The pathway of gene expression
RNA-‫תהליך עיבוד ה‬
‫גואניל טראנספראז מעביר ‪ G‬לקצה ה‪ '5-‬של ה‪RNA‬‬
‫בתאים אוקריוטים ל‪ mRNA‬מוסף מבנה ‪ CAP‬בקצה ה‪'5-‬‬
‫גואניל ‪ 7‬מתיל‬
‫טראנספראז‬
‫‪-O-'2‬מתיל‬
‫טראנספראז‬
‫גואניל טראנספראז‬
‫פוליאדנילישן סיגנל‬
‫‪CAP‬‬
‫פולי ‪ A‬פולימראז ‪ -‬אינזים המוסיף נוקלאוטידים ללא ‪emplate‬‬
Alternative polyadenylation
Capping, poly A, splicing
mRNA processing sum •
The pathway of gene expression
‫שיחבור‬
‫אינטרונים‬
‫אקסונים‬
‫רצפים שמורים‬
‫פוליפרימידין טראק‬
‫גן הבטא גלובין‬
‫ההומני‬
‫הכמיה של‬
‫ראקצית‬
‫ה‪splicing-‬‬
‫‪lariat‬‬
‫ראקציה דו‪-‬שלבית‬
‫המורכבת משתי ראקציות‬
‫טראנס‪-‬אסטרפיקציה עוקבות‬
‫האם ניתן לכתוב תוכנת מחשב שתאתר את‬
‫האינטרונים בתוך הגן?‬
‫•‬
‫•‬
‫•‬
‫•‬
‫•‬
‫‪ .1‬כן‪ ,‬התוכנה צריכה לחפש צמדי נוקלאוטידים ‪AG‬‬
‫‪.and GT‬‬
‫‪ .2‬לא‪ ,‬יש הרבה צמדי נוקלאוטידים ‪.AG and GT‬‬
‫שאינם ‪.splice site‬‬
‫‪ .3‬כן‪ ,‬בתנאי שהמרחק בין ‪ AG‬לבין ה‪ GT-‬אינו‬
‫עולה על ‪ 300‬נוקלאוטידים‪.‬‬
‫‪ .4‬כן‪ ,‬בתנאי שהמרחק בין ‪ AG‬לבין ה‪ GT-‬אינו‬
‫עולה על ‪ 1500‬נוקלאוטידים‪.‬‬
‫ראקציית הספליסינג מתרחשת בתוך קומפלקס שמכיל רנא וחלבון – נקראת‬
‫ספליסוזום‬
‫‪.‬‬
‫ראקצית ה ‪splicing‬‬
‫‪ 50-100‬חלבונים‬
‫‪U1, U2, U4, U5, U6‬‬
‫‪snRNP‬‬
‫‪Small nuclear‬‬
‫‪ribonucleoprotein‬‬
‫סנרפס‬
Pre-mRNA splicing involves 5 small nuclear RNAs (snRNAs)
U5
U1
‫חוט השידרה של ראקציית‬
‫הספליסינג הינה הדרך בה‬
‫חמשת המולקולות של הרנא‬
‫עוברות אינטראקציה אחת‬
‫עם השניה ועם הרצפים‬
‫השמורים על מנת לאפשר‬
.‫את ראקציית הספליסינג‬
U2
U6
U4
orange-interaction with the 5’ splice site
green-interaction with the branch site
blue-interaction between U2 and U6
tan-Sm-binding site (PuAU4-6GPu) flanked
by two stem-loop structures
Systemic Lupus Erythematosus (SLE)
Lupus is a type of immune system disorder known as an autoimmune disease. In
autoimmune diseases, the body harms its own healthy cells and tissues. This leads to
inflammation and damage of various body tissues. Lupus can affect many parts of the
body, including the joints, skin, kidneys, heart, lungs, blood vessels, and brain.
Although people with the disease may have many different symptoms, some of the most
common ones include extreme fatigue, painful or swollen joints (arthritis), unexplained
fever, skin rashes, and kidney problems. Lupus is also known as a rheumatic disease.
