biol 7.342 reading the blueprint of life: transcription,
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BIOL 7.342 Reading the Blueprint of Life: Transcription, Stem Cells and Differentiation
Fall 2006. Thursdays, 3 pm – 5 pm. Room 68-151
FALL 2006 - ADVANCED UNDERGRADUATE SEMINAR
Instructors:Matthew Guenther (guenther@wi.mit.edu, Young Lab)Roshan Kumar (roshan@wi.mit.edu, Young Lab) Organizer: Bob Horvitz
http://web.mit.edu/biology/www/undergrad/adv-ugsem.html
Stem cells have the unique ability to give rise to all human tissues and hold greatpotential for tissue regeneration and treating human disease. Realizing this potential will require an understanding of the fundamental mechanisms that allowstem cells to generate descendants that have a variety of fates and that lock in thespecialized states and distinctive RNA and protein expression patterns of differentiated cells. Transcriptional regulation is believed to account for a largepart of the specialized gene expression programs of cells. In this course, we will address how transcriptional regulators both prohibit and drive differentiation during the course of development. How does a stem cell know when to remaina stem cell and when to become a specific cell type? Are there global differences in the way the genome is read in multipotent and terminally differentiated cells? We will explore how stem cell pluripotency is preserved, how master regulators of cell-fate decisions execute developmental programs, and how chromatinregulators control undifferentiated versus differentiated states. Additionally,we will discuss how aberrant regulation of transcriptional regulators producesdisorders such as developmental defects and cancer.
Course Description
The Tools: Genome-wide discovery by expression analysis, location analysis
and more!
The Players: Cells, chromatin and transcriptional regulators
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Introductions and class structure
Introduction to subject matter:
Regulation of transcription
Stem cells
Finding and reading scientific literature
Outline
Name:
Major:
Year:
How did you become interested in biology in general or the course matter specifically:
Do you have research experience? If so, where?
Do you have experience reading primary literature?
E-mail:
Background
General:
Critical reading of original scientific literature (2 per class)
Attendance and participation in every class
Each student should be prepared to explain any figure
Assignments:
Email 2 question/comments about the upcoming papers to Roshan and Matt each week (1 per paper by 1 PM)
Write a 2 page research proposal
15 min oral presentation of proposal
Office hours: On demand, contact Roshan and Matt
Class Structure
Class Website: http://openwetware.org/wiki/7.342
Introductions and class structure
Introduction to subject matter:
Regulation of transcription
Stem cells
Finding and reading scientific literature
Outline
>200 Cell Types
1 Genome1 Cell
Cell uniqueness is determined by which
portions of the genome are expressed
Transcription
mRNA
Protein expression
Unique function ofcell
Cell Type Specificity
Central Questions
How does a stem cell remain a stem cell (not want to differentiate)
Once a stem cell differentiates to something else, why does it stay that way?
Are there fundamental differences in the way the genome is read in stem cells versus differentiated cells?
We will explore how regulation of transcription answers these questions
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Cell Type Specificity
DNA sequence DNA packaging (chromatin) Transcription Factors
11 nm
Higher Order Chromatin
DNA
stopstart
1977,1997 - Nucleosome crystal structureRichmond, Luger, Klug, Finch
Chromatin Structure
Chromatin Structure
1974 - Chromatin subunit modelKornberg
Marks et al., Nat Rev Cancer 1:194 (2001)
Luger et al., Nature 389:251 (1997)
Histone Tail Modifications
Transcription Factors
HDAC
acetylation
H3-K4 methylation
HAT
Pol II
HMT
Putting DNA + chromatin + transcription factors together
SAGA Nua4
Pol IIMediator
GTFs
Set1
Set2
PAF1
SWI/SNF
Isw1a
ORF
ORF
ORF
ORF
ORF
Isw1b
Me
MeTermination
Elongation
Initiation
Transcription of Yeast Protein-Coding Genes
Introductions and class structure
Introduction to subject matter:
Regulation of transcription
Stem cells
Finding and reading scientific literature
Outline
Culturing Embryonic Stem Cells
trophectoderm
Inner cell mass blastocyst
Oct4Sox2Nanog
Culturing Stem Cells: Pluripotency
Culturing Stem Cells: Pluripotency
Introductions and class structure
Introduction to subject matter:
Regulation of transcription
Stem cells
Finding and reading scientific literature
Outline
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pubmed
Finding a Journal Article
Abstract
Introduction
Results
Discussion
Concluding remarks
Reading the Paper
Be an active reader: write in margins, underline important phrasesor statements, ask why a certain experiment was performed
Ask yourself: What question(s) did the authors set out to answer?Ask yourself: Did the authors answer that question effectively?
Were the results to be expected? BoringWere the results unexpected? Exciting
What experiments would you have done differently?What experiments are missing?What experiments would you do next?
Reading the Paper
Structure of chromatin: “Beads-on-a-string”
Nuclease digestion of chromatin
Weintraub & Groudine Experiment
Harold Weintraub1945–1995
“It is hard to complete a picture of Hal without describing hisappearance: always sneakers, never a tie; no matter what theoccasion, better dressed for basketball than the opera.”
- Marc Kirschner
Structure of chromatin
Antisense regulation of gene expression
Discovery of MyoD
FRAP: Fluorescence Recovery After Photobleaching
FRAP: Fluorescence Recovery After Photobleaching
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