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Vertical zonation of the Barcroft granodiorite, White Mountains, California: Implications for magmatic processes (2012)

Ferré, Eric C. ; Michelsen, Karen J. ; Ernst, W. Gary ; Boyd, John D. ; Canon-Tapia, Edgardo

Mineralogical Society of America

In: American Mineralogist 97: 1049-1059.

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Publication Date: 2012-07-01

Description: Petrological and geochemical variations within plutons reflect their magmatic and emplacement histories. Here we present new magnetic susceptibility (Km) data on the ~163 Ma Barcroft granodiorite pluton in eastern California, which is exceptionally well exposed, especially in the vertical dimension. The Barcroft pluton offers exposures over a total of 2560 m of elevation and is an appropriate target to investigate variations of magnetic susceptibility. In ferromagnetic plutonic rocks, Km reflects mainly the abundance of magnetite, whereas in paramagnetic plutonic rocks it reflects primarily the abundance of mafic silicates. Magnetic susceptibility is also determined by magmatic processes such as crystal fractionation and by intensive parameters such as oxygen fugacity. Other magmatic processes, including magma replenishment, hybridization, and host-rock assimilation, may also influence Km variations. A first data set is based on 622 core samples that were measured in the laboratory. Our second data set comes from 1960 field measurements collected at 196 stations between ~1600 and 4000 m elevation. Detailed surveys were performed at the outcrop scale to evaluate the impact of the ~100 Ma McAfee Creek intrusion on the Barcroft background magnetic susceptibility. The combined data sets display a broad positive correlation between Km and elevation. Pluton mineralogy also appears to vary with elevation but is more difficult to quantify. At the outcrop scale, small dikes of the McAfee Creek granite transect the pluton and are responsible for a decrease in Km of the host granodioritic rocks toward the dikes due to late-stage magmatic or hydrothermal alteration. A contour map of Km shows a high degree of correlation with local topographic features such as deep canyons. Magnetic susceptibility of the Barcroft mafic rocks varies at the outcrop scale as a result of presence of petrological heterogeneities. However, these small-scale variations are embedded in a broader magnetic susceptibility trend due primarily to elevation, which reflects petrologic stratification of the pluton. The late-magmatic and hydrothermal alterations described in previous studies do not affect the spatial distribution of magnetic susceptibility. We propose that vertical increase of Km was primarily caused by crystal fractionation or another magmatic differentiation mechanism rather than by an externally driven increase in oxygen fugacity toward the roof of the intrusion.

Print ISSN: 0003-004X

Electronic ISSN: 1945-3027

Topics: Geosciences

Published by Mineralogical Society of America

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Calculating error bars for neutrino mixing parameters (2012)

H. R. Burroughs, B. K. Cogswell, J. Escamilla-Roa, D. C. Latimer, and D. J. Ernst

American Physical Society (APS)

In: Physical Review C

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Publication Date: 2012-06-20

Description: Author(s): H. R. Burroughs, B. K. Cogswell, J. Escamilla-Roa, D. C. Latimer, and D. J. Ernst One goal of contemporary particle physics is to determine the mixing angles and mass-squared differences that constitute the phenomenological constants that describe neutrino oscillations. Of great interest are not only the best-fit values of these constants but also their errors. Some of the neutri... [Phys. Rev. C 85, 068501] Published Tue Jun 19, 2012

Keywords: Electroweak Interaction, Symmetries

Print ISSN: 0556-2813

Electronic ISSN: 1089-490X

Topics: Physics

Published by American Physical Society (APS)

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A high-resolution map of human evolutionary constraint using 29 mammals (2011)

K. Lindblad-Toh ; M. Garber ; O. Zuk ; [et al.]

Nature Publishing Group (NPG)

In: Nature. 478(7370): 476-82. doi: 10.1038/nature10530.

