOO MUCH PROTEIN

59 What is siRNA?

siRNA = small interfering RNA

Gene of Interest

60 Advantages of siRNA as a drug

• siRNA prevents proteins from being made • Can target any protein – Don’t need to “get lucky” with a synthesized drug • Can target mutated protein – If there is an unmutated copy, it will be unaffected • BUT: do need to carefully test for off-target effects

61 What types of diseases could be targeted by siRNA? • Examples: – • • Hepatitis (B and C) – Cancer – Diseases that rely on protein-protein interactions – Huntington’s Disease

62 What is Huntington’s Disease?

• Genetic neurodegenerative disorder – One parent with disease has 50% chance of passing on to child • Usually begins between 35-44 – But 6% begin before 21, more aggressive disease • Symptoms: – Slow loss of muscle control – Brain degeneration into eventual dementia • No cure; average life expectancy from diagnosis is 20 years 63 Huntington’s Disease

Htt Mutant Htt

64 Huntington’s Disease

65 Huntington’s Disease

siRNA targets mutated protein

66 Huntington’s Disease

67 Summary

• siRNA treatments target unwanted proteins before they are made • What it could be used for – Diseases caused by over-production of proteins – Proteins that have been considered “un-druggable”

68 QUESTIONS?

USING RNA IN DISEASES CAUSED BY LACK OF A PROTEIN

72 Recap: mRNA

Protein coding transcript

73 Advantages of mRNA as a drug

• May not need to be as extensively tested as drugs – Off-target effects – Efficacy – Clearance from body • mRNA are inherently natural products

74 What types of diseases could be treated with mRNA?

• Good for diseases characterized by a loss of a certain protein – Cancers driven by loss of a tumor suppressor • BRCA loss in breast cancer, for example – Cystic fibrosis – A variety of other rare diseases

75 What is cystic fibrosis?

• Genetic disorder • Life expectancy 37-40 • Approximately 30,000 people in U.S.A. • Symptoms – Difficulty breathing – Lung infections – Poor growth/poor weight gain • No cure; often requires lung transplant 76 Cystic Fibrosis

Outside

Inside

77 Summary

• mRNA treatments add back needed proteins to the body • Useful for diseases caused by loss of a protein

78 QUESTIONS? THESE SOUND GREAT – WHY AREN’T THEY ALREADY IN USE? Challenges to RNA Delivery

• Hard for RNA to cross membrane – Charge – Size

Outside

Inside

81 Challenges to RNA Delivery

• Unstable as a molecule, so needs to be protected from its environment

82 One Method for Delivering RNA

Outside

Inside

83 One Method for Delivering RNA

Outside

Inside

84 One Method for Delivering RNA

Outside

Inside One Method for Delivering RNA

Outside

Inside Grand Summary

• RNA is the messenger between DNA and protein • RNA expression varies by cell-type in order to determine cell funcon • Most of the genome (76%) is transcribed but only a small poron (3%) encodes proteins • Noncoding RNAs are not translated into protein and play a variety of roles in the regulaon of gene expression at the level of DNA, RNA, and proteins • RNA treatments may one day be used in a variety of diseases

87 QUESTIONS? Thank you! SITN would like to acknowledge the following organizations for their generous support.

Harvard Medical School Office of Communications and External Relations Division of Medical Sciences

The Harvard Graduate School of Arts and Sciences (GSAS)

The Harvard Graduate Student Council (GSC)

The Harvard Biomedical Graduate Students Organization (BGSO)

The Harvard/MIT COOP

89