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Keywords: transcription
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Articles
Journal:
Biochemical Society Transactions
Biochem Soc Trans (2023) 51 (5): 1975–1988.
Published: 13 October 2023
...Ramzan Umarov; Chung-Chau Hon Enhancers are genomic regions that regulate gene transcription and are located far away from the transcription start sites of their target genes. Enhancers are highly enriched in disease-associated variants and thus deciphering the interactions between enhancers...
Articles
Journal:
Biochemical Society Transactions
Biochem Soc Trans (2023) 51 (3): 1023–1034.
Published: 12 May 2023
... by moving heterochromatin breaks (see section Genome Integrity — DNA DSB Repair Pathway) [ 1 , 2 , 8 , 9 , 30 ]. Besides gene relocation, myosin V helps regulate transcription. Both isoforms myosin Va and Vb are present in the nucleus of transcriptionally active cells, yet distribution differs...
Articles
Journal:
Biochemical Society Transactions
Biochem Soc Trans (2023) 51 (2): 557–569.
Published: 06 March 2023
...Liza Dahal; Nike Walther; Robert Tjian; Xavier Darzacq; Thomas G.W. Graham How molecules interact governs how they move. Single-molecule tracking (SMT) thus provides a unique window into the dynamic interactions of biomolecules within live cells. Using transcription regulation as a case study, we...
Articles
Journal:
Biochemical Society Transactions
Biochem Soc Trans (2023) 51 (1): 125–135.
Published: 18 January 2023
...Katerina Cermakova; Vaclav Veverka; H. Courtney Hodges Interaction scaffolds that selectively recognize disordered protein strongly shape protein interactomes. An important scaffold of this type that contributes to transcription is the TFIIS N-terminal domain (TND). The TND is a five-helical bundle...
Articles
Journal:
Biochemical Society Transactions
Biochem Soc Trans (2022) 50 (6): 1633–1642.
Published: 09 November 2022
...Hao Deng; Gaochen Jin; Bomyi Lim Proper enhancer–promoter interactions are essential to maintaining specific transcriptional patterns and preventing ectopic gene expression. Drosophila is an ideal model organism to study transcriptional regulation due to extensively characterized regulatory regions...
Articles
Journal:
Biochemical Society Transactions
Biochem Soc Trans (2022) 50 (3): 1227–1243.
Published: 13 June 2022
...Hailey E. Edwards; Daniel A. Gorelick Proteins that contain basic helix-loop-helix (bHLH) and Per-Arnt-Sim motifs (PAS) function as transcription factors. bHLH–PAS proteins exhibit essential and diverse functions throughout the body, from cell specification and differentiation in embryonic...
Articles
Journal:
Biochemical Society Transactions
Biochem Soc Trans (2021) 49 (6): 2639–2653.
Published: 08 November 2021
... for the spreading of the transcriptionally repressive H3K27me3 mark to neighboring nucleosomes resulting in heterochromatin boundaries [ 23 ]. Recent studies have shown that all three members of the PRC family of proteins work together in a hierarchical manner to regulate the transcriptional landscape during...
Articles
Journal:
Biochemical Society Transactions
Biochem Soc Trans (2021) 49 (6): 2483–2493.
Published: 08 November 2021
...Caroline A. Austin; Ian G. Cowell; Mushtaq M. Khazeem; Dawn Lok; Huei Teng Ng Transcription is regulated and mediated by multiprotein complexes in a chromatin context. Transcription causes changes in DNA topology which is modulated by DNA topoisomerases, enzymes that catalyse changes in DNA...
Articles
Journal:
Biochemical Society Transactions
Biochem Soc Trans (2021) 49 (3): 1325–1336.
Published: 01 June 2021
...Søren Lykke-Andersen; Jérôme O. Rouvière; Torben Heick Jensen ARS2/SRRT is an essential eukaryotic protein that has emerged as a critical factor in the sorting of functional from non-functional RNA polymerase II (Pol II) transcripts. Through its interaction with the Cap Binding Complex (CBC...
Articles
Journal:
Biochemical Society Transactions
Biochem Soc Trans (2021) 49 (3): 1299–1309.
Published: 01 June 2021
... with gene activity: when transcription was OFF, P–E distances were ∼700 nm r.m.s. This distance decreased to ∼340 nm r.m.s. right before transcription switches ON. Similarly, transcription switching from ON to OFF was accompanied by increased P–E distances. Interestingly, a more detailed analysis revealed...
