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Articles

Molecular mechanisms of transcription factor mediated cell reprogramming: conversion of liver to pancreas

Sebastian L. Wild, David Tosh

Biochem Soc Trans (2021) 49 (2): 579–590.

DOI: https://doi.org/10.1042/BST20200219

Published: 05 March 2021

... cells to alternative identities have advanced dramatically. Cellular identity is determined by the transcriptional profile which comprises the subset of mRNAs, and therefore proteins, being expressed by a cell at a given point in time. A better understanding of the levers governing transcription factor...

View article titled, Molecular mechanisms of transcription factor mediated cell reprogramming: conversion of liver to pancreas

Articles

Protein motion in the nucleus: from anomalous diffusion to weak interactions

Maxime Woringer, Xavier Darzacq

Biochem Soc Trans (2018) 46 (4): 945–956.

DOI: https://doi.org/10.1042/BST20170310

Published: 31 July 2018

...Maxime Woringer; Xavier Darzacq Understanding how transcription factors (TFs) regulate mammalian gene expression in space and time is a central topic in biology. To activate a gene, a TF has first to diffuse in the available space of the nucleus until it reaches a target DNA sequence or protein...

View article titled, Protein motion in the nucleus: from anomalous diffusion to weak interactions

Articles

Understanding life and death decisions in human leukaemias

David J. MacEwan, Lawrence N. Barrera, Sujitra Keadsanti, Stuart A. Rushworth, Niraj M. Shah, Tianma Yuan, Lyubov Zaitseva

Biochem Soc Trans (2014) 42 (4): 747–751.

DOI: https://doi.org/10.1042/BST20140127

Published: 11 August 2014

... in the clinic many drug-resistant forms of blood cancers. In the present article, we uncover the relationship that exists in human leukaemia life/death switching between the anti-apoptotic pro-inflammatory transcription factor NF-κB (nuclear factor κB) and the cytoprotective antioxidant-responsive transcription...

View article titled, Understanding life and death decisions in human leukaemias

Articles

Systematic genetic analysis of transcription factors to map the fission yeast transcription-regulatory network

Gordon Chua

Biochem Soc Trans (2013) 41 (6): 1696–1700.

DOI: https://doi.org/10.1042/BST20130224

Published: 20 November 2013

...Gordon Chua Mapping transcriptional-regulatory networks requires the identification of target genes, binding specificities and signalling pathways of transcription factors. However, the characterization of each transcription factor sufficiently for deciphering such networks remains laborious...

View article titled, Systematic genetic analysis of transcription factors to map the fission yeast transcription-regulatory network

Articles

Modern biophysical approaches probe transcription-factor-induced DNA bending and looping

Andreas Gietl, Dina Grohmann

Biochem Soc Trans (2013) 41 (1): 368–373.

DOI: https://doi.org/10.1042/BST20120301

Published: 29 January 2013

.... As these events play out on the nanometre scale, new biophysical approaches have been employed to monitor conformational changes in this regime at the single-molecule level. Focusing on transcription factor action on promoter DNA, we discuss how current biophysical techniques are able to quantitatively describe...

View article titled, Modern biophysical approaches probe transcription-factor-induced DNA bending and looping

Articles

The Pseudomonas aeruginosa DNR transcription factor: light and shade of nitric oxide-sensing mechanisms

Giorgio Giardina, Nicoletta Castiglione, Manuela Caruso, Francesca Cutruzzolà, Serena Rinaldo

Biochem Soc Trans (2011) 39 (1): 294–298.

DOI: https://doi.org/10.1042/BST0390294

Published: 19 January 2011

... transcription factors. These regulators are involved in many different pathways and distinct activation mechanism seems to be operative in several cases. Recent results indicate that DNR is a haem protein capable of discriminating between NO and CO (carbon monoxide). On the basis of the available structural...

View article titled, The Pseudomonas aeruginosa DNR transcription factor: light and shade of nitric oxide-sensing mechanisms

Articles

Translation deregulation in B-cell lymphomas

Emilie Horvilleur, Lindsay A. Wilson, Anne E. Willis

Biochem Soc Trans (2010) 38 (6): 1593–1597.

DOI: https://doi.org/10.1042/BST0381593

Published: 24 November 2010

... ribosomal entry segment (IRES) microRNA (miRNA) transcription factor Lymphomas are a disparate group of neoplastic disorders of lymphoid tissues. In the West, lymphomas have an incidence of one case per 5000 people, and, of these, 95% are of B-cell origin. Within B-cell lymphomas, distinction...

View article titled, Translation deregulation in B-cell lymphomas

Articles

Floral stem cells: from dynamic balance towards termination

Bo Sun, Toshiro Ito

Biochem Soc Trans (2010) 38 (2): 613–616.

