Key words: Mammalian Genetics/Genomics/Development/Mouse Models of Human Disease
Epigenetics and germ cell development: Polycomb repressive complex 2 (PRC2) catalyzes the methylation of histone H3 lysine 27 (H3K27), and functions as a critical epigenetic regulator of both stem cell pluripotency and somatic differentiation, but its role inmale germ cell development is unknown. Using conditional mutagenesis to remove thecore PRC2 subunits, EED and SUZ12, during male germ cell development, we identified a requirement for PRC2 in both mitotic and meiotic germ cells. We observed a paucity of mutant spermatogonial stem cells (SSCs), which appears independent of repression of the known cell cycle inhibitors Ink4a/Ink4b/Arf. Moreover, mutant spermatocytes exhibited ectopic expression of somatic lamins and an abnormal distribution of SUN1 proteins on the nuclear envelope. These defects were coincident with abnormal chromosome dynamics, affecting homologous chromosome pairing and synapsis. We observed acquisition of H3K27me3 on stage-specific genes during meiotic progression, indicating a requirement for PRC2 in regulating the meiotic transcriptional program. Together, these data demonstrate that transcriptionalrepression of soma-specific genes by PRC2 facilitates homeostasis and differentiation during mammalian spermatogenesis.
Chromatin modification dynamics during development: The early mammalian embryo utilizes histone H3 lysine 27 trimethylation (H3K27me3) to maintain essential developmental genes in a repressive chromatin state. As differentiation progresses, H3K27me3 is removed in a distinct fashion to activate lineage specific patterns of developmental gene expression. These rapid changes in early embryonic chromatin environment are thought to be dependent on H3K27 demethylases. We have taken a mouse genetics approach to remove activity of both H3K27 demethylases of the Kdm6 gene family,Utx (Kdm6a, X-linked gene) and Jmjd3 (Kdm6b, autosomal gene). Male embryos null for active H3K27 demethylation by the Kdm6 gene family survive to term. At mid-gestation, embryos demonstrate proper patterning and activation of Hox genes. These male embryos retain the Y-chromosome UTX homolog, UTY, which cannot demethylate H3K27me3 due to mutations in catalytic site of the Jumonji-C domain. Embryonic stem (ES) cells lacking all enzymatic KDM6 demethylation exhibit a typical decrease in global H3K27me3 levels with differentiation. Retinoic acid differentiations of these ES cells demonstrate loss of H3K27me3 and gain of H3K4me3 to Hox promoters and other transcription factors, and induce expression similar to control cells. A small subset of genes exhibit decreased expression associated with reduction of promoter H3K4me3 and some low-level accumulation of H3K27me3. Finally, Utx and Jmjd3 mutant mouse embryonic fibroblasts (MEFs) demonstrate dramatic loss of H3K27me3 from promoters of several Hox genes and transcription factors. Our results indicate that early embryonic H3K27me3 repression can be alleviated in the absence of active demethylation by the Kdm6 gene family.
Chromosome confirmation and X inactivation: X chromosome inactivation (XCI) is an epigenetic process that almost completely inactivates one of two X chromosomes in somatic cells of mammalian females. A few genes are known to escape XCI and the mechanism for this escape remains unclear. Here, using mouse trophoblast stem (TS) cells, we address whether particular chromosomal interactions facilitate escape from imprinted XCI. We demonstrate that promoters of genes escaping XCI do not congregate to any particular region of the genome in TS cells. Further, the escape status of a gene was uncorrelated with the types of genomic features and gene activity located in contacted regions. Our results suggest that genes escaping imprinted XCI do so by using the same regulatory sequences as their expressed alleles on the active X chromosome. We suggest a model where regulatory control of escape from imprinted XCI is mediated by genomic elements located in close linear proximity to escaping genes.
Chromatin remodeling complex dynamics: Every known SWI/SNF chromatin-remodeling complex incorporates an ARID DNA binding domain-containing subunit. Despite being a ubiquitous component of the complex, physiological roles for this domain remain undefined. We show that disruption of ARID1a-DNA binding in mice results in embryonic lethality, with mutant embryos manifesting prominent defects in the heart and extraembryonic vasculature. The DNA binding-defective mutant ARID1a subunit is stably expressed and capable of assembling into a SWI/SNF complex with core catalytic properties, but nucleosome substrate binding and promoter occupancy by ARID1a-containing SWI/SNF complexes (BAF-A) are impaired. Depletion of ARID domain-dependent, BAF-A associations at THROMBOSPONDIN 1(THBS1) led to the concomitant up regulation of this SWI/SNF target gene. Using a THBS1promoter-reporter gene, we show that BAF-A directly regulates THBS1 promoter activity in an ARID domain-dependent manner. Our data not only demonstrate that ARID1a-DNA interactions are physiologically relevant in higher eukaryotes but also indicate that these interactions facilitate SWI/SNF binding to target sites in vivo. These findings support the model wherein cooperative interactions among intrinsic subunit-chromatin interaction domains and sequence-specific transcription factors drive SWI/SNF recruitment.
