Nancy E. Cooke
Professor , Depts of Medicine and Genetics

Genetics and Gene Regulation Program

Address

547A Clinical Research Building
415 Curie Boulevard
Philadelphia, Pennsylvania 19104-6145

Office tel.: 215 898-4425
Lab tel.: 215 898-0391
Fax: 215-573-2326
E-mail: necooke@mail.med.upenn.edu

Link(s)

Lab's home page

Endocrinology, Diabetes, Metabolism Divisional web site

Genetics Departmental web site

Education

Wellesley College, Case Western Reserve University, B.S. (Chemistry),1970

Case Western Reserve University School of Medicine, M.D.,1974

Research Interests

• The role of chromatin structure in eukaryotic gene regulation.

Key words: epigenetics, chromatin structure, histone modifications, noncoding transcripts, growth hormone gene, chorionic somatomammotropin gene, Pit-1, pituitary, placenta, transcriptional controls, mRNA expression.

Description of Research

Long-Range, Epigenetic Gene Activation by the Growth Hormone Locus Control Region

The human growth hormone (hGH) gene cluster includes 5 genes: the pituitary hGH-N gene, and 4 paralogs expressed in placenta. These 5 genes are regulated by a locus control region (LCR) located in the far 5’ region of this multigene locus. The B-cell specific CD79b/Igß gene is interposed between the hGH LCR and the hGH-N gene. The LCR is made up of 5 DNaseI hypersensitive sites (HS) located between -14.5 kb (HSI) and -32 kb (HSV) 5' to hGH-N. These HS are only present in placenta and/or pituitary. When this 32 kb domain plus the linked GH genes are present in a transgenic construct, transgenic mice reproducibly and robustly express the hGH-N gene specifically in pituitary somatotropes and the four paralog genes specifically in the placenta. Expression in both tissues is copy-number-dependent and site-of-integration independent. In the pituitary, this expression is paralleled by the establishment of a 32 kb acetylated chromatin domain encompassing the hGH LCR and the contiguous hGH-N promoter. Levels of histone acetylation peak at the centrally located HSI,II. Determinants critical to hGH-N activation map to an array of three Pit-1 sites at HSI. Remarkably, deletion of HSI (99 bp) leads to a loss of histone acetylation throughout the 32 kb domain and >20-fold decrease in hGH-N expression. Of note, the epigenetic modifications within the LCR lead to “bystander transcriptional activation” of the adjacent B-cell specific CD79b/Igß gene. RT-PCR revealed non-coding, bi-directional RNA transcripts in the activated LCR. Recently we discovered that DNA looping between HSI and the hGH promoter occurs in a pituitary-dependent fashion. Deletion of HSI (99 bp) results in the marked and coordinate loss of the H3K4 tri-me, diminution of PolII recruitment within the LCR, and loss of the non-coding RNA transcripts and DNA looping. Insertion of a PolII terminator downstream of HSI,II blocks CD79b transcription, represses hGH-N expression as well as DNA looping, documenting a regulatory role for the noncoding transcripts and linking the “bystander” CD79b transcription to hGH-N regulation. Ongoing experiments will attempt to further understand the mechanistic role of noncoding and CD79b transcripts in hGH-N gene regulation; to understand how the LCR activates the four placental GH genes; and to dissect the protein determinants of HSI activation.

Selected Publications

Ho, Y, Tadevosyan A, Liebhaber SA, Cooke NE. The juxtaposition of a promoter with a locus control region transcriptional domain activates gene expression. EMBO Reports, in press, 2008.

Kimura AP, Sizova D, Handwerger S, Cooke NE, Liebhaber SA. Epigenetic activation of the human growth hormone gene cluster during placental cytotrophoblast differentiation. Mol Cell Biol, 27, 6555-6568, 2007.

Ho Y, Elefant F, Liebhaber SA, Cooke NE. Locus control region transcription plays an active role in long-range gene activation. Molecular Cell 23:365-75, 2006.

Yoo EJ, Cajiao I, Kim J-S, Kimura AP, Zhang A, Cooke NE, Liebhaber SA. Tissue-specific chromatin modifications at a multigene locus dictate asymmetric transcriptional interactions. Mol Cell Biol, 26(15), 5569-5579, 2006.

Cajiao I, Zhang A, Yoo EJ, Cooke NE, Liebhaber SA,. Bystander gene activation by a locus control element. EMBO J 23:3854-3863, 2004.

Search PubMed for more articles

Lab

Rotation Projects

Lab rotations are available in the area of chromatin structure/gene activation and may involve mouse models or cell lines. Students are encouraged to contact Dr. Cooke directly to discuss potential projects for rotation studies, as these will vary over time.

Lab personnel:

Yugong Ho, Ph.D. Instructor in Genetics
Eung Jae Yoo, Ph.D. Postdoctoral Researcher
Daria Sizova, Ph.D. Postdoctoral Researcher
Margaret Fleetwood, CAMB predoctoral student