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Publication Date: 2011-10-14

Description: The comparison of related genomes has emerged as a powerful lens for genome interpretation. Here we report the sequencing and comparative analysis of 29 eutherian genomes. We confirm that at least 5.5% of the human genome has undergone purifying selection, and locate constrained elements covering approximately 4.2% of the genome. We use evolutionary signatures and comparisons with experimental data sets to suggest candidate functions for approximately 60% of constrained bases. These elements reveal a small number of new coding exons, candidate stop codon readthrough events and over 10,000 regions of overlapping synonymous constraint within protein-coding exons. We find 220 candidate RNA structural families, and nearly a million elements overlapping potential promoter, enhancer and insulator regions. We report specific amino acid residues that have undergone positive selection, 280,000 non-coding elements exapted from mobile elements and more than 1,000 primate- and human-accelerated elements. Overlap with disease-associated variants indicates that our findings will be relevant for studies of human biology, health and disease.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3207357/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉 〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3207357/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Lindblad-Toh, Kerstin -- Garber, Manuel -- Zuk, Or -- Lin, Michael F -- Parker, Brian J -- Washietl, Stefan -- Kheradpour, Pouya -- Ernst, Jason -- Jordan, Gregory -- Mauceli, Evan -- Ward, Lucas D -- Lowe, Craig B -- Holloway, Alisha K -- Clamp, Michele -- Gnerre, Sante -- Alfoldi, Jessica -- Beal, Kathryn -- Chang, Jean -- Clawson, Hiram -- Cuff, James -- Di Palma, Federica -- Fitzgerald, Stephen -- Flicek, Paul -- Guttman, Mitchell -- Hubisz, Melissa J -- Jaffe, David B -- Jungreis, Irwin -- Kent, W James -- Kostka, Dennis -- Lara, Marcia -- Martins, Andre L -- Massingham, Tim -- Moltke, Ida -- Raney, Brian J -- Rasmussen, Matthew D -- Robinson, Jim -- Stark, Alexander -- Vilella, Albert J -- Wen, Jiayu -- Xie, Xiaohui -- Zody, Michael C -- Broad Institute Sequencing Platform and Whole Genome Assembly Team -- Baldwin, Jen -- Bloom, Toby -- Chin, Chee Whye -- Heiman, Dave -- Nicol, Robert -- Nusbaum, Chad -- Young, Sarah -- Wilkinson, Jane -- Worley, Kim C -- Kovar, Christie L -- Muzny, Donna M -- Gibbs, Richard A -- Baylor College of Medicine Human Genome Sequencing Center Sequencing Team -- Cree, Andrew -- Dihn, Huyen H -- Fowler, Gerald -- Jhangiani, Shalili -- Joshi, Vandita -- Lee, Sandra -- Lewis, Lora R -- Nazareth, Lynne V -- Okwuonu, Geoffrey -- Santibanez, Jireh -- Warren, Wesley C -- Mardis, Elaine R -- Weinstock, George M -- Wilson, Richard K -- Genome Institute at Washington University -- Delehaunty, Kim -- Dooling, David -- Fronik, Catrina -- Fulton, Lucinda -- Fulton, Bob -- Graves, Tina -- Minx, Patrick -- Sodergren, Erica -- Birney, Ewan -- Margulies, Elliott H -- Herrero, Javier -- Green, Eric D -- Haussler, David -- Siepel, Adam -- Goldman, Nick -- Pollard, Katherine S -- Pedersen, Jakob S -- Lander, Eric S -- Kellis, Manolis -- 095908/Wellcome Trust/United Kingdom -- GM82901/GM/NIGMS NIH HHS/ -- R01 HG003474/HG/NHGRI NIH HHS/ -- R01 HG004037/HG/NHGRI NIH HHS/ -- U54 HG003067/HG/NHGRI NIH HHS/ -- U54 HG003067-09/HG/NHGRI NIH HHS/ -- U54 HG003273/HG/NHGRI NIH HHS/ -- Howard Hughes Medical Institute/ -- England -- Nature. 2011 Oct 12;478(7370):476-82. doi: 10.1038/nature10530.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Broad Institute of Harvard and Massachusetts Institute of Technology, 7 Cambridge Center, Cambridge, Massachusetts 02142, USA. kersli@broadinstitute.org〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21993624" target="_blank"〉PubMed〈/a〉

Keywords: Animals ; Disease ; *Evolution, Molecular ; Exons/genetics ; Genome/*genetics ; Genome, Human/*genetics ; Genomics ; Health ; Humans ; Mammals/*genetics ; Molecular Sequence Annotation ; Phylogeny ; RNA/classification/genetics ; Selection, Genetic/genetics ; Sequence Alignment ; Sequence Analysis, DNA

Print ISSN: 0028-0836

Electronic ISSN: 1476-4687

Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics

Published by Nature Publishing Group (NPG)

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Mapping and analysis of chromatin state dynamics in nine human cell types (2011)

J. Ernst ; P. Kheradpour ; T. S. Mikkelsen ; [et al.]

Nature Publishing Group (NPG)

In: Nature. 473(7345): 43-9. doi: 10.1038/nature09906.

