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Articles

Pregnane X receptor inhibits the transdifferentiation of hepatic stellate cells by down-regulating periostin expression

Takumi Sato, Ryota Shizu, Ryonosuke Baba, Akira Ooka, Takuomi Hosaka, Yuichiro Kanno, Kouichi Yoshinari

Biochem J (2024) 481 (18): 1173–1186.

https://doi.org/10.1042/BCJ20240172

Published: 06 September 2024

View article titled, Pregnane X receptor inhibits the transdifferentiation of hepatic stellate cells by down-regulating periostin expression

Includes: Supplementary data

Articles

Thermoregulated transcriptomics: the molecular basis and biological significance of temperature-dependent alternative splicing

Tom Haltenhof, Marco Preußner, Florian Heyd

Biochem J (2024) 481 (15): 999–1013.

https://doi.org/10.1042/BCJ20230410

Published: 31 July 2024

View article titled, Thermoregulated transcriptomics: the molecular basis and biological significance of temperature-dependent alternative splicing

Articles

Insights into the mechanisms driven by H3K4 KMTs in pancreatic cancer

In Collection

Epigenetics

Kayla C. LaRue-Nolan, Glancis Luzeena Raja Arul, Ashley N. Sigafoos, Jiaqi Shi, Martin E. Fernandez-Zapico

Biochem J (2024) 481 (15): 983–997.

https://doi.org/10.1042/BCJ20230374

Published: 30 July 2024

View article titled, Insights into the mechanisms driven by H3K4 KMTs in pancreatic cancer

Articles

Inducible gene expression of IκB-kinase ε is dependent on nuclear factor-κB in human pulmonary epithelial cells

Amandah Necker-Brown, Cora Kooi, Andrew J. Thorne, Akanksha Bansal, Mahmoud M. Mostafa, Priyanka Chandramohan, Alex Gao, Keerthana Kalyanaraman, Arya Milani, Sachman Gill, Andrei Georgescu, Sarah K. Sasse, Anthony N. Gerber, Richard Leigh, Robert Newton

Biochem J (2024) 481 (14): 959–980.

https://doi.org/10.1042/BCJ20230461

Published: 12 July 2024

View article titled, Inducible gene expression of IκB-kinase ε is dependent on nuclear factor-κB in human pulmonary epithelial cells

Includes: Supplementary data

Articles

Aflatoxin biosynthesis regulators AflR and AflS: DNA binding affinity, stoichiometry, and kinetics

Asmaa Abbas, Ranjit K. Prajapati, Emil Aalto-Setälä, Alexander A. Baykov, Anssi M. Malinen

Biochem J (2024) 481 (12): 805–821.

https://doi.org/10.1042/BCJ20240084

Published: 17 June 2024

View article titled, Aflatoxin biosynthesis regulators AflR and AflS: DNA binding affinity, stoichiometry, and kinetics

Includes: Supplementary data

Articles

Mechanisms and pathologies of human mitochondrial DNA replication and deletion formation

Tiago M. Bernardino Gomes, Amy E. Vincent, Katja E. Menger, James B. Stewart, Thomas J. Nicholls

Biochem J (2024) 481 (11): 683–715.

https://doi.org/10.1042/BCJ20230262

Published: 28 May 2024

View article titled, Mechanisms and pathologies of human mitochondrial DNA replication and deletion formation

Articles

Epigenetic mechanisms linking early-life adversities and mental health

In Collection

Epigenetics

Eduardo T. Cánepa, Bruno G. Berardino

Biochem J (2024) 481 (10): 615–642.

https://doi.org/10.1042/BCJ20230306

Published: 09 May 2024

View article titled, Epigenetic mechanisms linking early-life adversities and mental health

Articles

Expression of neuronal NO synthase α- and β-isoforms in skeletal muscle of mice

Oliver Baum

Biochem J (2024) 481 (9): 601–613.

https://doi.org/10.1042/BCJ20230458

Published: 25 April 2024

View article titled, Expression of neuronal NO synthase α- and β-isoforms in skeletal muscle of mice

