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Yeast H2A.Z, FACT complex and RSC regulate transcription of tRNA gene through differential dynamics of flanking nucleosomes.

Mahapatra S, Dewari PS, Bhardwaj A, Bhargava P - Nucleic Acids Res. (2011)

Bottom Line: Histone variant H2A.Z is found in nucleosomes at the 5'-end of many genes.RSC maintains a nucleosome abutting the gene terminator downstream, which results in reduced transcription rate in active state while H2A.Z probably helps RSC in keeping the gene nucleosome-free and serves as stress-sensor.All these factors maintain an epigenetic state which allows the gene to return quickly from repressed to active state and tones down the expression from the active SUP4 gene, required probably to maintain the balance in cellular tRNA pool.

View Article: PubMed Central - PubMed

Affiliation: Centre for Cellular and Molecular Biology, Council of Scientific and Industrial Research, Uppal Road, Hyderabad 500007, India.

ABSTRACT
FACT complex is involved in elongation and ensures fidelity in the initiation step of transcription by RNA polymerase (pol) II. Histone variant H2A.Z is found in nucleosomes at the 5'-end of many genes. We report here H2A.Z-chaperone activity of the yeast FACT complex on the short, nucleosome-free, non-coding, pol III-transcribed yeast tRNA genes. On a prototype gene, yeast SUP4, chromatin remodeler RSC and FACT regulate its transcription through novel mechanisms, wherein the two gene-flanking nucleosomes containing H2A.Z, play different roles. Nhp6, which ensures transcription fidelity and helps load yFACT onto the gene flanking nucleosomes, has inhibitory role. RSC maintains a nucleosome abutting the gene terminator downstream, which results in reduced transcription rate in active state while H2A.Z probably helps RSC in keeping the gene nucleosome-free and serves as stress-sensor. All these factors maintain an epigenetic state which allows the gene to return quickly from repressed to active state and tones down the expression from the active SUP4 gene, required probably to maintain the balance in cellular tRNA pool.

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Relationship of transcription from SUP4 with H2A.Z level and nucleosome positions. Ovals represent nucleosomes, boxes and T1, T2 denote two terminators, bent arrow marks the TSS. Only downstream nucleosomes are shown with H2A.Z levels and transcriptional state of the gene shown on the right-hand side. (A) In wild-type cells, active state, nucleosmes are fuzzy and block T2. (B) In wild-type cells, following 2 h repression, +1 nucleosome is positioned at a short distance from the terminators. (C) In wild-type cells, after repression longer than 2 h, two nucleosomes may be positioned similar to that seen in rsc4-Δ4 cells. Both terminators are near the dyad axis of the gene-proximal nucleosome.
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Figure 6: Relationship of transcription from SUP4 with H2A.Z level and nucleosome positions. Ovals represent nucleosomes, boxes and T1, T2 denote two terminators, bent arrow marks the TSS. Only downstream nucleosomes are shown with H2A.Z levels and transcriptional state of the gene shown on the right-hand side. (A) In wild-type cells, active state, nucleosmes are fuzzy and block T2. (B) In wild-type cells, following 2 h repression, +1 nucleosome is positioned at a short distance from the terminators. (C) In wild-type cells, after repression longer than 2 h, two nucleosomes may be positioned similar to that seen in rsc4-Δ4 cells. Both terminators are near the dyad axis of the gene-proximal nucleosome.

Mentions: Loss of RSC is reported to shrink NFR (56) on pol II-transcribed genes and increase the nucleosome density on pol III-transcribed genes (57). We have shown that RSC is required to keep the nucleosome immediate downstream of the SUP4 terminator, fuzzy in vivo (Figure 6A). It changes the local density of nucleosmes near the SUP4 gene (Figure 6B and C), maintains nucleosome positions to suppress the transcription in active state, helps loading Nhp6/FACT for transcriptional fidelity and differential marking with H2A.Z according to the expression state. While leaving the +1, RSC persists on the −1 nucleosome under repression, keeping the gene poised for activation under repressed state.Figure 6.