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Publication Date: 2011-03-29

Description: Chromatin profiling has emerged as a powerful means of genome annotation and detection of regulatory activity. The approach is especially well suited to the characterization of non-coding portions of the genome, which critically contribute to cellular phenotypes yet remain largely uncharted. Here we map nine chromatin marks across nine cell types to systematically characterize regulatory elements, their cell-type specificities and their functional interactions. Focusing on cell-type-specific patterns of promoters and enhancers, we define multicell activity profiles for chromatin state, gene expression, regulatory motif enrichment and regulator expression. We use correlations between these profiles to link enhancers to putative target genes, and predict the cell-type-specific activators and repressors that modulate them. The resulting annotations and regulatory predictions have implications for the interpretation of genome-wide association studies. Top-scoring disease single nucleotide polymorphisms are frequently positioned within enhancer elements specifically active in relevant cell types, and in some cases affect a motif instance for a predicted regulator, thus suggesting a mechanism for the association. Our study presents a general framework for deciphering cis-regulatory connections and their roles in disease.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3088773/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉 〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3088773/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Ernst, Jason -- Kheradpour, Pouya -- Mikkelsen, Tarjei S -- Shoresh, Noam -- Ward, Lucas D -- Epstein, Charles B -- Zhang, Xiaolan -- Wang, Li -- Issner, Robbyn -- Coyne, Michael -- Ku, Manching -- Durham, Timothy -- Kellis, Manolis -- Bernstein, Bradley E -- R01 HG004037/HG/NHGRI NIH HHS/ -- R01HG004037/HG/NHGRI NIH HHS/ -- RC1HG005334/HG/NHGRI NIH HHS/ -- U54 HG004570/HG/NHGRI NIH HHS/ -- U54 HG004570-01/HG/NHGRI NIH HHS/ -- U54 HG004570-02/HG/NHGRI NIH HHS/ -- U54 HG004570-02S1/HG/NHGRI NIH HHS/ -- U54 HG004570-03/HG/NHGRI NIH HHS/ -- U54 HG004570-03S1/HG/NHGRI NIH HHS/ -- U54 HG004570-04/HG/NHGRI NIH HHS/ -- Howard Hughes Medical Institute/ -- England -- Nature. 2011 May 5;473(7345):43-9. doi: 10.1038/nature09906. Epub 2011 Mar 23.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21441907" target="_blank"〉PubMed〈/a〉

Keywords: Binding Sites ; Cell Line ; Cell Line, Tumor ; *Cell Physiological Phenomena ; Cells, Cultured ; Chromatin/*genetics/*metabolism ; *Chromosome Mapping ; Gene Expression Regulation ; Genome, Human/genetics ; Hep G2 Cells ; Humans ; Promoter Regions, Genetic/genetics ; Reproducibility of Results ; Transcription Factors/genetics

Print ISSN: 0028-0836

Electronic ISSN: 1476-4687

Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics

Published by Nature Publishing Group (NPG)

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Comprehensive analysis of the chromatin landscape in Drosophila melanogaster (2010)

P. V. Kharchenko ; A. A. Alekseyenko ; Y. B. Schwartz ; [et al.]

Nature Publishing Group (NPG)

In: Nature. 471(7339): 480-5. doi: 10.1038/nature09725.

