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Keywords: transcription
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Articles
Journal:
Biochemical Journal
Biochem J (2023) 480 (5): 297–306.
Published: 09 March 2023
...Josef Houser; Kristina Jendruchova; Andrea Knight; Martin Piskacek The nine-amino-acid transactivation domains (9aaTAD) was identified in numerous transcription factors including Gal4, p53, E2A, MLL, c-Myc, N-Myc, and also in SP, KLF, and SOX families. Most of the 9aaTAD domains interact...
Includes: Supplementary data
Articles
Journal:
Biochemical Journal
Biochem J (2022) 479 (11): 1205–1220.
Published: 13 June 2022
... , ZC3H11A ) lead to melanoma progression and metastasis through sequestration of distinct miRNAs species with tumor suppressor function [ 93 ]. Collectively, these results show that the regulation of NUCKS1 transcription is complex, and that NUCKS1 can be mis-regulated post-transcriptionally...
Articles
In Collection
Towards systems biochemistry
Journal:
Biochemical Journal
Biochem J (2022) 479 (6): 767–786.
Published: 28 March 2022
... responses. It has been suggested that basal gene expression profiles define, at least in part, cell type specific transitional responses to hypoxia, with genes transcriptionally active prior to hypoxia stimulation in a given cell type being susceptible to hypoxia induced transcriptional regulation [ 24...
Includes: Supplementary data
Articles
Journal:
Biochemical Journal
Biochem J (2021) 478 (6): 1261–1282.
Published: 19 March 2021
...Diti Chatterjee Bhowmick; Lydia Burnett; Zhanar Kudaibergenova; Aleksandar M. Jeremic Here, we investigated transcriptional and trafficking mechanisms of human islet amyloid polypeptide (hIAPP) in normal and stressed β-cells. In high glucose-challenged human islets and rat insulinoma cells...
Includes: Multimedia, Supplementary data
Articles
Journal:
Biochemical Journal
Biochem J (2020) 477 (12): 2401–2419.
Published: 26 June 2020
... with negative co-operativity to the full P rv2827c promoter, demonstrating an unexpectedly complex form of transcriptional regulation. Correspondence: Tim R. Blower ( [email protected] ) 6 5 2020 6 6 2020 10 6 2020 10 6 2020 © 2020 The Author(s) 2020...
Includes: Supplementary data
Articles
In Collection
Adipose biology
Journal:
Biochemical Journal
Biochem J (2020) 477 (6): 1137–1148.
Published: 27 March 2020
.... The recent recognition of the presence of brown or beige adipocytes in human adults has attracted much attention to elucidate the molecular mechanism underlying the thermogenic adipose program. Many key transcriptional regulators critical for the thermogenic gene program centering on activating the UCP1...
Articles
Journal:
Biochemical Journal
Biochem J (2018) 475 (24): 3921–3932.
Published: 14 December 2018
... this negative charge, loosening the histone's grip around DNA and opening the chromatin to make it more transcriptionally permissible. In addition, Lys-Ac acts as a binding site for proteins bearing a bromodomain [ 2 ], which for the most part include factors that help stimulate transcription, thus reinforcing...
Articles
Journal:
Biochemical Journal
Biochem J (2018) 475 (12): 2073–2090.
Published: 29 June 2018
...John Biddlestone; Michael Batie; Daniel Bandarra; Ivan Munoz; Sonia Rocha The SIN3A–HDAC (histone deacetylase) complex is a master transcriptional repressor, required for development but often deregulated in disease. Here, we report that the recently identified new component of this complex...
Includes: Supplementary data
Articles
Journal:
Biochemical Journal
Biochem J (2018) 475 (6): 1059–1062.
Published: 20 March 2018
...David Harrich; Hongping Jin The HIV-1 tat gene encodes a small 86–104 amino acid protein depending on the HIV-1 strain. Tat is essential for HIV-1 replication through interactions with numerous cellular transcription factors. The interaction between Tat and P-TEFb, which is a cellular protein...
