Our evolving knowledge of the transcriptional landscape

Transcriptional mechanisms that control expression of the macrophage colony-stimulating factor receptor locus

The proliferation, differentiation, and survival of cells of the macrophage lineage depends upon signals from the macrophage colony-stimulating factor (CSF) receptor (CSF1R). CSF1R is expressed by embryonic macrophages and induced early in adult hematopoiesis, upon commitment of multipotent progenitors to the myeloid lineage. Transcriptional activation of CSF1R requires interaction between members of the E26 transformation-specific family of transcription factors (Ets) (notably PU.1), C/EBP, RUNX, AP-1/ATF, interferon regulatory factor (IRF), STAT, KLF, REL, FUS/TLS (fused in sarcoma/ranslocated in liposarcoma) families, and conserved regulatory elements within the mouse and human CSF1R locus. One element, the Fms-intronic regulatory element (FIRE), within intron 2, is conserved functionally across all the amniotes. Lineage commitment in multipotent progenitors also requires down-regulation of specific transcription factors such as MYB, FLI1, basic leucine zipper transcriptional factor ATF-like (BATF3), GATA-1, and PAX5 that contribute to differentiation of alternative lineages and repress CSF1R transcription. Many of these transcription factors regulate each other, interact at the protein level, and are themselves downstream targets of CSF1R signaling. Control of CSF1R transcription involves feed–forward and feedback signaling in which CSF1R is both a target and a participant; and dysregulation of CSF1R expression and/or function is associated with numerous pathological conditions. In this review, we describe the regulatory network behind CSF1R expression during differentiation and development of cells of the mononuclear phagocyte system.

Cloning full-length transcripts and transcript variants using 5' and 3' RACE

Gene transcripts and transcript variants must be cloned to characterize gene function and regulation. However, obtaining full-length cDNAs with accurate sequences from the 5' end through to the 3' end can be challenging. Here we describe a reverse-transcriptase-based method for obtaining full-length cDNAs using the SMARTer ("Switching Mechanism At RNA Termini") RACE technology developed by Clontech. RNA is isolated from the tissue of interest and annealed to a primer (a modified oligo(dT) primer for polyA+ transcripts; random hexamers or a gene-specific primer for polyA- transcripts). A modified MMLV-reverse transcriptase uses the primer to initiate cDNA synthesis from RNA transcript(s) annealed to the primer and continues cDNA synthesis (reverse transcription) towards the 5' end of the transcript(s). Importantly, this reverse transcriptase possesses terminal transferase activity, so when it reaches the 5' end of a transcript it adds a 3-5 residue "tail" to the newly synthesized cDNA strand. Included in the reverse transcriptase reaction mix is an oligonucleotide containing a sequence tag as well as a terminal series of modified bases that anneal to the 3-5 residue tail on the newly synthesized cDNA. The reverse transcriptase proceeds from the end of the transcript onwards into the modified bases and the rest of the sequence-tagged oligo. The newly synthesized cDNA now has a sequence tag attached to it and can be used as a template for PCR, with one primer complementary to the sequence tag and the second primer specific to the gene of interest. The fragment can be cloned and sequenced or just sequenced directly. If high-quality, undegraded RNA is used, obtaining the true 5' end of a transcript is greatly enhanced. In combination with 3' RACE, full-length transcripts are easily cloned. This method provides sequence information on important regulatory regions, such as 5' and 3' UTRs and flanking regions, and is ideal for detecting transcript variants, including those with alternative transcriptional start sites, alternative splicing, and/or alternative polyadenylation.

Functional clustering and lineage markers: insights into cellular differentiation and gene function from large-scale microarray studies of purified primary cell populations

Very large microarray datasets showing gene expression across multiple tissues and cell populations provide a window on the transcriptional networks that underpin the differences in functional activity between biological systems. Clusters of co-expressed genes provide lineage markers, candidate regulators of cell function and, by applying the principle of guilt by association, candidate functions for genes of currently unknown function. We have analysed a dataset comprising pure cell populations from hemopoietic and non-hemopoietic cell types (http://biogps.gnf.org). Using a novel network visualisation and clustering approach, we demonstrate that it is possible to identify very tight expression signatures associated specifically with embryonic stem cells, mesenchymal cells and hematopoietic lineages. Selected examples validate the prediction that gene function can be inferred by co-expression. One expression cluster was enriched in phagocytes, which, alongside endosome-lysosome constituents, contains genes that may make up a 'pathway' for phagocyte differentiation. Promoters of these genes are enriched for binding sites for the ETS/PU.1 and MITF families. Another cluster was associated with the production of a specific extracellular matrix, with high levels of gene expression shared by cells of mesenchymal origin (fibroblasts, adipocytes, osteoblasts and myoblasts). We discuss the limitations placed upon such data by the presence of alternative promoters with distinct tissue specificity within many protein-coding genes.