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Publication Date: 2010-12-24

Description: Chromatin is composed of DNA and a variety of modified histones and non-histone proteins, which have an impact on cell differentiation, gene regulation and other key cellular processes. Here we present a genome-wide chromatin landscape for Drosophila melanogaster based on eighteen histone modifications, summarized by nine prevalent combinatorial patterns. Integrative analysis with other data (non-histone chromatin proteins, DNase I hypersensitivity, GRO-Seq reads produced by engaged polymerase, short/long RNA products) reveals discrete characteristics of chromosomes, genes, regulatory elements and other functional domains. We find that active genes display distinct chromatin signatures that are correlated with disparate gene lengths, exon patterns, regulatory functions and genomic contexts. We also demonstrate a diversity of signatures among Polycomb targets that include a subset with paused polymerase. This systematic profiling and integrative analysis of chromatin signatures provides insights into how genomic elements are regulated, and will serve as a resource for future experimental investigations of genome structure and function.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3109908/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉 〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3109908/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Kharchenko, Peter V -- Alekseyenko, Artyom A -- Schwartz, Yuri B -- Minoda, Aki -- Riddle, Nicole C -- Ernst, Jason -- Sabo, Peter J -- Larschan, Erica -- Gorchakov, Andrey A -- Gu, Tingting -- Linder-Basso, Daniela -- Plachetka, Annette -- Shanower, Gregory -- Tolstorukov, Michael Y -- Luquette, Lovelace J -- Xi, Ruibin -- Jung, Youngsook L -- Park, Richard W -- Bishop, Eric P -- Canfield, Theresa K -- Sandstrom, Richard -- Thurman, Robert E -- MacAlpine, David M -- Stamatoyannopoulos, John A -- Kellis, Manolis -- Elgin, Sarah C R -- Kuroda, Mitzi I -- Pirrotta, Vincenzo -- Karpen, Gary H -- Park, Peter J -- R01 GM071923/GM/NIGMS NIH HHS/ -- R01 GM082798/GM/NIGMS NIH HHS/ -- R01 HG004037/HG/NHGRI NIH HHS/ -- R37 GM45744/GM/NIGMS NIH HHS/ -- RC1 HG005334/HG/NHGRI NIH HHS/ -- RC2 HG005639/HG/NHGRI NIH HHS/ -- U01 HG004258/HG/NHGRI NIH HHS/ -- U01 HG004258-04/HG/NHGRI NIH HHS/ -- U01 HG004279/HG/NHGRI NIH HHS/ -- U01HG004258/HG/NHGRI NIH HHS/ -- U54 HG004592/HG/NHGRI NIH HHS/ -- England -- Nature. 2011 Mar 24;471(7339):480-5. doi: 10.1038/nature09725. Epub 2010 Dec 22.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Center for Biomedical Informatics, Harvard Medical School, Boston, Massachusetts 02115, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21179089" target="_blank"〉PubMed〈/a〉

Keywords: Animals ; Cell Line ; Chromatin/*genetics/*metabolism ; Chromatin Immunoprecipitation ; Chromosomal Proteins, Non-Histone/analysis/metabolism ; Deoxyribonuclease I/metabolism ; Drosophila Proteins/genetics ; Drosophila melanogaster/embryology/*genetics/growth & development ; Exons/genetics ; Gene Expression Regulation/genetics ; Genes, Insect/genetics ; Genome, Insect/genetics ; Histones/chemistry/metabolism ; Male ; Molecular Sequence Annotation ; Oligonucleotide Array Sequence Analysis ; Polycomb Repressive Complex 1 ; RNA/analysis/genetics ; Sequence Analysis ; Transcription, Genetic/genetics

Print ISSN: 0028-0836

Electronic ISSN: 1476-4687

Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics

Published by Nature Publishing Group (NPG)

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Identification of functional elements and regulatory circuits by Drosophila modENCODE (2010)

S. Roy ; J. Ernst ; P. V. Kharchenko ; [et al.]

American Association for the Advancement of Science (AAAS)

In: Science. 330(6012): 1787-97. doi: 10.1126/science.1198374.

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Publication Date: 2010-12-24