DOI: https://doi.org/10.1042/BST0380613

Published: 22 March 2010

... for the next generation. 1 To whom correspondence should be addressed (email itot@tll.org.sg ). 7 9 2009 © The Authors Journal compilation © 2010 Biochemical Society 2010 developmental timing floral meristem histone modification stem cell transcription factor From...

View article titled, Floral stem cells: from dynamic balance towards termination

Articles

Gene Expression in Neuronal Disease

Ian C. Wood, Nicola K. Gray, Lesley Jones

Biochem Soc Trans (2009) 37 (6): 1261–1262.

DOI: https://doi.org/10.1042/BST0371261

Published: 19 November 2009

... jonesl1@Cardiff.ac.uk ). 5 9 2009 © The Authors Journal compilation © 2009 Biochemical Society 2009 brain gene expression neuronal disease RNA transcription factor translation This papers in this issue of Biochemical Society Transactions arise from our meeting Gene...

View article titled, Gene Expression in Neuronal Disease

Articles

Unravelling neurogenetic networks implicated in developmental language disorders

Sonja C. Vernes, Simon E. Fisher

Biochem Soc Trans (2009) 37 (6): 1263–1269.

DOI: https://doi.org/10.1042/BST0371263

Published: 19 November 2009

... an unusual monogenic disorder, characterized by problems with articulating speech along with deficits in expressive and receptive language. FOXP2 encodes a regulatory protein, belonging to the forkhead box family of transcription factors, known to play important roles in modulating gene expression...

View article titled, Unravelling neurogenetic networks implicated in developmental language disorders

Articles

The reversal of epigenetic silencing of the EBV genome is regulated by viral bZIP protein

Questa H. Karlsson, Celine Schelcher, Elizabeth Verrall, Carlo Petosa, Alison J. Sinclair

Biochem Soc Trans (2008) 36 (4): 637–639.

DOI: https://doi.org/10.1042/BST0360637

Published: 22 July 2008

... To whom correspondence should be addressed (email A.J.Sinclair@Sussex.ac.uk ). 1 4 2008 © The Authors Journal compilation © 2008 Biochemical Society 2008 basic leucine zipper (bZIP) DNA binding epigenetics methylation transcription factor virus Infection with EBV...

View article titled, The reversal of epigenetic silencing of the EBV genome is regulated by viral bZIP protein

Articles

Computational approaches to study transcriptional regulation

M. Madan Babu

Biochem Soc Trans (2008) 36 (4): 758–765.

DOI: https://doi.org/10.1042/BST0360758

Published: 22 July 2008

... to understand the organization of regulatory interactions in an organism. I will then describe methods to predict transcription factors and cis -regulatory elements using information such as sequence, structure and evolutionary conservation. Finally, I will discuss approaches to infer genome-scale...

View article titled, Computational approaches to study transcriptional regulation

Articles

Alternative splicing in plants

Craig G. Simpson, Dominika Lewandowska, John Fuller, Monika Maronova, Maria Kalyna, Diane Davidson, Jim McNicol, Dorota Raczynska, Artur Jarmolowski, Andrea Barta, John W.S. Brown

Biochem Soc Trans (2008) 36 (3): 508–510.

DOI: https://doi.org/10.1042/BST0360508

Published: 21 May 2008

... ). 19 2 2008 © The Authors Journal compilation © 2008 Biochemical Society 2008 alternative splicing Arabidopsis precursor mRNA splicing factor transcription factor Pre-mRNA (precursor mRNA) splicing is the excision of intron sequences from pre-mRNAs mediated...

View article titled, Alternative splicing in plants

Articles

Ion channel switching and activation in smooth-muscle cells of occlusive vascular diseases

D.J. Beech

Biochem Soc Trans (2007) 35 (5): 890–894.

DOI: https://doi.org/10.1042/BST0350890

Published: 25 October 2007

... mitogen-activated protein kinase NF-κB nuclear factor κB REST repressor element 1-silencing transcription factor TRP transient receptor potential TRPC TRP canonical TRPV TRP vanilloid VSMC vascular smooth-muscle cell This study was funded by the British Heart...

View article titled, Ion channel switching and activation in smooth-muscle cells of occlusive vascular diseases

Articles

Ubiquitin signals in the NF-κB pathway

J. Terzic, I. Marinovic-Terzic, F. Ikeda, I. Dikic

Biochem Soc Trans (2007) 35 (5): 942–945.

DOI: https://doi.org/10.1042/BST0350942

Published: 25 October 2007

...J. Terzic; I. Marinovic-Terzic; F. Ikeda; I. Dikic The NF-κB (nuclear factor κB) transcription factors control cell survival, proliferation and innate and adaptive immune response. Post-translational modifications of key components of the NF-κB pathway provide the molecular basis for signal...

