Loss of the Brm-Type SWI/SNF Chromatin Remodeling Complex Is a Strong Barrier to the Tat-Independent Transcriptional Elongation of Human Immunodeficiency Virus Type 1 Transcripts

Abstract

To elucidate the epigenetic regulation of Tat-independent human immunodeficiency virus (HIV) transcription following proviral integration, we constructed an HIV type 1 (HIV-1)-based replication-defective viral vector that expresses a reporter green fluorescent protein (GFP) product from its intact long terminal repeat (LTR). We transduced this construct into human tumor cell lines that were either deficient in or competent for the Brm-type SWI/SNF complex. One day after transduction, single cells that expressed GFP were sorted, and the GFP expression profiles originating from each of these clones were analyzed. Unlike clones of the SWI/SNF-competent cell line, which exhibited clear unimodal expression patterns in all cases, many clones originating from Brm-deficient cell lines either showed a broad-range distribution of GFP expression or were fully silenced. The resorting of GFP-negative populations of these isolated clones showed that GFP silencing is either reversible or irreversible depending upon the proviral integration sites. We further observed that even in these silenced clones, proviral gene transcription initiates to accumulate short transcripts of around 60 bases in length, but no elongation occurs. We found that this termination is caused by tightly closed nucleosome-1 (nuc-1) at the 5 LTR. Also, nuc-1 is remodeled by exogenous Brm in some integrants. From these results, we propose that Brm is required for the occasional transcriptional elongation of the HIV-1 provirus in the absence of Tat. Since the Brm-type SWI/SNF complex is expressed at marginal levels in resting CD4؉ T cells and is drastically induced upon CD4 ؉ T-cell activation, we speculate that it plays crucial roles in the early Tat-independent phase of HIV transcription in affected patients.Human immunodeficiency virus type 1 (HIV-1) proviral DNA is semirandomly integrated into the host cell genome. The transcription of the HIV-1 provirus is characterized by an early Tat-independent phase and a late Tat-dependent phase. In the early Tat-independent phase, HIV-1 transcription is dependent upon the interaction of host transcription factors with cis-regulatory DNA elements with the viral 5Ј long terminal repeat (LTR) (23, 26) and the assembly of the transcription apparatus including RNA polymerase II (RNAPII) on these sequences. Importantly, RNAPII synthesizes mostly abortive transcripts during this Tat-independent phase (13, 16). Only a small fraction of the HIV-1 transcripts are in fact expected to be elongated and produce the transactivator Tat protein. Tat and its cellular coactivator, positive transcription factor b (pTEFb), bind the transacting responsive (TAR) element present in the 5Ј region of the HIV-1 proviral transcript and cause the hyperphosphorylation of RNAPII, which then elongates this transcript (20,31). Hence, for the successful elucidation of HIV-1 expression, host factors involved in the first stage of HIV-1 expression will be very important, although the low expression levels of these HIV-1 transcripts may make a detail...

Double Plant Homeodomain (PHD) Finger Proteins DPF3a and -3b Are Required as Transcriptional Co-activators in SWI/SNF Complex-dependent Activation of NF-κB RelA/p50 Heterodimer

“…Importantly, transactivation mediated through RelA/p50 (Fig. 1C, lanes 14 -18 compared with lane 13), RelB/p52 (lanes 20 -24 compared with lane 19), and c-Rel/p50 (lanes 8 -12 compared with lane 7) was enhanced by the endogenous expression of any of the five candidate proteins (lanes [7][8][9][10][11][12][13][14][15][16][17][18][19][20][21][22][23][24]. No significant differences were found among these five proteins in terms of the enhancement of any of the three NF-B dimers, suggesting that all potentially function as co-activators of NF-B in any context, at least when expressed at high levels.…”

Short Intracellular HIV-1 Transcripts as Biomarkers of Residual Immune Activation in Patients on Antiretroviral Therapy

“…In addition to these host factors, the viral trans-activating protein Tat also influences transcriptional elongation, not only by enhancing phosphorylation of the C-terminal domain of RNA polymerase II (33) but also by recruiting HATs to the HIV-1 LTR (34). However, in circulating resting CD4 ϩ T cells, NF-B and NFAT are sequestered in the cytoplasm, and the expression of Brm is downregulated (30).…”

“…Host factors involved in dynamic modifications of chromatin structure, such as the SWI/SNF chromatin remodeling complex, as well as histone deacetylases and histone acetyltransferases (HATs), are known to modify viral elongation (27)(28)(29). We previously reported the Brm-type SWI/SNF complex is required for the disruption of nuc-1 and enhances HIV-1 transcriptional elongation (30). Moreover, HIV-1 transcriptional activation is dependent upon host transcription factors.…”

Requiem Protein Links RelB/p52 and the Brm-type SWI/SNF Complex in a Noncanonical NF-κB Pathway

“…Indeed, Brm and BRG1 show clear differences in their biological activities. For example, Brm-type, but not BRG1-type, SWI/SNF complexes are essential for the maintenance of gene expression driven by the long terminal repeats of murine leukemia virus (5,6) and human immunodeficiency virus (7). Moreover, in gastrointestinal cells, Brm but not BRG1 can transactivate Cdx2-dependent villin expression, even though both proteins can interact with Cdx2 (8).…”