The rheumatic diseases are a group of disorders that cause aches, pain, and stiffness in
the joints, muscles, and bones.
Capping, poly A, splicing
mRNA processing sum •
Splicing of pre-mRNA movie
PloA
spliceosome
‫‪spliceosome‬‬
‫מעגל‬
‫מחזורי‬
‫של‬
‫ראקציית‬
‫השיחבור‬
‫ספליסוזום‬
The network of RNA interactions in the spliceosome
‫אבולוציה של ה ‪snRNP‬‬
‫אינטרונים אוטוקטליטים‬
‫כ‪ 15%-‬מהמוטציות שגורמות למחלות גנטיות נמצאות האזורים חשובים לראקצית‬
‫ה‪splicing-‬‬
‫‪Untreated β thalassemia‬‬
Treatment of thalassemia major
antisense
Human genome
2.91 billion base pairs
21,000 genes
1.5% exons (127 nucleotides)
24% introns (~3,000 nucleotides)
75% intergenic (no genes)
Average size of a gene is 27,894 bases
Contains an average of 8.8 exons
Titin contains 234 exons.
Gene number
C. elegans
~19,000
Drosophila melanogaster
~13,600
Arabidopsis thaliana
~25,500
Homo Sapiens
~21,000
Mouse
~21,000
Rice (Oryza sativa)
~50,000
Compared to
worm and fly,
human has
shorter exons
and longer
introns on the
extremes of the
distribution
150 nt – drosophila
125 nt – Ciona intes.
119 nt - human
5000 genes
234 introns
Multi-introns genes
7.8 introns per gene
‫זהות של ‪88%‬‬
‫ברצף האקסונים‬
‫בין אדם לעכבר‬
Alternative
Alternative splicing
splicing
‫פוליפרימידין טראק‬
40%
18%
8%
?
3%
‫איזופורם‬
‫‪18‬‬
‫איזופורמים‬
‫כ‪ 90%-‬מהגנים שלנו עוברים אלטרנטיב ספליסינג‬
‫‪1‬‬
Alternative splicing regulate pro or
anti apoptotic pathways.
pro-apoptotic
anti-apoptotic
‫כיצד מערכת השיחבור בוחרת את גבולות האקסון‪-‬אינטרון‬
‫‪RRM – RNA Recognition Motif‬‬
RNA processing
mRNA transport from the nucleus to the cytoplasm
mRNA
‫גרעין‬
‫תעלה‬
Nucleopore
‫ממברנת הגרעין‬
‫ציטופלזמה‬
‫מבנה ה‪nucleopore -‬‬
‫גרעין‬
‫‪RNP‬‬
‫ציטופלזמה‬
Protein import to the nucleus
mRNA movment •
mRNA mov
‫חלבונים המיועדים לגרעין צריכים להכיל רצף חומצות אמינו הנקרא‬
.Nuclear localization signal (NLS)
‫גרעינון‬
Nucleoli or Nucleolus
rRNA processing
Pre-rRNA processing
tRNA processing
RNase P
CCA adding
enzyme
‫זמן דור של התא‬
Transport from the nucleus to the cytoplasm .1
Precursor ribosomal RNA processing (pre-rRNA) .2
tRNA processing .3
Creation of a Bacterial Cell Controlled by a Chemically Synthesized Genome
How are short exons recognized
within vast intron oceans?
