The bromodomain-containing protein Ibd1 links multiple chromatin related protein complexes to highly expressed genes in Tetrahymena thermophila

Background: The chromatin remodelers of the SWI/SNF family are critical transcriptional regulators. Recognition of lysine acetylation through a bromodomain (BRD) component is key to SWI/SNF function; in most eukaryotes, this function is attributed to SNF2/Brg1. Results: Using affinity purification coupled to mass spectrometry (AP-MS) we identified members of a SWI/SNF complex (SWI/SNFTt) in Tetrahymena thermophila. SWI/SNFTt is composed of 11 proteins, Snf5Tt, Swi1Tt, Swi3Tt, Snf12Tt, Brg1Tt, two proteins with potential chromatin interacting domains and four proteins without orthologs to SWI/SNF proteins in yeast or mammals. SWI/SNFTt subunits localize exclusively to the transcriptionally active macronucleus (MAC) during growth and development, consistent with a role in transcription. While Tetrahymena Brg1 does not contain a BRD, our AP-MS results identified a BRD-containing SWI/SNFTt component, Ibd1 that associates with SWI/SNFTt during growth but not development. AP-MS analysis of epitope-tagged Ibd1 revealed it to be a subunit of several additional protein complexes, including putative SWRTt, and SAGATt complexes as well as a putative H3K4-specific histone methyl transferase complex. Recombinant Ibd1 recognizes acetyl-lysine marks on histones correlated with active transcription. Consistent with our AP-MS and histone array data suggesting a role in regulation of gene expression, ChIP-Seq analysis of Ibd1 indicated that it primarily binds near promoters and within gene bodies of highly expressed genes during growth. Conclusions: Our results suggest that through recognizing specific histones marks, Ibd1 targets active chromatin regions of highly expressed genes in Tetrahymena where it subsequently might coordinate the recruitment of several chromatin remodeling complexes to regulate the transcriptional landscape of vegetatively growing Tetrahymena cells.Comment: Published on BMC Epigenetics & Chromati

Scheduling Policies in Time and Frequency Domains for LTE Downlink Channel: A Performance Comparison

A key feature of the Long-Term Evolution (LTE) system is that the packet scheduler can make use of the channel quality information (CQI), which is periodically reported by user equipment either in an aggregate form for the whole downlink channel or distinguished for each available subchannel. This mechanism allows for wide discretion in resource allocation, thus promoting the flourishing of several scheduling algorithms, with different purposes. It is therefore of great interest to compare the performance of such algorithms under different scenarios. Here, we carry out a thorough performance analysis of different scheduling algorithms for saturated User Datagram Protocol (UDP) and Transmission Control Protocol (TCP) traffic sources, as well as consider both the time- and frequency-domain versions of the schedulers and for both flat and frequency-selective channels. The analysis makes it possible to appreciate the difference among the scheduling algorithms and to assess the performance gain, in terms of cell capacity, users' fairness, and packet service time, obtained by exploiting the richer, but heavier, information carried by subchannel CQI. An important part of this analysis is a throughput guarantee scheduler, which we propose in this paper. The analysis reveals that the proposed scheduler provides a good tradeoff between cell capacity and fairness both for TCP and UDP traffic sources