Articles

Dynamic interactions between SPX proteins, the ubiquitination machinery, and signalling molecules for stress adaptation at a whole-plant level

Emma Collins, Huixia Shou, Chuanzao Mao, James Whelan, Ricarda Jost

Biochem J (2024) 481 (5): 363–385.

https://doi.org/10.1042/BCJ20230163

Published: 29 February 2024

View article titled, Dynamic interactions between SPX proteins, the ubiquitination machinery, and signalling molecules for stress adaptation at a whole-plant level

Articles

AMP-activated protein kinase activation suppresses leptin expression independently of adipogenesis in primary murine adipocytes

Sophia Bustraan, Jane Bennett, Chad Whilding, Betheney R. Pennycook, David Smith, Alexis R. Barr, Jon Read, David Carling, Alice Pollard

Biochem J (2024) 481 (5): 345–362.

https://doi.org/10.1042/BCJ20240003

Published: 23 February 2024

View article titled, AMP-activated protein kinase activation suppresses leptin expression independently of adipogenesis in primary murine adipocytes

Includes: Supplementary data

Articles

Beyond the tail: the consequence of context in histone post-translational modification and chromatin research

In Collection

Epigenetics

Ellen N. Weinzapfel, Karlie N. Fedder-Semmes, Zu-Wen Sun, Michael-Christopher Keogh

Biochem J (2024) 481 (4): 219–244.

https://doi.org/10.1042/BCJ20230342

Published: 14 February 2024

View article titled, Beyond the tail: the consequence of context in histone post-translational modification and chromatin research

Articles

Pseudouridylation-mediated gene expression modulation

Jonathan L. Chen, W.-Matthias Leeder, Pedro Morais, Hironori Adachi, Yi-Tao Yu

Biochem J (2024) 481 (1): 1–16.

https://doi.org/10.1042/BCJ20230096

Published: 04 January 2024

View article titled, Pseudouridylation-mediated gene expression modulation

Articles

MicroRNA, miR-501 regulate the V(D)J recombination in B cells

Rupa Kumari, Urbi Roy, Sagar Desai, Arannya S. Mondal, Rajshree R. Nair, Namrata Nilavar, Bibha Choudhary, Sathees C. Raghavan

Biochem J (2023) 480 (24): 2061–2077.

https://doi.org/10.1042/BCJ20230250

Published: 20 December 2023

View article titled, MicroRNA, miR-501 regulate the V(D)J recombination in B cells

Includes: Supplementary data

Articles

Engineering of CYP82Y1, a cytochrome P450 monooxygenase: a key enzyme in noscapine biosynthesis in opium poppy

Zahra Aghaali, Mohammad Reza Naghavi

Biochem J (2023) 480 (23): 2009–2022.

https://doi.org/10.1042/BCJ20230243

Published: 08 December 2023

View article titled, Engineering of CYP82Y1, a cytochrome P450 monooxygenase: a key enzyme in noscapine biosynthesis in opium poppy

Articles

Lysine methylation signaling in skeletal muscle biology: from myogenesis to clinical insights

In Collection

Epigenetics

Eric Cordeiro-Spinetti, Scott B. Rothbart

Biochem J (2023) 480 (23): 1969–1986.

https://doi.org/10.1042/BCJ20230223

Published: 06 December 2023

View article titled, Lysine methylation signaling in skeletal muscle biology: from myogenesis to clinical insights

Articles

PHF1 compartmentalizes PRC2 via phase separation

Genzhe Lu, Pilong Li

Biochem J (2023) 480 (22): 1833–1844.

https://doi.org/10.1042/BCJ20230040

Published: 21 November 2023

View article titled, PHF1 compartmentalizes PRC2 via phase separation

Includes: Supplementary data

Articles

Microrchidia 2/histone deacetylase 1 complex regulates E-cadherin gene expression and function

Liz Thomas, Namita Chutani, Krishna R, Asha S. Nair, Nanda Kumar Yellapu, Prashanthi Karyala, Suresh B. Pakala

Biochem J (2023) 480 (20): 1675–1691.