Schwartz et al., Nature SMB, 2009
ttgagaactatttttctgactctagcactaaactcaaaatgtaatttcagatggaatttcctaggctcattcattttattttatttatggcttggccagtcatggatctaatcagtaacttgcaactgttgcttcaactacct
tgtcctggactttccagagattggctttaagaaagaaagaggacatccctgggataagattaccatgtgtatttttatgtacagattttgaaaaacatacaaatgaatgggatctttgcttatctcttccatgtagaaaaatt
attttacttctatttcaggttttcaataatgtagtaggacaagatgacatcactatatccctgttttttacacagatatattagagatgcattatcttattggaaattttaaactattcaataataaactattagtcttttag
atttctttttcctcaagtgttgataagtaactgaaagtctacaagcagacaagcagaattagtcggtggaacttcatttcttgctccatttttgtcctcagcagtagagggtggtgagatttcaacccagcctagcaggacca
taagtctggaaagaagtagctctagttcatattggcacctgctaattctagttctgaagaccatgggaaatctcttgcctatttagctcagtgatcatccaagatgggaaattcttgggctcagctgtgagggatcccaagtt
atatgtaacactaatgtctcacaaatcaagaatccaagagaatcaagagactatagttcattccttatattaaattcttaggactgccaactgggtggctacagttttgggggctagaagtctgatatcaaggtgccaactgg
ctggttccttctgaggaccacgagggcaggatctgttcaggcttgtagatggccttcttttccatgtgtcttcacattatcttcctctgtttgtatgtgtgtccaaatttcctcttctttttttttaatttagaaatttatac
gtctacaagctttatatagctttagttaaaaaaaagcaaaaaaaaaaaaaaatcaaaacaaaaacagtgaagccaagacactcttccaaagtctggacccttccggccttccaaatacaagagctctggaagttgtatatacc
aatttcctcttcttaaaatgtcaccagtcacattggattaaggcttaccctattaacaccattttaacttaatcacctctgtaaagaccctatctcctgatacagtcacattcggatgctcaggaagttagggtatcagtatc
ctatatgaatttgggagttgggggaggacacagtttagcccatgacagtcctgaatctcctttgctagatgcatgactgtgggccagtcacttcaccagttgggatactgccatctctatcagaaaaggggtttgggctaggt
atctataaagtcctttctgctctaaattgtaaatataatgagataccaacatttagtttaattgtttaaaattttagaagctaactggatgctttgctggtgtcaacactcccctttacaaaaaaaaattcggccgggcatgg
ggctcacgcctgtaatcccaacactttgggaggccgaggcaggcggatcacggggtcgagagattgagaccatctggccaacatggtgaaaccccgtctctactaaaaacacaaaaattagctgggcctggtggtgcacatct
tagtcccagctactcgggaagctgaggcaggagagtcacttgaacccgggaggcggagcttgcagtgagccgagatcgcgccactgcacctccagcctggcaacagagcgagactccgtctcaaaaaaataaataaataaata
aataaaataaaataaaataaaatctcactttctgtttctactgttctctcaagtacccctctgccttctgttacttctttgctgcattctgagaggaatggggtggggagcactctttcctgtagaaccccataacccatcta
tttcatcaatttatttgaaattcaaagccaggggttaaaatgtccactttcaatttgagatgtctaactttcagataaatctattaacatgcatttctaagtgacttttaagctaagcattttattttattgagctcgtatgg
agggtaactattatacttgtataataaagtgcactttcaaaaatactcggttcaaatgtaaaataatattcgtaatattttaagacaaacctcctagaacttatatgtgtctttcttcccagagcagtctctatgggtgccta
acaatactgcattattagatttttttcagtttataagccacacaagaaagttaacccatgtcatctctagaggcataaaaatagacagttgttctgagaaacatatctgtttattcctagttcagtaacagcgcaatgagatc
taaattatgaggtactttttgtttatcttattgtctcattggcaaccagcaactcctgttgcatttttgacatgggaatctatcagggtgtggttaataaagtacatttccatggtaagtattctttaagaaaaaataaacca
gatttcatcagagacagaaattactgcaaactgtacttaccagtttctggtgatttgtataactgagctttcaatttcaaaaattaaaaagttctctttagtgtaacatatttttgtgtccagtaattttacttcaaaaataa
