Genomes and Genes
Alexander S Brodsky
Affiliation: Harvard University
- Genomic mapping of RNA polymerase II reveals sites of co-transcriptional regulation in human cellsAlexander S Brodsky
Department of Systems Biology, Harvard Medical School and Department of Cancer Biology, Dana Farber Cancer Institute, 44 Binney St, Boston, MA 02115, USA
Genome Biol 6:R64. 2005..RNA polymerase II is thought to accumulate at the promoter and at sites of co-transcriptional alternative splicing where the rate of RNA synthesis slows...
- A microbead-based system for identifying and characterizing RNA-protein interactions by flow cytometryAlexander S Brodsky
Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School and the Dana Farber Cancer Institute, Boston, Massachusetts 02115, USA
Mol Cell Proteomics 1:922-9. 2002..We propose that this strategy, in combination with emerging coded bead systems, can identify RNAs and RNA sequences important for interacting with RNA-binding proteins on genomic scales...
- Analysis of RNA-protein interactions by flow cytometryAlexander S Brodsky
Dana Farber Cancer Institute, Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, 1 Jimmy Fund Way, SM 922, Boston, MA 02115, USA
Curr Opin Mol Ther 5:235-40. 2003..The microbead flow cytometric approach is flexible and provides new opportunities for functional genomic studies and small-molecule screening...
- Genome-wide analysis of estrogen receptor binding sitesJason S Carroll
Department of Medical Oncology, Dana Farber Cancer Institute, Harvard Medical School, 44 Binney St, Boston, Massachusetts 02115, USA
Nat Genet 38:1289-97. 2006..Furthermore, this resource has allowed the identification of cis-regulatory sites in previously unexplored regions of the genome and the cooperating transcription factors underlying estrogen signaling in breast cancer...
- Genomic localization of RNA binding proteins reveals links between pre-mRNA processing and transcriptionIan A Swinburne
Department of Systems Biology, Harvard Medical School, Boston, Massachusetts 02115, USA
Genome Res 16:912-21. 2006..In sum, we present the mapping in mammalian cells of RNA binding proteins across a portion of the genome that provides insight into the transcriptional assembly of RNA-protein complexes...
- Chromosome-wide mapping of estrogen receptor binding reveals long-range regulation requiring the forkhead protein FoxA1Jason S Carroll
Department of Medical Oncology, Dana Farber Cancer Institute, Harvard Medical School, 44 Binney Street, Boston, Massachusetts 02115, USA
Cell 122:33-43. 2005..Furthermore, knockdown of FoxA1 expression blocks the association of ER with chromatin and estrogen-induced gene expression demonstrating the necessity of FoxA1 in mediating an estrogen response in breast cancer cells...
- Exon expression profiling reveals stimulus-mediated exon use in neural cellsAdrienne E McKee
Department of Systems Biology, 200 Longwood Avenue, Harvard Medical School, Boston, Massachusetts 02115, USA
Genome Biol 8:R159. 2007..Although calcium-induced transcription and transcript variation have both been recognized as important sources of gene regulation, the interplay between these two phenomena has not been evaluated on a genome-wide scale...
- Identifying proteins that affect mRNA localization in living cellsAlexander S Brodsky
Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School and the Dana Farber Cancer Institute, Boston, MA 02115, USA
Methods 26:151-5. 2002..The technology also allows the swapping of different regions of the RNA to determine the cis requirements for transport. GFP RNA imaging opens many possibilities to examine RNA transport in real time in a variety of different organisms...
- Genome-wide identification of functionally distinct subsets of cellular mRNAs associated with two nucleocytoplasmic-shuttling mammalian splicing factorsMargarida Gama-Carvalho
Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Av, Prof, Egas Moniz, 1649 028 Lisboa, Portugal
Genome Biol 7:R113. 2006..This observation raises the question of whether U2AF associates with mature mRNA-ribonucleoprotein particles in transit to the cytoplasm, participating in additional cellular functions...
- Base flexibility in HIV-2 TAR RNA mapped by solution (15)N, (13)C NMR relaxationKwaku T Dayie
Department of Molecular Biology and The Skaggs Institute of Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
J Mol Biol 317:263-78. 2002..U23 in the bulge undergoes the largest dynamic change on binding argininamide, while U25 remains flexible, reflecting the large conformational change that is triggered upon ligand binding...