Rine Lab


Rine Lab News
Recommended Papers
Upcoming Meetings

Rine Lab News

02/01/14 - Debbie's SIR protein ChIP-seq paper hits the press! 11/12/13 - Debbie and Lenny's paper is published! 05/05/13 - Katie joins the lab! 05/1/12 - David joins the lab - welcome! 05/1/11- Sarah, Anne and Aisha join the lab! Welcome to the lab! 11/16/09 - Adam and Joy-el start their rotations. Welcome to the lab! 09/08/09- Caitlin starts her rotation. Welcome. 05/13/09 - Steakley qualifies 05/01/09 - Debbie joins the lab. Welcome again! 12/01/08 - Michael and Lisa start their rotations. Welcome! 10/31/08 - Qiaoning is selected to speak at the Chromatin & Epigenetics Keystone Meeting! 09/10/08 - Debbie Starts her rotation. Welcome, Debbie! 06/17/08 - Oliver's Paper hits the press! 04/29/08 - Jasper becomes a member of the National Academy of Sciences! 04/21/08 - Steakley's first day in the lab, Meru qualifies 11/29/07 - Started this wiki -MSs


Recent Reads

12/12/08 - Compensatory Interactions between Sir3p and the Nucleosomal LRS Surface Imply Their Direct Interaction - EO

11/12/08 - A silencer promotes the assembly of silenced chromatin independently of recruitment - EO

9/17/08 - Bypassing Sir2 and O-Acetyl-ADP-Ribose in Transcriptional Silencing - Chou_Gartenberg_2008.pdf - EO

9/17/08 - Structural and Functional Studies of the Rap1 C-Terminus Reveal Novel Separation-of-Function Mutants - Feeser_Wolberger_2008.pdf - EO

5/27/08 - http://www.molecule.org/content/article/abstract?uid=PIIS1097276502006950 Regulation of Subtelomeric Silencing during Stress Response Wandong Ai,1 Paula G. Bertram,1 Chi Kwan Tsang,1 Ting-Fung Chan,2 and X.F. Steven Zheng—2002 paper brought up in seminar this morning. LL

3/15/08 - Simultaneous Mutation of Methylated Lysine Residues in Histone H3 Causes Enhanced Gene Silencing, Cell Cycle Defects, and Cell Lethality in Saccharomyces cerevisiae - If you get a chance to read this, come talk to me. EO

2/13/08 - Epistatic Interaction Between the K-Homology Domain Protein HEK2 and SIR1 at HMR and Telomeres in Yeast - EO

11/30/07 - The obesity-associated FTO gene encodes a 2-oxoglutarate-dependent nucleic acid demethylase - JR

11/16/07 - Transgenerational Plasticity Is Adaptive in the Wild Environment/epigenetics interaction in plants. -MS

The Classics

Mating Type of Saccharomyces

A DELETION IN YEAST AND ITS BEARING ON THE STRUCTURE OF THE MATING TYPE LOCUS. The 'Hawthorne deletion' was the critical piece of data that led Strathern, et al. to develop the cassette model for mating type switching.

The Hawthorne deletion twenty-five years later. Herskowitz's Perspectives piece fills in the gap(s). Buh-dum-ching!

Control of cell type in yeast by the mating type locus. The alpha 1-alpha 2 hypothesis. Self evident.

Pubmed: Hicks and Herskowitz; Strathern and Herskowitz; Hicks and Strathern

Pubmed: Johnson, AD

Silencing and Position Effects in Yeast

A suppressor of mating-type locus mutations in Saccharomyces cerevisiae: evidence for and identification of cryptic mating-type loci. Bonus points if you've heard of ssp515.

Four genes responsible for a position effect on expression from HML and HMR in Saccharomyces cerevisiae. Sir1 was starting to get lonely...

Position effect at S. cerevisiae telomeres: reversible repression of Pol II transcription. Gottschling, et al. describe Telomere Position Effect for the first time.