Articles
Journal:
Biochemical Society Transactions
Biochem Soc Trans (2021) 49 (2): 867–880.
Published: 26 March 2021
...-transcriptionally, and most introns are removed before the addition of poly-A tails. However, occasionally some introns remain after splicing and polyadenylation. Transcripts with ‘detained introns’ are either sequestered in nucleus as a ‘reservoir’, or to be degraded. A recent report suggests a regulatory role...
Articles
Journal:
Biochemical Society Transactions
Biochem Soc Trans (2020) 48 (4): 1569–1581.
Published: 29 July 2020
... not readily available for the sequestration and subjugation by viruses. Transcription machineries encoded by the viral genome in turn, provide NCLDVs like ASFV with a strong selective advantage because they have become transcriptionally self-sufficient. This host-factor independence may also enable ASFV...
Articles
Journal:
Biochemical Society Transactions
Biochem Soc Trans (2020) 48 (3): 1121–1128.
Published: 05 May 2020
... biological outputs, with the main aim of restoring oxygen homeostasis. This includes a dynamic gene transcriptional response, the central drivers of which are the hypoxia-inducible factor (HIF) family of transcription factors. HIFs are regulated in an oxygen-dependent manner and while their role in hypoxia...
Articles
Journal:
Biochemical Society Transactions
Biochem Soc Trans (2019) 47 (6): 1597–1608.
Published: 26 November 2019
... of their active counterparts, assembly of signaling hubs, or modulation of protein localization. One such pseudokinase, named Tra1 in yeast and transformation/transcription domain-associated protein (TRRAP) in mammals, is the only member lacking all catalytic residues within the phosphatidylinositol 3-kinase...
Articles
Journal:
Biochemical Society Transactions
Biochem Soc Trans (2019) 47 (3): 847–860.
Published: 13 May 2019
... processes, such as transcription. The current state of research on mycobacteriophage-derived anti-TB treatment is reviewed in comparison with inhibitors from other phages, and with focus on transcription as the host target process. Treatment of drug-susceptible (DS)-TB is successful in 86% cases, MDR-TB...
Articles
Journal:
Biochemical Society Transactions
Biochem Soc Trans (2019) 47 (2): 679–689.
Published: 05 March 2019
...Amber Riaz-Bradley Transcription in cyanobacteria involves several fascinating features. Cyanobacteria comprise one of the very few groups in which no proofreading factors (Gre homologues) have been identified. Gre factors increase the efficiency of RNA cleavage, therefore helping to maintain...
Articles
Journal:
Biochemical Society Transactions
Biochem Soc Trans (2019) 47 (1): 399–410.
Published: 07 February 2019
...Alexis Verger; Didier Monté; Vincent Villeret Mediator is a large multiprotein complex conserved in all eukaryotes that plays an essential role in transcriptional regulation. Mediator comprises 25 subunits in yeast and 30 subunits in humans that form three main modules and a separable four-subunit...
Includes: Supplementary data
Articles
Journal:
Biochemical Society Transactions
Biochem Soc Trans (2019) 47 (1): 411–423.
Published: 01 February 2019
...Kevin Kramm; Christoph Engel; Dina Grohmann In all domains of life, the regulation of transcription by DNA-dependent RNA polymerases (RNAPs) is achieved at the level of initiation to a large extent. Whereas bacterial promoters are recognized by a σ-factor bound to the RNAP, a complex set...
Articles
Journal:
Biochemical Society Transactions
Biochem Soc Trans (2019) 47 (1): 339–350.
Published: 15 January 2019
...Hamed Mosaei; John Harbottle Transcription, the first phase of gene expression, is performed by the multi-subunit RNA polymerase (RNAP). Bacterial RNAP is a validated target for clinical antibiotics. Many natural and synthetic compounds are now known to target RNAP, inhibiting various stages...
Articles
Journal:
Biochemical Society Transactions
Biochem Soc Trans (2019) 47 (1): 209–217.
Published: 21 December 2018
... in which the DNA is double-stranded (closed), thereby preventing transcription. Promoter melting must occur to form the transcriptionally active open complex in which the DNA strands are separated. This enables RNA polymerase access to the template strand and elongation to start ( Figure 2 ). Indeed...
