Biomedical subjects

Carmen L de Hoog

Publications and source records attributed to Carmen L de Hoog.

3 recordsLinked to original sources

PubMed2006

A mammalian organelle map by protein correlation profiling.

Protein localization to membrane-enclosed organelles is a central feature of cellular organization. Using protein correlation profiling, we have mapped 1,404 proteins to ten subcellular locations in mouse liver, and these correspond with enzymatic assays, marker protein profiles, and confocal microscopy. These localizations allowed assessment of the specificity in published organellar proteomic inventories and demonstrate multiple locations for 39% of all organellar proteins. Integration of proteomic and genomic data enabled us to identify networks of coexpressed genes, cis-regulatory motifs, and putative transcriptional regulators involved in organelle biogenesis. Our analysis ties biochemistry, cell biology, and genomics into a common framework for organelle analysis.

Animals↗

PubMed2004

RNA and RNA binding proteins participate in early stages of cell spreading through spreading initiation centers.

Focal adhesions are specialized attachment and signaling centers that form at sites of cell-matrix contacts. We employed a quantitative mass spectrometry-based method called SILAC to identify and quantify proteins interacting in an attachment-dependent manner with focal adhesion proteins. Subsequent confocal microscopy revealed a previously undescribed structure, which we have termed a spreading initiation center (SIC), existing only in early stages of cell spreading. SICs contain focal adhesion markers, appear to be surrounded by an actin sheath, and, surprisingly, contain numerous RNA binding proteins, ribosomal RNA, and perhaps other RNAs. Interfering with the function of FUS/TLS, hnRNP K, and hnRNP E1 results in increased spreading. Spreading initiation centers are ribonucleoprotein complexes distinct from focal adhesions and demonstrate a role for RNA and RNA binding proteins in the initiation of cell spreading.

Actins↗

PubMed2004

Proteomics.

The genome sequences of important model systems are available and the focus is now shifting to large-scale experiments enabled by this data. Following in the footsteps of genomics, we have functional genomics, proteomics, and even metabolomics, roughly paralleling the biological hierarchy of the transcription, translation, and production of small molecules. Proteomics is initially concerned with determining the structure, expression, localization, biochemical activity, interactions, and cellular roles of as many proteins as possible. There has been great progress owing to novel instrumentation, experimental strategies, and bioinformatics methods. The area of protein-protein interactions has been especially fruitful. First pass interaction maps of some model organisms exist, and the proteins in many important organelles are about to be determined. Researchers are also beginning to integrate large-scale data sets from various "omics" disciplines in targeted investigations of specific biomedical areas and in pursuit of a general framework for systems biology.

Genomics↗