Yeasty Evolution

Yeast as a model to study evolution

Genetic isolation, speciation of the sensu stricto yeasts

Evolution of Sir silencing

Chromatin Journal Club

Chromatin JC Page

Protocols and Other Lab Documents

Protein Protocols

07/25/14 - Simple fast yeast lysate prep.docx - LR

07/25/14 - Cycloheximide-chase assay.docx - LR

07/25/14 - Coimmunoprecipitation Assay.docx - LR

09/22/08 - cerevisiae TCA whole cell extract.doc - LL

12/04/07 - cerevisiae NaOH whole cell extract protocol.doc - MS

11/30/07 - Ultimate Western Protocol.doc - EO

Cloning/Strain Building/DNA Protocols

10/10/08 - Modified Qiagen mini prep protocol for genomic DNA (yeast).doc- YC

09/29/08 - Expand Long Template PCR Protocol.doc - EO

12/04/07 - Knockout Cassettes.doc - MS

11/30/07 - UManitoba Best Yeast Transformation Protocol.doc - EO

11/30/07 - Yeast Colony PCR.doc - EO

11/30/07 - Yeast DNA Extraction for Southern Blot.doc - EO

5/21/09 - S_bayanus_Transformation_Protocol.doc - OZ

8/16/11 - Overlap Extension PCR.doc - DT

8/16/11 - Useful pJR plasmids.doc - DT

07/25/14 - Non-radioactive Southern Blot (in progress).docx

RNA Protocols

09/11/04 - Lennys_qRT-PCR.doc - EO

09/08/08 - RTQPCRnew.doc - JG

Inventories & Templates

08/01/08 - yournamehere Inventory.xls - EO

10/31/08 - chemical inventory oct 2008.xls - MD

10/31/08 - qPCR template.xls - LL

03/19/09 - Brem Lab Gal Overexpression collection.xls - MS

03/31/09 - mat-alpha deletion collection map.xls - MS

03/31/09 - mat-a deletion collection map.xls - MS

03/31/09 - diploid deletion collection map.xls - MS

Worksheets and Order Forms

03/19/14 - Tetrad Dissection Worksheet_11Rows.xlsx - KJS

03/19/14 - Dissection Checklist.xls - KJS

Next-Gen Sequencing

I am working on custom protocols for Illumina/Solexa sequencing of genomic DNA, and ChIP-seq. Will post these soon.

In the meantime, please see these websites for relevant info:

QB3 GSL site Illumina's protocols are posted here. Be sure to check out the Links page.

UC-Davis genome center site Lots of helpful info here.

http://seqanswers.com/ Awesome Next-Gen sequencing community blog/discussion site!

- OZ, 5/10/09

Upload some protocols!

Former Lab Member Plasmid, Strain, and Oligo Collections

Lauren Richardson oligos: oLR collection.xlsx

Lauren Richardson plasmids: pLR complete collection.xlsx

Lauren Richardson yeast strains: yLR collection.xlsx

Upcoming Meetings

2014 Yeast Genetics Meeting Seattle, WA. July 29 - August 3, 2014

Past Meetings

Keystone Epigenetics, Chromatin, & Human Disease. Breckenridge, CO. January 3 - 10, 2009.

Chromatin and Chromosomes. Asilomar, CA. December 11 - 14, 2008.

Chromatin Modifications & Epigenetic Phenomena. Snowmass, CO. April 7 - 12, 2008.

Transcriptional Control During Cell Growth, Differentiation, & Development. FASEB. Snowmass, CO. June 22 - 27, 2008.

Cellular & Molecular Fungal Biology. Gordon Conference. Holderness, NH. June 29 - July 4, 2008.

Yeast Genetics & Molecular Biology. Toronto, Canada. July 22 - 27, 2008.

The Berkeley MCB Retreat! Breckenridge, CA. September 26 - 28, 2008.