Articles
Journal:
Biochemical Society Transactions
Biochem Soc Trans (2019) 47 (1): 219–228.
Published: 21 December 2018
...David Forrest Transcription, the first step of gene expression, is accomplished in all domains of life by the multisubunit RNA polymerase (msRNAP). Accordingly, the msRNAP is an ancient enzyme that is ubiquitous across all cellular organisms. Conserved in absolutely all msRNAPs is the catalytic...
Articles
Journal:
Biochemical Society Transactions
Biochem Soc Trans (2016) 44 (1): 279–285.
Published: 09 February 2016
... in inositide metabolism, nuclear signalling and transcriptional regulation. 1 To whom correspondence should be addressed (email ray.blind@vanderbilt.edu). 30 11 2015 © 2016 Authors; published by Portland Press Limited 2016 IPMK ipk2 ArgR inositide multikinase transcription...
Articles
Journal:
Biochemical Society Transactions
Biochem Soc Trans (2014) 42 (4): 1123–1128.
Published: 11 August 2014
... in the production of toxic RNA and/or protein or causes transcriptional repression and silencing of the host gene. Although the molecular mechanisms of expansion diseases are not well understood, mounting evidence suggests that transcription through expanded repeats plays an essential role in disease pathology...
Articles
Journal:
Biochemical Society Transactions
Biochem Soc Trans (2013) 41 (6): 1666–1672.
Published: 20 November 2013
... concomitantly with polII (RNA polymerase II) transcription, it has become evident that QC acts at the transcriptional level in addition to degrading aberrant RNAs. In the present review, we discuss mechanisms that allow cells to co-transcriptionally initiate the removal of RNAs as well as down-regulate...
Articles
Journal:
Biochemical Society Transactions
Biochem Soc Trans (2013) 41 (6): 1673–1678.
Published: 20 November 2013
... by the Yamamoto laboratory as a suppressor of the uncontrolled meiosis driven by a pat1 mutant. Numerous studies from this laboratory and others have established the role of the Ste11 transcription factor as the master regulator of the switch between proliferation and differentiation in fission yeast...
Articles
Journal:
Biochemical Society Transactions
Biochem Soc Trans (2013) 41 (6): 1660–1665.
Published: 20 November 2013
...Miriam Sansó; Robert P. Fisher CDKs (cyclin-dependent kinases) ensure directionality and fidelity of the eukaryotic cell division cycle. In a similar fashion, the transcription cycle is governed by a conserved subfamily of CDKs that phosphorylate Pol II (RNA polymerase II) and other substrates...
Articles
Journal:
Biochemical Society Transactions
Biochem Soc Trans (2013) 41 (4): 1008–1016.
Published: 18 July 2013
... of the structural biology of the CDK family has been extended by determination of structures for members of the transcriptional CDK and CDK-like kinase branches of the extended family. We include these recent structures in the present review and consider them in the light of current models for CDK activation...
Articles
Journal:
Biochemical Society Transactions
Biochem Soc Trans (2013) 41 (3): 727–740.
Published: 23 May 2013
...-modifying activities that are thought to contribute to transcriptional repression and maintain heterochromatic regions of the genome. In contrast with DNA methylation, which is found broadly across vertebrate genomes, non-methylated DNA is concentrated in regions known as CGIs (CpG islands). Recently...
Articles
Journal:
Biochemical Society Transactions
Biochem Soc Trans (2013) 41 (2): 542–547.
Published: 21 March 2013
...Charles J. Dorman DNA supercoiling and NAPs (nucleoid-associated proteins) contribute to the regulation of transcription of many bacterial genes. The horizontally acquired SPI ( Salmonella pathogenicity island) genes respond positively to DNA relaxation, they are activated and repressed by the Fis...
Articles
Journal:
Biochemical Society Transactions
Biochem Soc Trans (2013) 41 (1): 356–361.
Published: 29 January 2013
... shibatae RNAP) in complex with dsDNA (double-stranded DNA) constitutes a new piece of information helping the understanding of the mechanisms for DNA stabilization at the position downstream of the catalytic site during transcription. In Archaea, in contrast with Eukarya, downstream DNA stabilization...
Articles
Journal:
Biochemical Society Transactions
Biochem Soc Trans (2012) 40 (4): 846–849.
