Super-resolution imaging reveals three-dimensional folding dynamics of the ß-globin locus upon gene activation.
Authorsvan de Corput MP, de Boer E, Knoch TA, van Cappellen WA, Quintanilla A, Ferrand L, Grosveld FG,
JournalJ Cell Sci
PubMed ID22767512
The chromatin architecture is constantly changing because of cellular processes such as proliferation, differentiation and changes in the expression profile during gene activation or silencing. Unravelling the changes that occur in the chromatin structure during these processes has been a topic of interest for many years. It is known that ... More
Heterogeneous nuclear ribonucleoprotein (hnRNP) E1 binds to hnRNP A2 and inhibits translation of A2 response element mRNAs.
AuthorsKosturko LD, Maggipinto MJ, Korza G, Lee JW, Carson JH, Barbarese E
JournalMol Biol Cell
PubMed ID16775011
'Heterogeneous nuclear ribonucleoprotein (hnRNP) A2 is a trans-acting RNA-binding protein that mediates trafficking of RNAs containing the cis-acting A2 response element (A2RE). Previous work has shown that A2RE RNAs are transported to myelin in oligodendrocytes and to dendrites in neurons. hnRNP E1 is an RNA-binding protein that regulates translation of ... More
Effects of RNA interference of Trypanosoma brucei structure-specific endonuclease-I on kinetoplast DNA replication.
AuthorsLiu Y, Motyka SA, Englund PT
JournalJ Biol Chem
PubMed ID16096280
'Kinetoplast DNA, the mitochondrial DNA of trypanosomatid protozoa, is a network containing several thousand topologically interlocked DNA minicircles. Kinetoplast DNA synthesis involves release of minicircles from the network, replication of the free minicircles, and reattachment of the progeny back onto the network. One enzyme involved in this process is structure-specific ... More
A beta-catenin survival signal is required for normal lobular development in the mammary gland.
AuthorsTepera SB, McCrea PD, Rosen JM,
JournalJ Cell Sci
PubMed ID12584256
'The Wnt (wingless) family of secreted glycoproteins initiates a signalling pathway implicated in the regulation of both normal mouse mammary gland development and tumorigenesis. Multiple Wnt signals ultimately converge on the multifunctional protein beta-catenin to activate the transcription of target genes. Although beta-catenin plays a crucial role in canonical Wnt ... More
The genetic architecture of Down syndrome phenotypes revealed by high-resolution analysis of human segmental trisomies.
AuthorsKorbel JO, Tirosh-Wagner T, Urban AE, Chen XN, Kasowski M, Dai L, Grubert F, Erdman C, Gao MC, Lange K, Sobel EM, Barlow GM, Aylsworth AS, Carpenter NJ, Clark RD, Cohen MY, Doran E, Falik-Zaccai T, Lewin SO, Lott IT, McGillivray BC, Moeschler JB, Pettenati MJ, Pueschel SM, Rao KW, Shaffer LG, Shohat M, Van Riper AJ, Warburton D, Weissman S, Gerstein MB, Snyder M, Korenberg JR,
JournalProc Natl Acad Sci U S A
PubMed ID19597142
'Down syndrome (DS), or trisomy 21, is a common disorder associated with several complex clinical phenotypes. Although several hypotheses have been put forward, it is unclear as to whether particular gene loci on chromosome 21 (HSA21) are sufficient to cause DS and its associated features. Here we present a high-resolution ... More
High-density polymerase-mediated incorporation of fluorochrome-labeled nucleotides.
AuthorsRamanathan A, Pape L, Schwartz DC
JournalAnal Biochem
PubMed ID15649370
'DNA-polymerase-mediated incorporation of different fluorochrome-labeled nucleotides (FdNTPs) was investigated with the goals of optimizing the high-density labeling of probes and exploring DNA sequencing strategies that rely on the controlled, sequential addition of such compounds. By systematically evaluating variables--including polymerase type, buffer conditions, and fluorochrome chemistries--a rational strategy for the sequential ... More
Mapping of genomic clones by fluorescence in situ hybridization.