Articles
Journal:
Biochemical Journal
Biochem J (2016) 473 (21): 3741–3753.
Published: 27 October 2016
...Nan Zhang; Vidya C. Darbari; Robert Glyde; Xiaodong Zhang; Martin Buck Transcription initiation is highly regulated in bacterial cells, allowing adaptive gene regulation in response to environment cues. One class of promoter specificity factor called sigma54 enables such adaptive gene expression...
Articles
Journal:
Biochemical Journal
Biochem J (2016) 473 (19): 3065–3079.
Published: 27 September 2016
...M. Gomar-Alba; M. del Olmo Hyperosmotic stress response involves the adaptative mechanisms needed for cell survival. Under high osmolarity conditions, many stress response genes are activated by several unrelated transcription factors that are controlled by the Hog1 kinase. Osmostress transcription...
Includes: Supplementary data
Articles
Matthew Velinder, Jason Singer, Diana Bareyan, Jessica Meznarich, Christopher M. Tracy, James M. Fulcher, David McClellan, Helena Lucente, Sarah Franklin, Sunil Sharma, Michael E. Engel
Journal:
Biochemical Journal
Biochem J (2016) 473 (19): 3355–3369.
Published: 27 September 2016
...Matthew Velinder; Jason Singer; Diana Bareyan; Jessica Meznarich; Christopher M. Tracy; James M. Fulcher; David McClellan; Helena Lucente; Sarah Franklin; Sunil Sharma; Michael E. Engel Proper hematopoietic cell fate decisions require co-ordinated functions of transcription factors...
Includes: Supplementary data
Articles
Journal:
Biochemical Journal
Biochem J (2015) 469 (3): 391–398.
Published: 23 July 2015
...Beiying Qiu; Xiaohe Shi; Qiling Zhou; Hui Shan Chen; Joy Lim; Weiping Han; Vinay Tergaonkar Nuclear ubiquitous casein and cyclin-dependent kinase substrate (NUCKS) is highly expressed in the brain and peripheral metabolic organs, and regulates transcription of a number of genes involved in insulin...
Articles
Journal:
Biochemical Journal
Biochem J (2015) 466 (3): 587–599.
Published: 06 March 2015
... ) on a few transcription factors known to be activated by CARM1. However, O-GlcNAc-depleted CARM1 generated by wheat germ agglutinin (WGA) enrichment, O-GlcNAcase (OGA) treatment and mutation of putative O-GlcNAcylation sites displays different substrate specificity from that of CARM1 WT . Our findings...
Includes: Supplementary data
Articles
Journal:
Biochemical Journal
Biochem J (2014) 462 (3): 385–395.
Published: 22 August 2014
... that gene expression is co-ordinated by changes in transcription and translation in hypoxia, much less is known about how chromatin changes allow for transcription to take place. The missing link between co-ordinating chromatin structure and the hypoxia-induced transcriptional programme could be in the form...
Articles
Fabian Blombach, Helene Launay, Ambrosius P. L. Snijders, Violeta Zorraquino, Hao Wu, Bart de Koning, Stan J. J. Brouns, Thijs J. G. Ettema, Carlo Camilloni, Andrea Cavalli, Michele Vendruscolo, Mark J. Dickman, Lisa D. Cabrita, Anna La Teana, Dario Benelli, Paola Londei, John Christodoulou, John van der Oost
Journal:
Biochemical Journal
Biochem J (2014) 462 (2): 373–384.
Published: 07 August 2014
... van der Oost MBF1 (multi-protein bridging factor 1) is a protein containing a conserved HTH (helix–turn–helix) domain in both eukaryotes and archaea. Eukaryotic MBF1 has been reported to function as a transcriptional co-activator that physically bridges transcription regulators with the core...
Includes: Supplementary data
Articles
Journal:
Biochemical Journal
Biochem J (2014) 461 (1): 15–32.
