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Prof. Austin Cooney

Associate Professor
Baylor College of Medicine
One Baylor Plaza

Brief Biography:

Name:  Austin J. Cooney, Ph.D.
Date of Birth: November 29, 1960. Citizenship: US
* Undergraduate Education: National University of Ireland, University College, Galway, Ireland, B.S., Biochemistry 1985.
* Graduate Education: National University of Ireland, University College, Galway, Ireland, Ph.D., Biochemistry 1990
* Postgraduate Training: Baylor College of Medicine, Molecular Biology, Houston TX, Postdoctoral Associate with B.W. O’Malley, MD. 1989

Academic Appointments:
* Faculty Positions at BCM: Associate Professor tenure: 08/12/08 – Present. Department of Molecular and Cellular Biology
* Associate Professor non-tenure track: 05/01/05 – .07/12/08: Department of Molecular and Cellular Biology
* Assistant Professor tenure track: 08/01/00 – 04/30/05: Department of Molecular and Cellular Biology
* Research Assistant Professor: 08/01/94 – 07/30/00: Department of Molecular and Cellular Biology
* Instructor: 09/01/92 – 07/31/94: Department of Molecular and Cellular Biology
* Associate member of the BCM StAR Center


Academic positions:

1985-1989: Graduate Student, University College Galway, Ireland
1989-1992: Research Associate, Baylor College of Medicine, Houston, Texas
1992-1994: Instructor, Department of Molecular and Cellular Biology, BCM, Houston, TX
1994-2000: Assistant Professor, Department of Molecular and Cellular Biology, BCM, Houston, Texas.
2000–2005: Assistant Professor Tenure Track, Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas.
2005–Present: Associate Professor, Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas.


Research interests:

The focus of our lab is to understand the genetic and epigenetic components of gene regulation. Our model system is the regulation of Oct4 gene expression I embryonic stem cells as they transition from the pluripotent self-renewing undifferentiated state to various differentiated states. The expression of the Oct4 gene is regulated by conserved response elements through which we have shown that the orphan receptor Liver Receptor Homolog1 (LRH-1) maintains Oct4 expression. During ES cell differentiation LRH-1 expression is down-regulated and another orphan receptor Germ Cell Nuclear factor (GCNF) is up-regulated. GCNF binds to the same response element as LRH-1 and leads to the repression and subsequent silencing of the Oct4 gene. LRH-1 and GCNF directly interact, this heterodimer however is unable to bind DNA. The prediction is that if LRH-1 is in excess Oct4 expression is maintained as LRH-1 binds to the promoter. However, when GCNF is in excess the Oct4 gene is repressed and silenced. This model predicts a binary switch that regulates Oct4 expression during differentiation. Oct4 is either expressed or repressed depending on the relative ratio of GCNF and LRH-1. Proving this yin-yang model for regulation of Oct4 has been hampered by limits of detection of gene expression, promoter occupancy. What is required is a single cell analysis of this binary switch. Currently tandem arrays of promoters and response element s are applied to single cell analysis of transcriptional regulation. However these systems are artificial. The frontier would be to analyze the regulation of an endogenous gene is a single cell. The Nikon….offers this opportunity. Thus, we proposed to analyze the binding of Lrh-1 and GCNF both tagged with complementary fluorescent reporters at the not only the single cell level but the single molecule level. Thus, we will analyze the binding of LRH-1 and GCNF to ES cell chromatin during ES cell differentiation.  This will establish a map of binding sites for these factors in situ. However, to study the regulation of an individual gene such as Oct4 we will need to be able to identify it as one of many genes bound by these factors in situ. We will take advantage of the ability to genetically engineer ES cells. We have generated a Tet regulatable expression system for the expression of recombinant tagged proteins from the ROSA locus in ES cells. We will use this system to express our LRH-1 and GCF fusion proteins. In addition we will genetically alter one of the endogenous Oct4 genes. We will recombine a Lac operator into a non-essential part of the gene. This response element will then be used to tag the Oct4 gene with a transcriptional inert tet-GFP fusion, expressed by our system. Thus, the tagged Oct4 gene will appear as a single fluorescent dot in the in situ chromatin analysis. Using complementry fluroophores we will be able to analyze the regulation of the endogenous Oct4 gene by LRH-1 and GCNF during ES cell differentiation using the Tet-GFP as a proximity anchor.


Any other information:

Other Experience and Professional Memberships

2002-2006: Member NIH Special Emphasis Panel ZRG1F06 for fellowship reviews.

2003-2004: Editorial Board Biology of Reproduction.

2003-2007: Member of the AHA Western Affiliates Study Section.

2003-2007: Director of the Texas Chapter of Biolink USA-Ireland.

2003-2005: Co-Director of The Mellon Foundation Center for Contraceptive Research, BCM.

2006 & 2008: Ad Hoc Member of DEV1 NIH Study Section.

2007-2008: Ad Hoc Member of MGB2 NIH Study Section.

2009: Ad Hoc Member of RAG NIH Study Section.

2007-2009: Ad Hoc Member of NCF NIH Study Section.

2007: Ad Hoc Member of CMIR NIH Study Section.

2009-2013: Member of NCF NIH Study Section.

2008: Chaired NIH SEP ZHD1 DSR-L.

2009: Member of NIH SEP ZGM1-GDB-7-CR.

2010: Member of NIH SEP ZRG1 MDCN-F(86).

2007-2010: Texas Representative of the Executive Committee of AAS-SWARM.

2008: MCB Award of Excellence for Education and Research.

2009-2012: Editorial Board Molecular Endocrinology

2010-2011: Editorial Board PLoS ONE

2011: Editorial Board The Scientific World Journal; Genetics


1983,84&85: 1st Prize in Department of Biochemistry Student Competitions, University College, Galway.

1983&84: 1st Prize in All of Science Student Competitions, University College, Galway.

1986-1989: Limerick County Council Graduate fellowship award.

1994: Travel Award from Keystone Symposium on Steroid/Thyroid/Retinoic Acid Super Gene Family.

1995: Texas Triangle Award for Outstanding Accomplishments.

2000: The Marc Dresden Excellence in graduate Education Award.

2007: Donald J. Nash Memorial Award, AAAS-SWARM.

2008: Fulbright & Jaworski L. L. P. Faculty Excellence Award for Teaching and Evaluation

2008-2013: Membership of the BCM Academy of Distinguished Educators


What I think of the idea behind WebmedCentral:

I think the prosoed endeavour is an outstanding idea in connection with the direction science and scientifice publication should be going. I am on the editorial board of two like minded eJournals-PLoS One and The Scientific World Journal; Genetics.