Published: 20 July 2012
...Steven West Splicing is a key process for mRNA maturation, particularly in higher eukaryotes where most protein-coding transcripts contain multiple introns. It is achieved by the concerted action of five snRNAs (small nuclear RNAs) and hundreds of accessory proteins that form the spliceosome...
Articles
Journal:
Biochemical Society Transactions
Biochem Soc Trans (2012) 40 (4): 762–767.
Published: 20 July 2012
... transcription The miRNA family of endogenous short single-stranded RNAs down-regulate gene expression post-transcriptionally. Sequence-specific miRNA binding at recognition sites in the 3′-UTRs (untranslated regions) of target mRNAs leads to translational repression and/or mRNA destabilization via...
Articles
Journal:
Biochemical Society Transactions
Biochem Soc Trans (2012) 40 (2): 311–323.
Published: 21 March 2012
...) and SUMO (small ubiquitin-related modifier) E3 ligases [hPC2 (human polycomb protein 2) and PIAS1 (protein inhibitor of activated signal transducer and activator of transcription 1)] [ 39 ] that remodel target gene chromatin into transcriptionally inactive facultative heterochromatin. Curiously, however...
Articles
Journal:
Biochemical Society Transactions
Biochem Soc Trans (2012) 40 (1): 1–5.
Published: 19 January 2012
.... Central to this is the coupling of cAMP elevation to the mobilization of two C/EBP (CCAAT/enhancer-binding protein) family transcription factors, resulting in the induction of the SOCS3 (suppressor of cytokine signalling 3) gene, which attenuates pro-inflammatory cytokine signalling in VECs. These novel...
Articles
Journal:
Biochemical Society Transactions
Biochem Soc Trans (2011) 39 (1): 122–127.
Published: 19 January 2011
...Dina Grohmann; Daniel Klose; Daniel Fielden; Finn Werner The complex organization of the transcription machinery has been revealed mainly by biochemical and crystallographic studies. X-ray structures describe RNA polymerases and transcription complexes on an atomic level, but fail to portray...
Articles
Magdalena Wojtas, Bibiana Peralta, Marina Ondiviela, Maria Mogni, Stephen D. Bell, Nicola G.A. Abrescia
Journal:
Biochemical Society Transactions
Biochem Soc Trans (2011) 39 (1): 25–30.
Published: 19 January 2011
... step towards the understanding of Rpo13's role in archaeal transcription. 1 To whom correspondence should be addressed (email nabrescia@cicbiogune.es ). 29 9 2010 RNAP from S. shibatae packs in three different space groups: P 2 1 2 1 2 and P 2 1 2 1 2 1 , as described...
Articles
Journal:
Biochemical Society Transactions
Biochem Soc Trans (2010) 38 (6): 1598–1601.
Published: 24 November 2010
... in methyl cap levels correlated with increased translation and protein expression of the genes in question. Formation of the methyl cap was observed to be regulated by Myc on a significant number of genes, including most transcriptional target genes and some genes not transcriptionally regulated by Myc...
Articles
Journal:
Biochemical Society Transactions
Biochem Soc Trans (2010) 38 (6): 1543–1547.
Published: 24 November 2010
... into the nucleus and incorporated into pre-ribosomal subunits at the nucleolus, where they bind to the rRNA co-transcriptionally [ 20 ]. The nucleolus is divided into three morphologically distinct subcompartments: transcription, early processing and rRNA modifications occur within the innermost FC (fibrillar...
Articles
Journal:
Biochemical Society Transactions
Biochem Soc Trans (2010) 38 (1): 217–222.
Published: 19 January 2010
... The CCND1 gene-encoded cyclin D1 protein is tightly regulated by a variety of signalling pathways at the transcriptional level as well as post-transcriptionally, through modulation of RNA splicing and stability, nucleocytoplasmic transport, protein stability and degradation ( Figure 1 ). Cyclin D1 differs...
Articles
Journal:
Biochemical Society Transactions
Biochem Soc Trans (2009) 37 (6): 1375–1377.
Published: 19 November 2009
... of the transcription factor zif268 (egr1). Hence, it is predicted that zif268 may regulate transcription of genes associated with glutamate receptors and/or GABA A Rs. It turns out that receptor regulation by zif268 tends to be indirect. Induction of zif268 in neurons leads to altered expression of proteasome subunit...