Published: 13 June 2014
..., the physiological relevance and function of WT1 as a regulator of post-transcriptional processes is still not clear. It been proposed that WT1 −KTS isoforms function optimally as transcriptional factors, whereas the +KTS isoforms might act post-transcriptionally [ 95 ]. WT1 +KTS isoforms were found to localize...
Articles
Journal:
Biochemical Journal
Biochem J (2014) 458 (1): 153–158.
Published: 20 January 2014
..., but not at the nucleosome dyad. We show further that in vivo TALEs bind to transcriptionally repressed chromatin and that transcription increases binding by only 2-fold. These data therefore imply that TALEs are likely to bind to their target in vivo even at inactive loci. 1 These authors contributed equally...
Includes: Supplementary data
Articles
Journal:
Biochemical Journal
Biochem J (2014) 457 (3): 401–413.
Published: 10 January 2014
...Maja Milanovic; Michael Kracht; M. Lienhard Schmitz The transcription factor NF-κB (nuclear factor κB) serves to up-regulate gene expression in response to precarious signals such as the pro-inflammatory cytokines TNF (tumour necrosis factor) and IL-1 (interleukin 1). In the present study we show...
Includes: Supplementary data
Articles
Journal:
Biochemical Journal
Biochem J (2014) 457 (2): 231–242.
Published: 20 December 2013
... eukaryotes independently of their catalytic activities [ 11 – 13 ]. Although capping occurs predominantly during transcription, accumulating evidence suggests that cap-like structures can be also formed post-transcriptionally [ 14 ]. Figure 2 7mG synthesis in S. cerevisiae , Schizosaccharomyces...
Articles
Regulation of the transcriptional activation of the androgen receptor by the UXT-binding protein VHL
Journal:
Biochemical Journal
Biochem J (2013) 456 (1): 55–66.
Published: 24 October 2013
...Shuliang Chen; Ke Chen; Qinghua Zhang; Hanhua Cheng; Rongjia Zhou Loss and/or inactivation of the VHL (von Hippel–Lindau) tumour suppressor causes various tumours. Using a yeast two-hybrid system, we have identified the AR (androgen receptor) co-activator UXT (ubiquitously expressed transcript...
Includes: Supplementary data
Articles
Journal:
Biochemical Journal
Biochem J (2013) 455 (1): 67–73.
Published: 13 September 2013
... [ 8 ]. Although methyl cap formation occurs predominantly at the initiation of transcription, recent evidence has demonstrated that the formation of mRNA cap structures can occur post-transcriptionally [ 9 ]. The human cap methyltransferase consists of the catalytic subunit and an obligate...
Articles
Chau H. Nguyen, Benjamin J. Lang, Ryan C. C. Chai, Jessica L. Vieusseux, Michelle M. Kouspou, John T. Price
Journal:
Biochemical Journal
Biochem J (2013) 452 (2): 321–329.
Published: 10 May 2013
...) mutant p53 stress transcription HSF1 (heat-shock factor 1) is transcriptionally activated by cells in response to a variety of extrinsic and intrinsic stresses, including heat shock, oxidative stress, nutrient deprivation and oncogene activation [ 1 ]. Its activation results in the expression...
Articles
Journal:
Biochemical Journal
Biochem J (2013) 449 (3): 707–717.
Published: 09 January 2013
... docking site (Mf2 domain) in an intrinsically disordered domain of IRF-1 [IFN (interferon) regulatory factor-1], a short-lived IFNγ-regulated transcription factor, in ubiquitination of the protein. Ubiquitin modification of full-length IRF-1 by E3 ligases such as CHIP [C-terminus of the Hsc (heat-shock...
Includes: Supplementary data
Articles
Journal:
Biochemical Journal
Biochem J (2012) 443 (3): 757–768.
Published: 16 April 2012
... [SRE (sterol-regulatory element)-binding protein 2] that activates PCSK9 gene transcription through an SRE motif of the promoter. In addition to SREBP2, HNF1α (hepatic nuclear factor 1α) positively regulates PCSK9 gene transcription in hepatic cells through a binding site located 28 bp upstream from...