View article titled, Ubiquitin signals in the NF-κB pathway

Articles

Mechanisms controlling the expression of the components of the exocytotic apparatus under physiological and pathological conditions

A. Abderrahmani, V. Plaisance, P. Lovis, R. Regazzi

Biochem Soc Trans (2006) 34 (5): 696–700.

DOI: https://doi.org/10.1042/BST0340696

Published: 25 October 2006

... of the genes involved in exocytosis is urgently needed. Recent studies have led to the identification of transcription factors and other regulatory molecules such as microRNAs that modulate the cellular level of key controllers of the exocytotic process. These findings furnish a new perspective...

View article titled, Mechanisms controlling the expression of the components of the exocytotic apparatus under physiological and pathological conditions

Articles

Regulation by Per-Arnt-Sim (PAS) kinase of pancreatic duodenal homeobox-1 nuclear import in pancreatic β-cells

R. An, G. da Silva Xavier, H.-X. Hao, F. Semplici, J. Rutter, G.A. Rutter

Biochem Soc Trans (2006) 34 (5): 791–793.

DOI: https://doi.org/10.1042/BST0340791

Published: 25 October 2006

...R. An; G. da Silva Xavier; H.-X. Hao; F. Semplici; J. Rutter; G.A. Rutter The transcription factor PDX-1 ( p ancreatic d uodenal homeobo x -1) is required for normal pancreatic development and for the function of insulin-producing islet β-cells in mammals. We have shown previously that glucose...

View article titled, Regulation by Per-Arnt-Sim (PAS) kinase of pancreatic duodenal homeobox-1 nuclear import in pancreatic β-cells

Articles

Transcriptional regulation and metabolism

M.P. Brynildsen, W.W. Wong, J.C. Liao

Biochem Soc Trans (2005) 33 (6): 1423–1426.

DOI: https://doi.org/10.1042/BST0331423

Published: 26 October 2005

... to elucidate transcription factor dynamics in Saccharomyces cerevisiae cell-cycle regulation, detect cross-talks in Escherichia coli two-component signalling pathways, and characterize E. coli carbon source transition. An ultimate test of system-wide understanding is the ability to design and construct novel...

View article titled, Transcriptional regulation and metabolism

Articles

Amazing grass: developmental genetics of maize domestication

E. Vollbrecht, B. Sigmon

Biochem Soc Trans (2005) 33 (6): 1502–1506.

DOI: https://doi.org/10.1042/BST0331502

Published: 26 October 2005

... are representative, approx. 1200 genes were targeted during maize domestication. © 2005 The Biochemical Society 2005 developmental genetics meristem plant architecture plant domestication ramosa1 transcription factor Plants, through their ability to harvest light energy and convert...

View article titled, Amazing grass: developmental genetics of maize domestication

Articles

Sucrose-induced translational repression of plant bZIP-type transcription factors

A. Wiese, N. Elzinga, B. Wobbes, S. Smeekens

Biochem Soc Trans (2005) 33 (1): 272–275.

DOI: https://doi.org/10.1042/BST0330272

Published: 01 February 2005

...) type transcription factor AtbZIP11 / ATB2 . This sucrose-induced repression of translation (SIRT) depends on translation of a highly conserved upstream open reading frame (uORF) in the 5′ UTR of the gene. This conserved uORF is exclusively encoded in 5′ UTRs of several plant S-class bZIP transcription...

View article titled, Sucrose-induced translational repression of plant bZIP-type transcription factors

Articles

Regulation of lipoprotein trafficking in the kidney: role of inflammatory mediators and transcription factors

X.Z. Ruan, J.F. Moorhead, R. Fernando, D.C. Wheeler, S.H. Powis, Z. Varghese

Biochem Soc Trans (2004) 32 (1): 88–91.

DOI: https://doi.org/10.1042/bst0320088

Published: 01 February 2004

... and the formation of foam cells, and that AP-1 (activator protein 1)/ets were necessary transcriptional factors for Scr induction in HMCs (human kidney mesangial cells). Most cells are protected from excessive native LDL (low-density lipoprotein) accumulation by tight feedback regulation of the LDLr (LDL receptor...

View article titled, Regulation of lipoprotein trafficking in the kidney: role of inflammatory mediators and transcription factors

Articles

Fatty acid recycling in adipocytes: a role for glyceroneogenesis and phosphoenolpyruvate carboxykinase

C. Forest, J. Tordjman, M. Glorian, E. Duplus, G. Chauvet, J. Quette, E.G. Beale, B. Antoine

Biochem Soc Trans (2003) 31 (6): 1125–1129.

DOI: https://doi.org/10.1042/bst0311125

Published: 01 December 2003

...-activated receptor re-esterification thiazolidinedione transcription factor Abbreviations used: COUP-TF, chicken ovalbumin upstream promoter–transcription factor; DR1, direct repeat 1; G3P, glycerol 3-phosphate; FA, fatty acid; PEPCK-C, cytosolic phosphoenolpyruvate carboxykinase (GTP); PPAR...