Description: To gain insight into how genomic information is translated into cellular and developmental programs, the Drosophila model organism Encyclopedia of DNA Elements (modENCODE) project is comprehensively mapping transcripts, histone modifications, chromosomal proteins, transcription factors, replication proteins and intermediates, and nucleosome properties across a developmental time course and in multiple cell lines. We have generated more than 700 data sets and discovered protein-coding, noncoding, RNA regulatory, replication, and chromatin elements, more than tripling the annotated portion of the Drosophila genome. Correlated activity patterns of these elements reveal a functional regulatory network, which predicts putative new functions for genes, reveals stage- and tissue-specific regulators, and enables gene-expression prediction. Our results provide a foundation for directed experimental and computational studies in Drosophila and related species and also a model for systematic data integration toward comprehensive genomic and functional annotation.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3192495/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉 〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3192495/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉modENCODE Consortium -- Roy, Sushmita -- Ernst, Jason -- Kharchenko, Peter V -- Kheradpour, Pouya -- Negre, Nicolas -- Eaton, Matthew L -- Landolin, Jane M -- Bristow, Christopher A -- Ma, Lijia -- Lin, Michael F -- Washietl, Stefan -- Arshinoff, Bradley I -- Ay, Ferhat -- Meyer, Patrick E -- Robine, Nicolas -- Washington, Nicole L -- Di Stefano, Luisa -- Berezikov, Eugene -- Brown, Christopher D -- Candeias, Rogerio -- Carlson, Joseph W -- Carr, Adrian -- Jungreis, Irwin -- Marbach, Daniel -- Sealfon, Rachel -- Tolstorukov, Michael Y -- Will, Sebastian -- Alekseyenko, Artyom A -- Artieri, Carlo -- Booth, Benjamin W -- Brooks, Angela N -- Dai, Qi -- Davis, Carrie A -- Duff, Michael O -- Feng, Xin -- Gorchakov, Andrey A -- Gu, Tingting -- Henikoff, Jorja G -- Kapranov, Philipp -- Li, Renhua -- MacAlpine, Heather K -- Malone, John -- Minoda, Aki -- Nordman, Jared -- Okamura, Katsutomo -- Perry, Marc -- Powell, Sara K -- Riddle, Nicole C -- Sakai, Akiko -- Samsonova, Anastasia -- Sandler, Jeremy E -- Schwartz, Yuri B -- Sher, Noa -- Spokony, Rebecca -- Sturgill, David -- van Baren, Marijke -- Wan, Kenneth H -- Yang, Li -- Yu, Charles -- Feingold, Elise -- Good, Peter -- Guyer, Mark -- Lowdon, Rebecca -- Ahmad, Kami -- Andrews, Justen -- Berger, Bonnie -- Brenner, Steven E -- Brent, Michael R -- Cherbas, Lucy -- Elgin, Sarah C R -- Gingeras, Thomas R -- Grossman, Robert -- Hoskins, Roger A -- Kaufman, Thomas C -- Kent, William -- Kuroda, Mitzi I -- Orr-Weaver, Terry -- Perrimon, Norbert -- Pirrotta, Vincenzo -- Posakony, James W -- Ren, Bing -- Russell, Steven -- Cherbas, Peter -- Graveley, Brenton R -- Lewis, Suzanna -- Micklem, Gos -- Oliver, Brian -- Park, Peter J -- Celniker, Susan E -- Henikoff, Steven -- Karpen, Gary H -- Lai, Eric C -- MacAlpine, David M -- Stein, Lincoln D -- White, Kevin P -- Kellis, Manolis -- R01 HG004037/HG/NHGRI NIH HHS/ -- R01HG004037/HG/NHGRI NIH HHS/ -- RC2HG005639/HG/NHGRI NIH HHS/ -- U01 HG004258/HG/NHGRI NIH HHS/ -- U01 HG004271/HG/NHGRI NIH HHS/ -- U01 HG004279/HG/NHGRI NIH HHS/ -- U01HG004258/HG/NHGRI NIH HHS/ -- U01HG004261/HG/NHGRI NIH HHS/ -- U01HG004264/HG/NHGRI NIH HHS/ -- U01HG004271/HG/NHGRI NIH HHS/ -- U01HG004274/HG/NHGRI NIH HHS/ -- U01HG004279/HG/NHGRI NIH HHS/ -- U41HG004269/HG/NHGRI NIH HHS/ -- ZIA DK015600-14/Intramural NIH HHS/ -- Howard Hughes Medical Institute/ -- New York, N.Y. -- Science. 2010 Dec 24;330(6012):1787-97. doi: 10.1126/science.1198374. Epub 2010 Dec 22.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21177974" target="_blank"〉PubMed〈/a〉