Includes: Supplementary data
Articles
Journal:
Biochemical Journal
Biochem J (2012) 441 (1): 481–485.
Published: 14 December 2011
...María-Antonia Sánchez-Romero; David J. Lee; Eugenio Sánchez-Morán; Stephen J. W. Busby In the present paper, we report that transcription affects the location of a DNA target in Escherichia coli K-12. A strain whose chromosome had been engineered to encode a lac repressor–GFP (green fluorescent...
Articles
Journal:
Biochemical Journal
Biochem J (2012) 441 (1): 61–76.
Published: 14 December 2011
... studies show that the metabolite 1,25(OH) 2 D (1,25-dihydroxyvitamin D) is a biologically active metabolite that works through vitamin D receptor to regulate gene transcription. In the present review we discuss the literature relevant to the molecular events that may account for the beneficial impact...
Articles
Journal:
Biochemical Journal
Biochem J (2011) 439 (3): 487–502.
Published: 13 October 2011
...Jin Zhao; Wee Leng Siew; Weiqi Sun; Norbert Lehming The nucleosomes occupying the chromosomal start sites of transcription contain the histone H2A variant H2A.Z in place of H2A. Upon galactose induction, nucleosomes are evicted from the GAL1 locus in Saccharomyces cerevisiae cells. H2A.Z (which...
Includes: Supplementary data
Articles
Masakazu Yoshida, Akihiko Ishimura, Minoru Terashima, Zanabazar Enkhbaatar, Naohito Nozaki, Kenji Satou, Takeshi Suzuki
Journal:
Biochemical Journal
Biochem J (2011) 437 (3): 555–564.
Published: 13 July 2011
... that CD82, which was transcriptionally regulated by KAT5, might be a candidate effector of cell invasion promoted by PLU1. The present study demonstrated a functional contribution of PLU1 overexpression with concomitant epigenetic dysregulation in cancer progression. ChIP experiments were performed...
Includes: Supplementary data
Articles
Journal:
Biochemical Journal
Biochem J (2011) 435 (3): 641–649.
Published: 13 April 2011
... reports about the functional role of the degradation of transcriptional activators and indicate that gene expression studies interfering with proteasome degradation should take the stabilization of potential repressors into account. 1 To whom correspondence should be addressed (email micln...
Includes: Supplementary data
Articles
Jing Sang, Kai Yang, Yueping Sun, Yan Han, Hui Cang, Yuying Chen, Guiying Shi, Kangmin Wang, Jie Zhou, Xiangrui Wang, Jing Yi
Journal:
Biochemical Journal
Biochem J (2011) 435 (2): 489–498.
Published: 29 March 2011
... cannot be differentiated between and are thus referred to as SUMO2/3. Whether these two isoforms are regulated in distinct manners has never been addressed. In the present paper we report that the expression of SUMO3, but not SUMO2, can be down-regulated at the transcription level by cellular oxidative...
Includes: Supplementary data
Articles
Xrel3/XrelA attenuates β-catenin-mediated transcription during mesoderm formation in Xenopus embryos
Journal:
Biochemical Journal
Biochem J (2011) 435 (1): 247–257.
Published: 15 March 2011
... wild-type β-catenin or constitutively active β-catenin S37A abrogated β-catenin-induced axis duplication and attenuated β-catenin-stimulated reporter transcription. Lastly, we provide evidence that Xrel3, but not XrelA, can interact with β-catenin without affecting the association of β-catenin...
Articles
Journal:
Biochemical Journal
Biochem J (2011) 435 (1): 259–266.
Published: 15 March 2011
... suggested that the ZRG17 gene is regulated in response to zinc status by the Zap1 transcription factor. Zap1 activates the expression of many genes in zinc-deficient cells. In the present study, we assessed whether ZRG17 is a direct Zap1 target gene. We showed that ZRG17 mRNA levels were elevated in zinc...