View article titled, Fatty acid recycling in adipocytes: a role for glyceroneogenesis and phosphoenolpyruvate carboxykinase

Articles

Structure and mechanism of the oestrogen receptor

E.H. Kong, A.C.W. Pike, R.E. Hubbard

Biochem Soc Trans (2003) 31 (1): 56–59.

DOI: https://doi.org/10.1042/bst0310056

Published: 01 February 2003

...-activated transcription factor and a member of the steroid hormone nuclear receptor (NR) superfamily, all of which share the same structural features, such as having distinct DNA- and hormone-binding domains [3]. Hormone binding initiates receptor conformational changes, which allows the ER to interact...

View article titled, Structure and mechanism of the oestrogen receptor

Articles

AMP-activated protein kinase regulates gene expression by direct phosphorylation of nuclear proteins

T. Leff

Biochem Soc Trans (2003) 31 (1): 224–227.

DOI: https://doi.org/10.1042/bst0310224

Published: 01 February 2003

... and regulates proteins involved in gene transcription. There are now several examples of transcription factors, cofactors and components of the transcriptional core machinery that are directly phosphorylated and regulated by AMPK. Here I review these examples and discuss the significance of AMPK activity...

View article titled, AMP-activated protein kinase regulates gene expression by direct phosphorylation of nuclear proteins

Articles

Sterol regulatory element-binding proteins: transcriptional activators of lipid synthesis

J. D. Horton

Biochem Soc Trans (2002) 30 (6): 1091–1095.

DOI: https://doi.org/10.1042/bst0301091

Published: 01 November 2002

...J. D. Horton Sterol regulatory element-binding proteins (SREBPs) are a family of transcription factors that regulate lipid homoeostasis. Three SREBP iso-forms control the expression of more than 30 genes required for the biosynthesis of cholesterol, fatty acids, triacylglycerols and phospholipids...

View article titled, Sterol regulatory element-binding proteins: transcriptional activators of lipid synthesis

Articles

Structural aspects of agonism and antagonism in the oestrogen receptor

A. C. W. Pike, A. M. Brzozowski, J. Walton, R. E. Hubbard, T. Bonn, J-Å. Gustafsson, M. Carlquist

Biochem Soc Trans (2000) 28 (4): 396–400.

DOI: https://doi.org/10.1042/bst0280396

Published: 01 August 2000

... binding steroid receptor transcription factor © 2000 Biochemical Society 2000 13 4 2000 1 To whom correspondence should be addressed (e-mail rod@ysbl.york.ac.uk ) Biochemical Society Transactions (2000) Volume 28, part 4 6 Chen, J. D., Umesono, K. and Evans, R M. ( I 996) Proc...

View article titled, Structural aspects of agonism and antagonism in the oestrogen receptor

NARROW

Molecular mechanisms of transcription factor mediated cell reprogramming: conversion of liver to pancreas

Protein motion in the nucleus: from anomalous diffusion to weak interactions

Understanding life and death decisions in human leukaemias

Systematic genetic analysis of transcription factors to map the fission yeast transcription-regulatory network

Modern biophysical approaches probe transcription-factor-induced DNA bending and looping

The Pseudomonas aeruginosa DNR transcription factor: light and shade of nitric oxide-sensing mechanisms

Translation deregulation in B-cell lymphomas

Floral stem cells: from dynamic balance towards termination

Gene Expression in Neuronal Disease

Unravelling neurogenetic networks implicated in developmental language disorders

The reversal of epigenetic silencing of the EBV genome is regulated by viral bZIP protein

Computational approaches to study transcriptional regulation

Alternative splicing in plants

Ion channel switching and activation in smooth-muscle cells of occlusive vascular diseases

Ubiquitin signals in the NF-κB pathway

Mechanisms controlling the expression of the components of the exocytotic apparatus under physiological and pathological conditions

Regulation by Per-Arnt-Sim (PAS) kinase of pancreatic duodenal homeobox-1 nuclear import in pancreatic β-cells

Transcriptional regulation and metabolism

Amazing grass: developmental genetics of maize domestication

Sucrose-induced translational repression of plant bZIP-type transcription factors

Regulation of lipoprotein trafficking in the kidney: role of inflammatory mediators and transcription factors

Fatty acid recycling in adipocytes: a role for glyceroneogenesis and phosphoenolpyruvate carboxykinase

Structure and mechanism of the oestrogen receptor

AMP-activated protein kinase regulates gene expression by direct phosphorylation of nuclear proteins

Sterol regulatory element-binding proteins: transcriptional activators of lipid synthesis

Structural aspects of agonism and antagonism in the oestrogen receptor

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