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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

SAGANua4

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