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Research: Glucocorticoid receptor quaternary structure drives chromatin occupancy and transcriptional outcome
- Ville Paakinaho,
- Thomas A. Johnson,
- Diego M. Presman,
- and Gordon L. Hager
Genome Res. August 2019 29: 1223-1234; Published in Advance July 23, 2019, doi:10.1101/gr.244814.118
...that drives both the activating and repressive actions of glucocorticoids.The multimeric structure adopted by transcription factor complexes at their genomic sites of interaction is a longstanding problem in transcription biology. Information bearing on this question is often inferred from indirect data...
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Research: Nascent transcript analysis of glucocorticoid crosstalk with TNF defines primary and cooperative inflammatory repression
- Sarah K. Sasse,
- Margaret Gruca,
- Mary A. Allen,
- Vineela Kadiyala,
- Tengyao Song,
- Fabienne Gally,
- Arnav Gupta,
- Miles A. Pufall,
- Robin D. Dowell,
- and Anthony N. Gerber
Genome Res. November 2019 29: 1753-1765; Published in Advance September 13, 2019, doi:10.1101/gr.248187.119
...epithelial cells treated for 1 h with the potent synthetic glucocorticoid, dexamethasone (dex), TNF, and both dex and TNF (Kadiyala et al. 2016). Whereas our studies revealed rapid and robust reduction in RNAPII occupancy across a host of pro-inflammatory genes when cells were treated with dex + TNF versus...
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Research: Glucocorticoid receptor recruits to enhancers and drives activation by motif-directed binding
- Ian C. McDowell,
- Alejandro Barrera,
- Anthony M. D'Ippolito,
- Christopher M. Vockley,
- Linda K. Hong,
- Sarah M. Leichter,
- Luke C. Bartelt,
- William H. Majoros,
- Lingyun Song,
- Alexias Safi,
- D. Dewran Koçak,
- Charles A. Gersbach,
- Alexander J. Hartemink,
- Gregory E. Crawford,
- Barbara E. Engelhardt,
- and Timothy E. Reddy
Genome Res. September 2018 28: 1272-1284; Published in Advance August 10, 2018, doi:10.1101/gr.233346.117
...of GR binding and activity. To identify genomic and epigenetic contributions to GR binding specificity and the downstream changes resultant from GR binding, we performed hundreds of -wide measurements of TF binding, epigenetic state, and gene expression across a 12-h time course of glucocorticoid...
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Method: SelexGLM differentiates androgen and glucocorticoid receptor DNA-binding preference over an extended binding site
- Liyang Zhang,
- Gabriella D. Martini,
- H. Tomas Rube,
- Judith F. Kribelbauer,
- Chaitanya Rastogi,
- Vincent D. FitzPatrick,
- Jon C. Houtman,
- Harmen J. Bussemaker,
- and Miles A. Pufall
Genome Res. January 2018 28: 111-121; Published in Advance December 1, 2017, doi:10.1101/gr.222844.117
...These authors contributed equally to this work. Corresponding authors: miles-pufall@uiowa.edu, hjb2004@columbia.eduAbstractThe DNA-binding interfaces of the androgen (AR) and glucocorticoid (GR) receptors are virtually identical, yet these transcription factors share only about a third of their genomic binding...
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Research: Accessibility of promoter DNA is not the primary determinant of chromatin-mediated gene regulation
- Răzvan V. Chereji,
- Peter R. Eriksson,
- Josefina Ocampo,
- Hemant K. Prajapati,
- and David J. Clark
Genome Res. December 2019 29: 1985-1995; Published in Advance September 11, 2019, doi:10.1101/gr.249326.119
...3. Genomic analysis of AluI accessibility reveals imperfect nucleosome phasing in yeast. (A) Mean accessibility as a function of distance from the center of the +1 nucleosome (defined by Chereji et al. 2018) on all approximately 5000 yeast genes. (B) Heterogeneous nucleosome positioning model...
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Perspective: Genomic approaches for understanding the genetics of complex disease
- William L. Lowe, Jr. and
- Timothy E. Reddy
Genome Res. October 2015 25: 1432-1441; doi:10.1101/gr.190603.115
...motivate a deeper investigation into the genetic architecture of gene regulation, with a particular focus on determining the specific variants that alter regulatory element activity. Allele-specific genomic activity reveals candidate mechanisms of disease The use of high-throughput sequencing as readout...