Keywords: Animals ; Binding Sites ; *Chromatin/genetics/metabolism ; Computational Biology/methods ; Drosophila Proteins/genetics/metabolism ; Drosophila melanogaster/*genetics/growth & development/metabolism ; Epigenesis, Genetic ; Gene Expression Regulation ; *Gene Regulatory Networks ; Genes, Insect ; *Genome, Insect ; Genomics/methods ; Histones/metabolism ; *Molecular Sequence Annotation ; Nucleosomes/genetics/metabolism ; Promoter Regions, Genetic ; RNA, Small Untranslated/genetics/metabolism ; Transcription Factors/metabolism ; Transcription, Genetic

Print ISSN: 0036-8075

Electronic ISSN: 1095-9203

Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics

Published by American Association for the Advancement of Science (AAAS)

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Loss-of-function HDAC8 mutations cause a phenotypic spectrum of Cornelia de Lange syndrome-like features, ocular hypertelorism, large fontanelle and X-linked inheritance (2014)

Kaiser, F. J., Ansari, M., Braunholz, D., Concepcion Gil-Rodriguez, M., Decroos, C., Wilde, J. J., Fincher, C. T., Kaur, M., Bando, M., Amor, D. J., Atwal, P. S., Bahlo, M., Bowman, C. M., Bradley, J. J., Brunner, H. G., Clark, D., Del Campo, M., Di Donato, N., Diakumis, P., Dubbs, H., Dyment, D. A., Eckhold, J., Ernst, S., Ferreira, J. C., Francey, L. J., Gehlken, U., Guillen-Navarro, E., Gyftodimou, Y., Hall, B. D., Hennekam, R., Hudgins, L., Hullings, M., Hunter, J. M., Yntema, H., Innes, A. M., Kline, A. D., Krumina, Z., Lee, H., Leppig, K., Lynch, S. A., Mallozzi, M. B., Mannini, L., Mckee, S., Mehta, S. G., Micule, I., Care4; Rare Canada Consortium, Mohammed, S., Moran, E., Mortier, G. R., Moser, J.-A. S., Noon, S. E., Nozaki, N., Nunes, L., Pappas, J. G., Penney, L. S., Perez-Aytes, A., Petersen, M. B., Puisac, B., Revencu, N., Roeder, E., Saitta, S., Scheuerle, A. E., Schindeler, K. L., Siu, V. M., Stark, Z., Strom, S. P., Thiese, H., Vater, I., Willems, P., Williamson, K., Wilson, L. C., University of Washington Center for Mendelian Genomics, Hakonarson, H., Quintero-Rivera, F., Wierzba, J., Musio, A., Gillessen-Kaesbach, G., Ramos, F. J., Jackson, L. G., Shirahige, K., Pie, J., Christianson, D. W., Krantz, I. D., Fitzpatrick, D. R., Deardorff, M. A.

Oxford University Press

In: Human Molecular Genetics

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Publication Date: 2014-05-09

Description: Cornelia de Lange syndrome (CdLS) is a multisystem genetic disorder with distinct facies, growth failure, intellectual disability, distal limb anomalies, gastrointestinal and neurological disease. Mutations in NIPBL , encoding a cohesin regulatory protein, account for 〉80% of cases with typical facies. Mutations in the core cohesin complex proteins, encoded by the SMC1A , SMC3 and RAD21 genes, together account for ~5% of subjects, often with atypical CdLS features. Recently, we identified mutations in the X-linked gene HDAC8 as the cause of a small number of CdLS cases. Here, we report a cohort of 38 individuals with an emerging spectrum of features caused by HDAC8 mutations. For several individuals, the diagnosis of CdLS was not considered prior to genomic testing . Most mutations identified are missense and de novo . Many cases are heterozygous females, each with marked skewing of X-inactivation in peripheral blood DNA. We also identified eight hemizygous males who are more severely affected. The craniofacial appearance caused by HDAC8 mutations overlaps that of typical CdLS but often displays delayed anterior fontanelle closure, ocular hypertelorism, hooding of the eyelids, a broader nose and dental anomalies, which may be useful discriminating features. HDAC8 encodes the lysine deacetylase for the cohesin subunit SMC3 and analysis of the functional consequences of the missense mutations indicates that all cause a loss of enzymatic function. These data demonstrate that loss-of-function mutations in HDAC8 cause a range of overlapping human developmental phenotypes, including a phenotypically distinct subgroup of CdLS.

Print ISSN: 0964-6906

Electronic ISSN: 1460-2083

Topics: Biology , Medicine

Published by Oxford University Press

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