Human Negative Elongation Factor Activates Transcription and Regulates Alternative Transcription Initiation

The human Negative Elongation Factor (NELF) is a four-subunit protein complex that inhibits the movement of RNA polymerase II (RNAPII) at an early elongation stage in vitro. NELF-mediated stalling of RNAPII also attenuates transcription of a number of inducible genes in human cells. To obtain a genome-wide understanding of human NELF-mediated transcriptional regulation in vivo, we carried out an exon-array study in T47D breast cancer cells with transient siRNA knockdown of individual NELF subunits. Upon depletion of NELF-A, -C, or -E, the vast majority of NELF-regulated genes were down-regulated. Many of the down-regulated genes encode proteins that play key roles in cell cycle progression. Consequently, NELF knockdown resulted in significant reduction in DNA synthesis and cell proliferation. Chromatin immunoprecipitation showed that NELF knockdown led to dissociation of RNAPII from the promoter-proximal region of the cell cycle-regulating genes. This was accompanied by decreased histone modifications associated with active transcription initiation (H3K9Ac) and elongation (H3K36Me3), as well as reduced recruitment of the general transcription factor TFIIB and increased overall histone occupancy at a subset of the down-regulated promoters. Lastly, our study indicates that NELF regulates alternative transcription initiation of Basigin gene (BSG) by differentially influencing RNAPII density at the two neighboring exons at the 5’ end of the gene. Taken together, our data suggest a diverse transcriptional consequence of NELF-mediated RNAPII pausing in the human genome. Gene expression analysis of RNA samples from NELF-depleted T47D breast cancer cell line. We analyzed gene expression of T47D cells transfected with siRNAs for control and each of the four NELF subunits by exon array. Each knockdown condition contains three technical repeats. Differentially expressed genes and exons between knockdown of the individual NELF subunits and the control are analyzed by the Arrayassist software from Stratagene. The commonly affected genes and exons among all four NELF subunits knockdown samples are chosen for further studies.