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Ashleigh J Jackobel, Yan Han, Yuan He, Bruce A Knutson
While structures of the RNA polymerase (Pol) II initiation complex have been resolved and extensively studied, the Pol I initiation complex remained elusive. Here, we review the recent structural analyses of the yeast Pol I transcription initiation complex that reveal several unique and unexpected Pol I-specific properties.
December 21, 2017: Transcription
Michael C Church, Alastair B Fleming
Recently, we reported that a major function of histone acetylation at the yeast FLO1 gene was to regulate transcription elongation. Here, we discuss possible mechanisms by which histone acetylation might regulate RNA polymerase II processivity, and comment on the contribution to transcription of chromatin remodelling at gene coding regions and promoters.
December 8, 2017: Transcription
Deokjae Lee, Jun Hong Park, Shinseog Kim, Seon-Gyeong Lee, Kyungjae Myung
There are hundreds of copies of rDNA repeats in mammalian chromosomes and the ratio of active, poised, or inactive rDNA is regulated in epigenetic manners. Recent studies demonstrated that a post-DNA replication repair enzyme, SHPRH affects rRNA transcription by recognizing epigenetic markers on rDNA promoters and unveiled potential links between DNA repair and ribosome biogenesis (1) . This study suggests that SHPRH could be a link between mTOR-mediated epigenetic regulations and rRNA transcription, while concomitantly affecting genomic integrity...
November 15, 2017: Transcription
Kevin Roy, Guillaume F Chanfreau
The role of transcription factors (TFs) on nucleosome positioning, RNA polymerase recruitment, and transcription initiation has been extensively characterized. Here, we propose that a subset of TFs such as Reb1, Abf1, Rap1, and TFIIIB also serve a major function in partitioning transcription units by assisting the Nrd1p-Nab3p-Sen1p Pol II termination pathway.
November 6, 2017: Transcription
Julie Dubois-Chevalier, Parisa Mazrooei, Mathieu Lupien, Bart Staels, Philippe Lefebvre, Jérôme Eeckhoute
Gene transcriptional regulation relies on cis-regulatory DNA modules (CRMs), which serve as nexus sites for integration of multiple transcription factor (TF) activities. Here, we provide evidence and discuss recent literature indicating that TF recruitment to CRMs is organized into combinations of trans-regulatory protein modules (TRMs). We propose that TRMs are functional entities composed of TFs displaying the most highly interdependent chromatin binding which are, in addition, able to modulate their recruitment to CRMs through inter-TRM effects...
November 6, 2017: Transcription
Masahiko Imashimizu, David B Lukatsky
Transcription of DNA by RNA polymerase (RNAP) takes place in a cell environment dominated by thermal fluctuations. How are transcription reactions including initiation, elongation, and termination on genomic DNA so well-controlled during such fluctuations? A recent statistical mechanical approach using high-throughput sequencing data reveals that repetitive DNA sequence elements embedded into a genomic sequence provide the key mechanism to functionally bias the fluctuations of transcription elongation complexes...
November 6, 2017: Transcription
Didier Auboeuf
Recent large-scale RNA sequencing efforts have revealed the extensive diversity of mRNA molecules produced from most eukaryotic coding genes, which arises from the usage of alternative, cryptic or non-canonical splicing and intronic polyadenylation sites. The prevailing view regarding the tremendous diversity of coding gene transcripts is that mRNA processing is a flexible and more-or-less noisy process leading to a diversity of proteins on which natural selection can act depending on protein-mediated cellular functions...
November 3, 2017: Transcription
Shrutii Sarda, Sridhar Hannenhalli
CpG islands (CGIs) are associated with ∼60% of mammalian promoters. Most unmethylated CGIs exhibit transcriptional activity, which has led to their co-option as promoters by retrogenes. CGIs may also serve as alternative promoters for downstream genes with methylated promoters, with implications on aberrant activation of oncogenes in cancer phenotypes.
November 3, 2017: Transcription
Marta Russo, Gioacchino Natoli, Serena Ghisletti
Cell type-specific and housekeeping enhancers and promoters collectively control the transcriptional output of mammalian cells. Recent data clarify how DNA sequence features on the one hand control functional coupling of promoters with selected enhancers, and on the other impart high level of activity to a broad range of regulatory elements.
October 9, 2017: Transcription
Susan Duncan, Stefanie Rosa
Single molecule RNA fluorescent in situ hybridization (smFISH) enables gene transcription to be assessed at the cellular level. In this point of view article, we describe our recent smFISH research in the model plant Arabidopsis thaliana and discuss how this technique could further knowledge of plant gene transcription in the future.
October 9, 2017: Transcription
Feda H Hamdan, Steven A Johnsen
Significant attention has recently been given to a class of enhancers termed "super enhancers", while implying that "typical enhancers" are less important. In this report, we examine criteria for identification of super enhancers and address the need to evaluate the differences between BRD4-occupied "typical" and "super" enhancers.