Silencing of regulatory elements on the X chromosome: The inactive X chromosome’s (Xi) physical territory is microscopically devoid of transcriptional hallmarks and enriched in silencing-associated modifications. How these microscopic signatures relate to specific Xi sequences is unknown. We profiled Xi gene expression and chromatin states at high resolution via allele-specific sequencing in mouse trophoblast stem cells. Most notably, X-inactivated transcription start sites harbored distinct epigenetic signatures relative to surrounding Xi DNA. These sites displayed H3-lysine27-trimethylation enrichment and DNaseI hypersensitivity, similar to autosomal Polycomb targets, yet excluded Pol II and other transcriptional hallmarks, similar to nontranscribed genes. CTCF bound X-inactivated and escaping genes, irrespective of measured chromatin boundaries. Escape from X inactivation occurred within, and X inactivation was maintained exterior to, the area encompassed by Xist in cells subject to imprinted and random X inactivation. The data support a model whereby inactivation of specific regulatory elements, rather than a simple chromosome- wide separation from transcription machinery, governs gene silencing over the Xi.
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Terry Magnuson in UNC Genetics News
April 15, 2021
Dr. Terry Magnuson Reappointed Vice Chancellor for Research
Following the completion of administrative review, Dr. Terry Magnuson (Kay M. & Van L. Weatherspoon Eminent Distinguished Professor of Genetics) has been reappointed as Vice Chancellor for Research for another five-year term.
November 6, 2020
UNC Researchers Lead International Consortium to Improve Understanding of Genetics of Mouse Models
An international consortium led by UNC Departments of Genetics and Computer Science published a manuscript on the development and testing of a new tool to enhance the value of the laboratory mouse in biomedical research.
November 2, 2020
Department of Genetics Publications for October 11-31, 2020
Department of Genetics faculty, postdocs, students and collaborators published 18 papers during October 11-31, 2020. Survival, Pathologic Response, and Genomics in CALGB 40601 (Alliance), a Neoadjuvant Phase III Trial of Paclitaxel-Trastuzumab With or Without Lapatinib in HER2-Positive Breast Cancer. Fernandez-Martinez A, Krop IE, Hillman DW, Polley MY, Parker JS, Huebner L, Hoadley KA, …
August 28, 2020
MMRRC Awarded Administrative Supplement from NIH Office of the Director
Dr. Terry Magnuson, Vice Chancellor for Research and Kay M. and Van L. Weatherspoon Eminent Distinguished Professor of Genetics was awarded an administrative supplement to the U42 Cooperative Agreement “A Carolina Center to Characterize and Maintain Mutant Mice”.
June 29, 2020
Department of Genetics Publications for June 14-27, 2020
Department of Genetics faculty, postdocs, students and collaborators published nine papers during June 14-27, 2020.
March 23, 2020
Department of Genetics Publications for March 8-21, 2020
Department of Genetics faculty, postdocs, students and collaborators published twelve papers during March 8-21, 2020.
December 17, 2019
Department of Genetics Publications for Dec. 1-14, 2019
Department of Genetics faculty, postdocs, students and collaborators published nine papers during Dec. 1-14, 2019.
July 15, 2019
Department of Genetics Publications for June 30 – July 13, 2019
Department of Genetics faculty, postdocs, students and collaborators published four papers during June 30 – July 13, 2019.
May 6, 2019
Department of Genetics Publications from April 21-May 4, 2019
Department of Genetics faculty, postdocs, students and collaborators published fourteen papers during April 21-May 4, 2019.
November 7, 2016
Genetics Faculty Publications for Oct 15 – Nov 4, 2016
During the last three weeks, Department of Genetics faculty members, along with their colleagues, have published 21 manuscripts on a wide variety of topics. A survey of current practices for genomic sequencing test interpretation and reporting processes in US laboratories. O’Daniel JM, McLaughlin HM, Amendola LM, Bale SJ, Berg JS, Bick D, Bowling KM, Chao …