Articles
Journal:
Biochemical Society Transactions
Biochem Soc Trans (2009) 37 (6): 1147–1160.
Published: 19 November 2009
... (NMDAR) oxidative stress transcription 1 email Giles.Hardingham@ed.ac.uk 7 8 2009 © The Authors Journal compilation © 2009 Biochemical Society 2009 NMDARs [NMDA ( N -methyl- D -aspartate) receptors] are cation-passing channels gated by the neurotransmitter glutamate...
Articles
Journal:
Biochemical Society Transactions
Biochem Soc Trans (2009) 37 (1): 12–17.
Published: 20 January 2009
..., nucleic acid binding, catalysis and specific regulatory interactions with transcription factors. The recent development of methods to reconstitute archaeal RNAP from recombinant materials in conjunction with structural information of multisubunit RNAPs present a potent opportunity to investigate...
Articles
Journal:
Biochemical Society Transactions
Biochem Soc Trans (2009) 37 (1): 52–57.
Published: 20 January 2009
...Bart de Koning; Fabian Blombach; Hao Wu; Stan J.J. Brouns; John van der Oost MBF1 (multiprotein bridging factor 1) is a highly conserved protein in archaea and eukaryotes. It was originally identified as a mediator of the eukaryotic transcription regulator BmFTZ-F1 ( Bombyx mori regulator of fushi...
Articles
Journal:
Biochemical Society Transactions
Biochem Soc Trans (2009) 37 (1): 18–22.
Published: 20 January 2009
... enzyme shows close structural similarity to eukaryotic RNAP, particularly to polymerase II, and can therefore be used as model for analyses of the eukaryotic transcriptional machinery. The cleft loops in the active centre of RNAP were deleted and modified to unravel their function in interaction...
Articles
Journal:
Biochemical Society Transactions
Biochem Soc Trans (2008) 36 (6): 1160–1164.
Published: 19 November 2008
... and the signals that they sense has greatly increased. The present article reviews recent developments, with a particular focus on bacterial sensors of nitric oxide. bacterium metalloregulatory protein nitric oxide regulatory protein transcription transition metal cofactor Transition Metals...
Articles
Journal:
Biochemical Society Transactions
Biochem Soc Trans (2008) 36 (6): 1262–1266.
Published: 19 November 2008
..., including Type 2 diabetes, Alzheimer's disease and cancer, highlights the importance of zinc-regulated gene expression. Mechanisms elucidated in bacteria and yeast provide examples of different possible modes of zinc-sensitive gene regulation, involving the zinc-regulated binding of transcriptional...
Articles
Journal:
Biochemical Society Transactions
Biochem Soc Trans (2008) 36 (4): 590–594.
Published: 22 July 2008
... transcription and RNA processing. Recent work has demonstrated that the CTD of the large subunit of pol II and its phosphorylation are required for 3′-box-dependent RNA 3′-end formation in vivo [ 6 , 25 ], indicating that processing occurs co-transcriptionally. The CTD plays a major role in co-ordinating...
Articles
Journal:
Biochemical Society Transactions
Biochem Soc Trans (2008) 36 (4): 619–624.
Published: 22 July 2008
... ], perhaps promoting steps to convert rDNA chromatin into a transcriptionally competent form. Interestingly, however, UBF does not appear to be required to maintain transcriptional competence, since adenoviral infection of cells, which leads to a sequestration of the majority of UBF away from the nucleolus...
Articles
Journal:
Biochemical Society Transactions
Biochem Soc Trans (2008) 36 (4): 595–598.
Published: 22 July 2008
...Laura M. Elsby; Stefan G.E. Roberts Transcription by RNA polymerase II requires the assembly of the general transcription factors at the promoter to form a pre-initiation complex. The general transcription factor TF (transcription factor) IIB plays a central role in the assembly of the pre...
Articles
Journal:
Biochemical Society Transactions
Biochem Soc Trans (2008) 36 (4): 625–628.
Published: 22 July 2008
...Richard D. Palermo; Helen M. Webb; Andrea Gunnell; Michelle J. West The EBNA 2 (Epstein–Barr nuclear antigen 2) transcription factor is essential for B-cell transformation by the cancer-associated EBV (Epstein–Barr virus) and for the continuous proliferation of infected cells. EBNA 2 activates...
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