Articles
Hiroko Inoue, Stavros Giannakopoulos, Christopher N. Parkhurst, Tatsushi Matsumura, Evelyn A. Kono, Takako Furukawa, Naoko Tanese
Journal:
Biochemical Journal
Biochem J (2011) 434 (1): 83–92.
Published: 27 January 2011
... / BAF250b that are unique to the BAF complex and absent in the related PBAF (Polybromo BAF). hOsa / BAF250 has been shown to interact with transcriptional activators and bind to DNA suggesting that it acts to target the remodelling complex to chromatin. To better understand the functions of hOsa2, we...
Articles
Lynley D. Pound, Yan Hang, Suparna A. Sarkar, Yingda Wang, Laurel A. Milam, James K. Oeser, Richard L. Printz, Catherine E. Lee, Roland Stein, John C. Hutton, Richard M. O'Brien
Journal:
Biochemical Journal
Biochem J (2011) 433 (1): 95–105.
Published: 15 December 2010
... immunoprecipitation) assays revealed that the islet-enriched transcription factor Pdx-1 binds enhancer A in vitro and in situ respectively. Mutation of two Pdx-1-binding sites in enhancer A markedly reduces fusion gene expression suggesting that this factor contributes to Slc30a8 expression in β-cells, a conclusion...
Includes: Supplementary data
Articles
Journal:
Biochemical Journal
Biochem J (2010) 432 (3): 473–486.
Published: 25 November 2010
... Society 2010 gene expression luteinizing hormone pituitary steroidogenesis transcription To date, SF-1 is known to directly enhance the transcription of more than 20 genes. Numerous target genes are required for cholesterol mobilization and steroid hormone biosynthesis...
Includes: Supplementary data
Articles
Journal:
Biochemical Journal
Biochem J (2010) 431 (2): 179–187.
Published: 28 September 2010
...Eun-Jung Park; Shin-Kyoung Hur; Jongbum Kwon Recent studies have shown that the SWI/SNF family of ATP-dependent chromatin-remodelling complexes play important roles in DNA repair as well as in transcription. The INO80 complex, the most recently described member of this family, has been shown...
Articles
Journal:
Biochemical Journal
Biochem J (2010) 430 (1): 107–117.
Published: 28 July 2010
.... These results suggest that appropriate control of NEU3 gene expression is required for homoeostasis of cellular functions. To gain insights into regulation mechanisms, we determined the gene structure and assessed transcription factor involvement. Oligo-capping analysis indicated the existence of alternative...
Includes: Supplementary data
Articles
Journal:
Biochemical Journal
Biochem J (2010) 428 (2): 247–254.
Published: 13 May 2010
... to be elicited. This dynamism is controlled by two competing conjugating and deconjugating activities. The latter activity is mediated by the SENP [SUMO1/sentrin/SMT3 (suppressor of mif two 3 homologue 1)-specific peptidase] family of SUMO-specific proteases. The transcription factor Elk-1 [ETS (E twenty-six...
Articles
Journal:
Biochemical Journal
Biochem J (2010) 427 (3): 499–511.
Published: 14 April 2010
...Yiming Zhang; Shen Gao; Zhengxin Wang We previously demonstrated that the Groucho protein AES (amino-terminal enhancer of split) functions as a co-repressor of the AR (androgen receptor). It physically interacts with the N-terminal domain of AR and inhibits AR-driven transcription...
Articles
Journal:
Biochemical Journal
Biochem J (2010) 427 (3): 541–550.
Published: 14 April 2010
...-hypersensitive site mapping. Gel-shift assays and chromatin immunoprecipitation of the core region of a hypersensitive site 4.4 kb upstream of BCL6 transcription initiation (HSS-4.4) showed an E-box element-binding ZEB1 (zinc finger E-boxbinding homeobox 1) and the co-repressor CtBP (C-terminal binding protein...
Includes: Supplementary data
Articles
Journal:
Biochemical Journal
Biochem J (2010) 425 (2): 295–302.