Yeast H2A.Z, FACT complex and RSC regulate transcription of tRNA gene through differential dynamics of flanking nucleosomes.

Mahapatra S, Dewari PS, Bhardwaj A, Bhargava P - Nucleic Acids Res. (2011)

Relationship of transcription from SUP4 with H2A.Z level and nucleosome positions. Ovals represent nucleosomes, boxes and T1, T2 denote two terminators, bent arrow marks the TSS. Only downstream nucleosomes are shown with H2A.Z levels and transcriptional state of the gene shown on the right-hand side. (A) In wild-type cells, active state, nucleosmes are fuzzy and block T2. (B) In wild-type cells, following 2 h repression, +1 nucleosome is positioned at a short distance from the terminators. (C) In wild-type cells, after repression longer than 2 h, two nucleosomes may be positioned similar to that seen in rsc4-Δ4 cells. Both terminators are near the dyad axis of the gene-proximal nucleosome.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

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Show All Figures
getmorefigures.php?uid=PMC3105386&req=5

Figure 6: Relationship of transcription from SUP4 with H2A.Z level and nucleosome positions. Ovals represent nucleosomes, boxes and T1, T2 denote two terminators, bent arrow marks the TSS. Only downstream nucleosomes are shown with H2A.Z levels and transcriptional state of the gene shown on the right-hand side. (A) In wild-type cells, active state, nucleosmes are fuzzy and block T2. (B) In wild-type cells, following 2 h repression, +1 nucleosome is positioned at a short distance from the terminators. (C) In wild-type cells, after repression longer than 2 h, two nucleosomes may be positioned similar to that seen in rsc4-Δ4 cells. Both terminators are near the dyad axis of the gene-proximal nucleosome.
Mentions: Loss of RSC is reported to shrink NFR (56) on pol II-transcribed genes and increase the nucleosome density on pol III-transcribed genes (57). We have shown that RSC is required to keep the nucleosome immediate downstream of the SUP4 terminator, fuzzy in vivo (Figure 6A). It changes the local density of nucleosmes near the SUP4 gene (Figure 6B and C), maintains nucleosome positions to suppress the transcription in active state, helps loading Nhp6/FACT for transcriptional fidelity and differential marking with H2A.Z according to the expression state. While leaving the +1, RSC persists on the −1 nucleosome under repression, keeping the gene poised for activation under repressed state.Figure 6.

Bottom Line: Histone variant H2A.Z is found in nucleosomes at the 5'-end of many genes.RSC maintains a nucleosome abutting the gene terminator downstream, which results in reduced transcription rate in active state while H2A.Z probably helps RSC in keeping the gene nucleosome-free and serves as stress-sensor.All these factors maintain an epigenetic state which allows the gene to return quickly from repressed to active state and tones down the expression from the active SUP4 gene, required probably to maintain the balance in cellular tRNA pool.

View Article: PubMed Central - PubMed

Affiliation: Centre for Cellular and Molecular Biology, Council of Scientific and Industrial Research, Uppal Road, Hyderabad 500007, India.

ABSTRACT
FACT complex is involved in elongation and ensures fidelity in the initiation step of transcription by RNA polymerase (pol) II. Histone variant H2A.Z is found in nucleosomes at the 5'-end of many genes. We report here H2A.Z-chaperone activity of the yeast FACT complex on the short, nucleosome-free, non-coding, pol III-transcribed yeast tRNA genes. On a prototype gene, yeast SUP4, chromatin remodeler RSC and FACT regulate its transcription through novel mechanisms, wherein the two gene-flanking nucleosomes containing H2A.Z, play different roles. Nhp6, which ensures transcription fidelity and helps load yFACT onto the gene flanking nucleosomes, has inhibitory role. RSC maintains a nucleosome abutting the gene terminator downstream, which results in reduced transcription rate in active state while H2A.Z probably helps RSC in keeping the gene nucleosome-free and serves as stress-sensor. All these factors maintain an epigenetic state which allows the gene to return quickly from repressed to active state and tones down the expression from the active SUP4 gene, required probably to maintain the balance in cellular tRNA pool.

Show MeSH
Related in: MedlinePlus