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Research: Whole-epigenome analysis in multiple myeloma reveals DNA hypermethylation of B cell-specific enhancers
- Xabier Agirre,
- Giancarlo Castellano,
- Marien Pascual,
- Simon Heath,
- Marta Kulis,
- Victor Segura,
- Anke Bergmann,
- Anna Esteve,
- Angelika Merkel,
- Emanuele Raineri,
- Lidia Agueda,
- Julie Blanc,
- David Richardson,
- Laura Clarke,
- Avik Datta,
- Nuria Russiñol,
- Ana C. Queirós,
- Renée Beekman,
- Juan R. Rodríguez-Madoz,
- Edurne San José-Enériz,
- Fang Fang,
- Norma C. Gutiérrez,
- José M. García-Verdugo,
- Michael I. Robson,
- Eric C. Schirmer,
- Elisabeth Guruceaga,
- Joost H.A. Martens,
- Marta Gut,
- Maria J. Calasanz,
- Paul Flicek,
- Reiner Siebert,
- Elías Campo,
- Jesús F. San Miguel,
- Ari Melnick,
- Hendrik G. Stunnenberg,
- Ivo G. Gut,
- Felipe Prosper,
- and José I. Martín-Subero
Genome Res. April 2015 25: 478-487; Published in Advance February 2, 2015, doi:10.1101/gr.180240.114
...-seq and in vitro reporter assays indicated that enhancer hypermethylation is globally associated with down-regulation of its host genes. ChIP-seq and DNase-seq further revealed that DNA hypermethylation in these regions is related to enhancer decommissioning. Hypermethylated enhancer regions overlapped...
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Research: Dynamic shifts in occupancy by TAL1 are guided by GATA factors and drive large-scale reprogramming of gene expression during hematopoiesis
- Weisheng Wu,
- Christapher S. Morrissey,
- Cheryl A. Keller,
- Tejaswini Mishra,
- Maxim Pimkin,
- Gerd A. Blobel,
- Mitchell J. Weiss,
- and Ross C. Hardison
Genome Res. December 2014 24: 1945-1962; Published in Advance October 15, 2014, doi:10.1101/gr.164830.113
...Pimkin C Morrissey Christapher Morrissey Keller Cheryl A. genome;gr.164830.113 10.1101/gr.164830.113 1549-5469 1088-9051 Dynamic shifts in occupancy by TAL1 are guided by GATA factors and drive large-scale reprogramming of gene expression during hematopoiesis Wu et al. Dynamics of TAL1 occupancy in mouse...
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Research: Effects of sequence variation on differential allelic transcription factor occupancy and gene expression
- Timothy E. Reddy,
- Jason Gertz,
- Florencia Pauli,
- Katerina S. Kucera,
- Katherine E. Varley,
- Kimberly M. Newberry,
- Georgi K. Marinov,
- Ali Mortazavi,
- Brian A. Williams,
- Lingyun Song,
- Gregory E. Crawford,
- Barbara Wold,
- Huntington F. Willard,
- and Richard M. Myers
Genome Res. May 2012 22: 860-869; Published in Advance February 2, 2012, doi:10.1101/gr.131201.111
...Present address: Developmental &amp; Cell Biology, University of California, Irvine CA 92697, USA. Abstract A complex interplay between transcription factors (TFs) and the genome regulates transcription. However, connecting variation in genome sequence with variation in TF binding and gene...
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Resource: The GENCODE v7 catalog of human long noncoding RNAs: Analysis of their gene structure, evolution, and expression
- Thomas Derrien,
- Rory Johnson,
- Giovanni Bussotti,
- Andrea Tanzer,
- Sarah Djebali,
- Hagen Tilgner,
- Gregory Guernec,
- David Martin,
- Angelika Merkel,
- David G. Knowles,
- Julien Lagarde,
- Lavanya Veeravalli,
- Xiaoan Ruan,
- Yijun Ruan,
- Timo Lassmann,
- Piero Carninci,
- James B. Brown,
- Leonard Lipovich,
- Jose M. Gonzalez,
- Mark Thomas,
- Carrie A. Davis,
- Ramin Shiekhattar,
- Thomas R. Gingeras,
- Tim J. Hubbard,
- Cedric Notredame,
- Jennifer Harrow,
- and Roderic Guigó
Genome Res. September 2012 22: 1775-1789; doi:10.1101/gr.132159.111
...RNAdb reveals many that intersect with protein-coding genes and/or small RNAs. A full characterization of the GENCODE v7 lncRNA set can be downloaded as Supplemental Table S1 from: http://big.crg.cat/bioinformatics_and_genomics/ lncrna_data. LncRNAs do not show evidence of protein-coding potential There is some...
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