Published: 23 December 2009
... transcription elongation. This is discussed in more detail below in the discussion of the mechanism of mRNA cap methylation. Figure 3 mRNA cap methylation occurs co-transcriptionally RNA polymerase II is recruited to chromatin with the CTD hypophosphorylated. At the initiation of transcription, TFIIH...
Articles
Victoria A. Payne, Wo-Shing Au, Christopher E. Lowe, Shaikh M. Rahman, Jacob E. Friedman, Stephen O'Rahilly, Justin J. Rochford
Journal:
Biochemical Journal
Biochem J (2010) 425 (1): 215–224.
Published: 14 December 2009
...Victoria A. Payne; Wo-Shing Au; Christopher E. Lowe; Shaikh M. Rahman; Jacob E. Friedman; Stephen O'Rahilly; Justin J. Rochford The transcription factor SREBP1c (sterol-regulatory-element-binding protein 1c) is highly expressed in adipose tissue and plays a central role in several aspects...
Includes: Supplementary data
Articles
Journal:
Biochemical Journal
Biochem J (2009) 422 (3): 521–531.
Published: 27 August 2009
...Anna-Maria G. Psarra; Stefan Hermann; George Panayotou; Giannis Spyrou Trx2 (mitochondrial thioredoxin) is an antioxidant and anti-apoptotic factor essential for cell viability. Trx1 (cytoplasmic thioredoxin) is a co-factor and regulator of redox-sensitive transcription factors such as the GR...
Articles
Journal:
Biochemical Journal
Biochem J (2009) 422 (3): 493–501.
Published: 27 August 2009
...Phillip G. P. Andrews; Zhijian He; Cathy Popadiuk; Kenneth R. Kao Pygopus is a core component of the β-catenin/TCF (T-cell factor) transcriptional activation complex required for the expression of canonical Wnt target genes. Recent evidence suggests that Pygopus could interpret histone methylation...
Includes: Supplementary data
Articles
Journal:
Biochemical Journal
Biochem J (2009) 422 (3): 543–551.
Published: 27 August 2009
...Hanshao Liu; Hoi Chin Hew; Zheng-Guang Lu; Tomoko Yamaguchi; Yoshio Miki; Kiyotsugu Yoshida Transcriptional regulation of the p53 tumour suppressor gene plays an important role in the control of the expression of various target genes involved in the DNA damage response. However, the molecular basis...
Articles
Journal:
Biochemical Journal
Biochem J (2009) 422 (2): 363–372.
Published: 13 August 2009
... previous work showed that S100A9 was severely down-regulated in human ESCC (oesophageal squamous cell carcinoma). To further investigate the transcriptional regulation of S100A9, we analysed the S100A9 promoter region and found several putative p53BS (p53-binding sites). Luciferase reporter assays showed...
Includes: Supplementary data
Articles
Journal:
Biochemical Journal
Biochem J (2009) 421 (3): 339–343.
Published: 15 July 2009
... the transcription cycle. We have characterized the molecular interactions between the F/E complex and the RNAP core. F/E binds to RNAP with submicromolar affinity and is not in a dynamic exchange with unbound F/E. 1 To whom correspondence should be addressed (email [email protected] ). 22 5...
Articles
Journal:
Biochemical Journal
Biochem J (2009) 420 (3): 421–428.
Published: 27 May 2009
...Wen Tang; Wanhui You; Feng Shi; Tianyang Qi; Ling Wang; Zina Djouder; Wenguang Liu; Xianlu Zeng Actin, the major component of the cytoplasmic skeleton, has been shown to exist in the nucleus. Nuclear actin functions in several steps of the transcription process, including chromatin remodelling...
Articles
Journal:
Biochemical Journal
Biochem J (2009) 419 (1): 167–176.
Published: 13 March 2009
...Moritz Hentschke; Ute Süsens; Uwe Borgmeyer Modification with SUMOs (small ubiquitin-related modifiers) has emerged as an important means of regulating the activity of transcription factors, often by repressing their activity. The ERRγ [oestrogen receptor-related receptor γ; ERR3 or NR3B3 (nuclear...
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