agagaattttctttaccatcaaacaacgttgctgtaatgagtggtgatatatttagtcctagaggaccaaagagaaataaaatggctttgattatgctggtttaagaaaatatatccgatgaaacagaggttaatatttgtga
gtttgatttagtaaaattataagactaccaaagaaaactagaagagcaaaataaccaaaatttatataaagaattcaatgttgataattcaaaggtttagaattttttccacctttcaaatactaagttgctgttatagattt
ctaccattattacccagattttctattttactaaaaaataataacacagttcgttatgataaatcagtatagatctttaggctcaacacaaccctgctaccttttaaacttttttattatacaacaaacacatatgcattatc
agaaaagatgagtttagcaaaatgaagaaaaatagtcttatcaactagaaataagcaccattaaaatttctgtgtgttaaaagataatatgctgctgaaactttttttttcttgaaatgtccctcttttctttcacttttcat
ttcttaatccctaaccttctactgttgaattttctggaccaccgttataccccctcatcaatagggcatttttttctgcagtagctgagcacaatggtcatattgaagaaattcccttgtgggggctttgcctagaggtaaaa
cctcttggccgggtgcgttggctcatgcctgtaatcccagcactttgggaagctgaggcgggagcatcttctgaggtcaggagtttgagattagcctggccaacgtggtgaaatgccgtctctactaaaaatacaaaaaatta
ccgtcatagtgtgcattcctgtaatcccacctactcgggaggctgaggcaggagaattgcttgaatgccggaggcagaggttgtagtgagccaagatctagattgtgccactgtgctccagcctgggtgacagagcaagactc
gtctaaaacaaaacaaaacaaaacaacaacaacaaaaacaaagtaaaaccctcttcactgtgatgactctaaagcttgcttttgtctctctaaatcacaacaaaccgtttgcagtgtgatgctgtgctcaaaattgagaattc
cactgactgttccaggcatctgtctactcattcttgccatgctgagggctgtcatttctcaccactgaatgcctttttttttttttttgtgcttctttttaaaagtcttttcctgtttgctttgaacttcaataaaaacaggg
gtaagaaggtaatatgcttttattttgtctgtggggtttttttcttccttcttttggttccttttcagatcctagctcatcaaggccatttgccacactgacactggaataagcctgaatgggggtctatatttcttccagta
ttagtttaattcggtcattgagctgttgctctatttgtaaccgtcatgctagatccgagggctgactattcctgagaaagtgtggagatcctttcagactgccatggtgctagggcagagtttcagtcattatcttctgtgtc
gctaattcttgcatcatttcttctactctgtaacctggttggctatgaaaagtgattcttcctcactgatgctgcaggcaatgggtgaatatccaattgttctctcaggttcttgtcatcggatacaaagaacaaatttcatg
gtccctgtttctgagaggttcaaagggagcaaatgcacagattctagcttaggatgacttccagcttctaactatttgtctgtgcattccatttcctcacccctgcgagaggttgcagtcatggtaacggctgttctgagaaa
tcagtgcccaaactggagggaggggaacacaaactcagcttcttcccaagcttcagggcagggctggcaagttttgccttccccgccagcaagagccctggctttaggggtcttgctacagttttcccagactggaggtcttg
ggctggattctggttcttagcgaattcttgccaaacacctcccctttccccagtatccatttgttttgaaggttctttgcaggcttcttgccaataattgtcttaaaacaaatggagttgtttgcatacctagatggagtaaa
tatttaggaaactattctacaaatatgaaacagcccagatttgggccagaagtcctggtcctgagtctcttgttagccactcttaactgtgaattattggacaaatcatttctcgcactctgtgtaatctgtcacctgggtac
tgatgatttaaaccaggaattgtggcccttctcataatactgtctcctaaatattgggtgaatttagtatatcaaggagggcagggcactatacccgtaggggactctctctctccctctgtctctttgcctttctcagatat
catctttggtggcagacctggggttcaaaccacagttgttttgaaatttctctttccttctccactatgctccccctcactgaaactttaataataaaagtagcacacttattgggcatgtatttgttatgtgccaggttctg
gctaacagctttaagtgcattattccacgtattttcacaacaagcctgtgaggaagaggttatttccacttatagataaagaaactgagacttggagaatgtaagtgattttacccacaaacacagggcagtaagtgggaggc