October 5, 2017: Transcription
Joseph T Wade, David C Grainger
Most RNA polymerases can initiate transcription from diverse DNA template sequences with relatively few outright sequence restraints. Recent reports have demonstrated that failure to subdue the promiscuity of RNA polymerase in vivo can severely impede cell function. This phenomenon appears common to all cell types with undesirable effects ranging from growth inhibition in prokaryotes to cancer in higher organisms. Here we discuss similarities and differences in strategies employed by cells to minimise spurious transcription across life's domains...
October 5, 2017: Transcription
Jun-Ichi Sakamaki, Jaclyn S Long, Maria New, Tim Van Acker, Sharon A Tooze, Kevin M Ryan
Autophagy is an essential cellular process that degrades cytoplasmic organelles and components. Precise control of autophagic activity is achieved by context-dependent signaling pathways. Recent studies have highlighted the involvement of transcriptional programs during autophagic responses to various signals. Here, we summarize the current understanding of the transcriptional regulation of autophagy.
October 5, 2017: Transcription
Roy Baas, Hetty A A M van Teeffelen, Sjoerd J D Tjalsma, H Th Marc Timmers
Sma and Mad related (SMAD)-mediated Transforming Growth Factor β (TGF-β) and Bone Morphogenetic Protein (BMP) signaling is required for various cellular processes. The activated heterotrimeric SMAD protein complexes associate with nuclear proteins such as the histone acetyltransferases p300, PCAF and the Mixed Lineage Leukemia 4 (MLL4) subunit Pax Transactivation domain-Interacting Protein (PTIP) to regulate gene transcription. We investigated the functional role of PTIP and PTIP Interacting protein 1 (PA1) in relation to TGF-β-activated SMAD signaling...
October 4, 2017: Transcription
Junwoo Lee, Eun Shik Choi, Daeyoup Lee
The ability of elongating RNA polymerase II (RNAPII) to regulate the nucleosome barrier is poorly understood because we do not know enough about the involved factors and we lack a conceptual framework to model this process. Our group recently identified the conserved Fun30/SMARCAD1 family chromatin-remodeling factor, Fun30(Fft3), as being critical for relieving the nucleosome barrier during RNAPII-mediated elongation, and proposed a model illustrating how Fun30(Fft3) may contribute to nucleosome disassembly during RNAPII-mediated elongation...
September 19, 2017: Transcription
Zhengjian Zhang, Robert Tjian
Transcription of protein-encoding genes in eukaryotic cells is a dynamically coordinated process. Many of the key transcription regulators contain functionally essential intrinsically disordered regions (IDRs), the dynamic nature of which creates extra challenges to traditional biochemical analyses. Recent advances in single-molecule fluorescence imaging technology have enabled direct visualization of these rapid, complex and dynamic molecular interactions in real time.
September 18, 2017: Transcription
Zhong Han, Odil Porrua
Helicases are enzymes that remodel nucleic acids or protein-nucleic acid complexes in an ATP-dependent manner. They are ubiquitous and can play many diverse functions related to the metabolism of nucleic acids. A few helicases from both the prokaryotic and the eukaryotic worlds have the ability to induce transcription termination. Here we discuss how the same biological function is achieved by different helicases with quite divergent structures and mechanisms of action.
September 8, 2017: Transcription
Marion Grasser, Klaus D Grasser
Characterisation of the Arabidopsis RNA polymerase II (RNAPII) elongation complex revealed an assembly of a conserved set of transcript elongation factors associated with chromatin remodellers, histone modifiers as well as with various pre-mRNA splicing and polyadenylation factors. Therefore, transcribing RNAPII streamlines the processes of mRNA synthesis and processing in plants.
September 8, 2017: Transcription
Jerome Gouge, Alessandro Vannini
Here, we discuss the role of Brf2, an RNA Polymerase III core transcription factor, as a master switch of the oxidative stress response. We highlight the interplay of Brf2 with the Nrf2/Keap1 pathway, as well as the role of Brf2 in cancer and other possible regulations.
August 30, 2017: Transcription
Yuri A Nedialkov, Kristopher Opron, Hailey L Caudill, Fadi Assaf, Amanda J Anderson, Robert I Cukier, Guowei Wei, Zachary F Burton
Based on molecular dynamics simulations and functional studies, a conformational mechanism is posited for forward translocation by RNA polymerase (RNAP). In a simulation of a ternary elongation complex, the clamp and downstream cleft were observed to close. Hinges within the bridge helix and trigger loop supported generation of translocation force against the RNA-DNA hybrid resulting in opening of the furthest upstream i-8 RNA-DNA bp, establishing conditions for RNAP sliding. The β flap tip helix and the most N-terminal β' Zn finger engage the RNA, indicating a path of RNA threading out of the exit channel...
August 30, 2017: Transcription
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