AuthorsLeversha MA
JournalMethods Mol Biol
PubMed ID11462829
Sensitive fluorescence in situ hybridization signal detection in maize using directly labeled probes produced by high concentration DNA polymerase nick translation.
AuthorsKato A, Albert PS, Vega JM, Birchler JA
JournalBiotech Histochem
PubMed ID16908431
The signal produced by fluorescence in situ hybridization (FISH) often is inconsistent among cells and sensitivity is low. Small DNA targets on the chromatin are difficult to detect. We report here an improved nick translation procedure for Texas red and Alexa Fluor 488 direct labeling of FISH probes. Brighter probes ... More
Visualizing chromatin and chromosomes in living cells.
AuthorsZink D, Sadoni N, Stelzer E
JournalMethods
PubMed ID12543070
The dynamic organization of eukaryotic genomes in cell nuclei recently came into the focus of research interest. The kinetics of genome dynamics can be addressed only by approaches involving live cell microscopy. Different methods are available to visualize chromatin, specific chromatin fractions, or individual chromosome territories within nuclei of living ... More
Association between the Igk and Igh immunoglobulin loci mediated by the 3' Igk enhancer induces 'decontraction' of the Igh locus in pre-B cells.
AuthorsHewitt SL, Farmer D, Marszalek K, Cadera E, Liang HE, Xu Y, Schlissel MS, Skok JA,
JournalNat Immunol
PubMed ID18297074
Variable-(diversity)-joining (V(D)J) recombination at loci encoding the immunoglobulin heavy chain (Igh) and immunoglobulin light chain (Igk) takes place sequentially during successive stages in B cell development. Using three-dimensional DNA fluorescence in situ hybridization, here we identify a lineage-specific and stage-specific interchromosomal association between these two loci that marks the transition ... More
Cytogenetic evidence for asexual evolution of bdelloid rotifers.
AuthorsMark Welch JL, Mark Welch DB, Meselson M
JournalProc Natl Acad Sci U S A
PubMed ID14747655
DNA sequencing has shown individual bdelloid rotifer genomes to contain two or more diverged copies of every gene examined and has revealed no closely similar copies. These and other findings are consistent with long-term asexual evolution of bdelloids. It is not entirely ruled out, however, that bdelloid genomes consist of ... More
The positioning and dynamics of origins of replication in the budding yeast nucleus.
AuthorsHeun P, Laroche T, Raghuraman MK, Gasser SM
JournalJ Cell Biol
PubMed ID11266454
We have analyzed the subnuclear position of early- and late-firing origins of DNA replication in intact yeast cells using fluorescence in situ hybridization and green fluorescent protein (GFP)-tagged chromosomal domains. In both cases, origin position was determined with respect to the nuclear envelope, as identified by nuclear pore staining or ... More
A novel multiple FISH array for the detection of genetic aberrations in cancer.
AuthorsLi R, Liu Z, Fan T, Jiang F
JournalLab Invest
PubMed ID16518404
Interphase multicolor fluorescence in situ hybridization (IM-FISH) has great promise for improving cancer diagnosis because it can directly visualize multiple changes in chromosomes and gene copy number on a cell-to-cell basis. However, no more than four targets can be detected simultaneously by current commercially available IM-FISH protocols, and the DNA ... More
Suppression of preadipocyte differentiation and promotion of adipocyte death by HIV protease inhibitors.
AuthorsDowell P, Flexner C, Kwiterovich PO, Lane MD
JournalJ Biol Chem
PubMed ID11018036
Many human immunodeficiency virus (HIV)-infected patients taking combination antiretroviral therapy that includes HIV protease inhibitors experience atrophy of peripheral subcutaneous adipose tissue. We investigated the effects of HIV protease inhibitors on adipogenesis and adipocyte survival using the 3T3-L1 preadipocyte cell line. Several HIV protease inhibitors were found either to inhibit ... More