ctgttcaccttagaacacctggcttctatcattcatggtgctgtttctagtgtggtttgaagaacctgagatccaaactgctatacaagtgacctgctgctttcttggagagagaaatctgaaagacagtggagccctcacat
gtctttgcctgtgcacagcagatactgccaattttgggtgggttacacttgtttaccacgttgcttacttcagaaatcaataaaattctcttcatgcttttattttacagGTTCTTACGTCTGTTGCTAGATTATCGTCCAAA
GTGTTAATGCCCAAGTGACTGACATCAACTCCAAGGGATTGGAATTGAGGAAGACTGTTACTACAGTTGAGACTCAGAACTTGGAAGGCCTGCATCATGATGGCCAATTCTGCCATAAGCCCTGTCCTCCAGgtatgttacac
aaacatccagagattacagtgaaagtcacagttaggagtagcacatagtaatcatgactataataattttacagtttttggttcccctatattatataacataactgagagaaaaacaactatgaaattattttccaaagatg
gttttatttatatttatcacgcttatttgatgtggttatggataaatttaatttacaagtgacatgcacctctgaaatgagaagactggtctatttggctccatttttttctaagcaaaaatgactcatttgtgaatatgaaa
cttatcatgtcaaaactgattaggatctaccataacaatagtggaactctgaaagcaagagacttctcctcttaagggatatgtctcagcacttcccttcaatcagaaggtctctaagaaagctgtcctggcactgaagcctg
aaaatatatttgcattttgcagctgaataactagacgaataagaaaagcaacaggcagaaaccaacagcttttttttttaaatcaatactttgaagggcaaactaatttcagatcacaaatccttcaaacactggtaaattag
agctaagcaaaatgcaattgtgcaaacatttcttcaactttgagtagagttgaaaaaaggaaaatagcacatgggttcatgtgatagattaatagaacaaaaaaggactgtagtatgtttcatggttgtcctcccaggcttcc
gcactcaagctgtaaaacaggatgggtcctgtttgtgaaaagattctaccagtctccctgtgcttcatgtccagattttaataaccgttatggaaaaatctcccctataacccaacccatttatacttaaacccatttacact
aaatcttctccaacacgaataaagaatggcgtcctggctttattataacctgctaaacacaatcaatttgctctatgaattgaaatctttgttcataattttaaaacctaaaatgtaaattaaaatgaacaaaatatgctttg
acatcaaactgtcaaggatttttgtctattgctttttcggttttgctttgttttattttaatttaagaagtgaatgtaaattgttacaaacttttaagaaatacatttggatatatgagtcaaaaatttgaaaaaaaattttt
ttaacttttttttcttattattatactttaagttttagggtacacatgcacaatctgcaggttagttacatatgtatacatgtgccatgctggtgcactgcacccactaactcgtcatctagcattaggtatatctcccaatg
tatccctcccccctccccccaacccactgtttatacttgctaagatagcaattaatttatacgaaaataccctgagaaaataatcaaaaataaaggaaaatattgtacacatgatatttcattatcaatatgatgtaggattc
ttaggtaaattctggaatatttaaagactgaaatagtatgtatcaaagtcatgttttctgatatatttctaatataatcctcaattatataaaccttcttaagtaatttccaactgatctggctggattaactgattctccct
atccgtctataaaatatcctggatggcatccaaccatgttaaatactcttcccacttcaattccctcttgttgaattttaggcttatcaatatctaagttgcttccaaatctgtttatgctcattagtgttgtgatattcata
gtaatttgattgaatattgcataaattaatgaaatacaaatacagagaaaagacagattttatttctaagaaaactaggttgagtgctttggagaattcaataaagatgagctgctaaaatgttgttgatgaattttgtgagg
aaaaataaaagttaagtagtaggaaaaatcacaaaaatctctaaagccattcatagagattattggtatgtttatgttttcctttcatcaaaaacgaagggagggagggagggagggagggaggagaaaaaaagaaagaaatg
Nucleosomes mark exon-intron structure
What drives nucleosomes to
exons?
Nucleosome positioning is dependent on
nucleotide composition
Eran Segal from
the WIC
Nucleosomes mark exon-intron structure
ChIP-seq in a nutshell
Nucleosomes mark exon-intron structure
Exon length and DNA length wrapped
around nucleosomes are
conserved through evolution