https://doi.org/10.1042/BCJ20230304

Published: 19 October 2023

View article titled, Microrchidia 2/histone deacetylase 1 complex regulates E-cadherin gene expression and function

Includes: Supplementary data

Articles

Seasonal cold induces divergent structural/biochemical adaptations in different skeletal muscles of Columba livia : evidence for nonshivering thermogenesis in adult birds

Punyadhara Pani, Gourabamani Swalsingh, Sunil Pani, Unmod Senapati, Bijayashree Sahu, Benudhara Pati, Subhasmita Rout, Naresh C. Bal

Biochem J (2023) 480 (17): 1397–1409.

https://doi.org/10.1042/BCJ20230245

Published: 04 September 2023

View article titled, Seasonal cold induces divergent structural/biochemical adaptations in different skeletal muscles of Columba livia : evidence for nonshivering thermogenesis in adult birds

Includes: Supplementary data

Articles

Development of an OTUD1 ubiquitin variant inhibitor

Qi Liu, Evan Mallette, Hui Zheng, Wei Zhang

Biochem J (2023) 480 (16): 1317–1330.

https://doi.org/10.1042/BCJ20230119

Published: 25 August 2023

View article titled, Development of an OTUD1 ubiquitin variant inhibitor

Includes: Supplementary data

Articles

SUFU promotes GLI activity in a Hedgehog-independent manner in pancreatic cancer

Brooke D. Paradise, Vladimir G. Gainullin, Luciana L. Almada, Ashley N. Sigafoos, Sandhya Sen, Renzo E. Vera, Glancis Luzeena Raja Arul, Murat Toruner, David R. Pease, Alina L. Gonzalez, Fatima M. Mentucci, Daniel H. Grasso, Martin E. Fernandez-Zapico

Biochem J (2023) 480 (15): 1199–1216.

https://doi.org/10.1042/BCJ20220439

Published: 02 August 2023

View article titled, SUFU promotes GLI activity in a Hedgehog-independent manner in pancreatic cancer

Articles

Calcium signalling components underlying NPK homeostasis: potential avenues for exploration

In Collection

Plants and climate change: the role of plants in achieving net zero

Sonam Pahuja, Malathi Bheri, Diksha Bisht, Girdhar K. Pandey

Biochem J (2023) 480 (13): 1015–1034.

https://doi.org/10.1042/BCJ20230156

Published: 07 July 2023

View article titled, Calcium signalling components underlying NPK homeostasis: potential avenues for exploration

Articles

Respiratory epithelial cell types, states and fates in the era of single-cell RNA-sequencing

Oleksandr Dudchenko, Jose Ordovas-Montanes, Colin D. Bingle

Biochem J (2023) 480 (13): 921–939.

https://doi.org/10.1042/BCJ20220572

Published: 06 July 2023

View article titled, Respiratory epithelial cell types, states and fates in the era of single-cell RNA-sequencing

Articles

Root system growth and development responses to elevated CO 2 : underlying signalling mechanisms and role in improving plant CO 2 capture and soil C storage

In Collection

Plants and climate change: the role of plants in achieving net zero

Liên Bach, Alain Gojon

Biochem J (2023) 480 (11): 753–771.

https://doi.org/10.1042/BCJ20220245

Published: 02 June 2023

View article titled, Root system growth and development responses to elevated CO 2 : underlying signalling mechanisms and role in improving plant CO 2 capture and soil C storage

Articles

Novel insights into the recognition of acetylated histone H4 tail by the TRIM24 PHD-Bromo module

Ishita Bardhan, Soumen Barman, Anirban Roy, Babu Sudhamalla

Biochem J (2023) 480 (9): 629–647.

https://doi.org/10.1042/BCJ20230011

Published: 10 May 2023

View article titled, Novel insights into the recognition of acetylated histone H4 tail by the TRIM24 PHD-Bromo module

Includes: Supplementary data

Articles

Identification and characterization of the Doublesex gene and its mRNA isoforms in the brine shrimp Artemia franciscana

Wen-Tao Wu, Lian-Ying Xu, Zhi-Jun Yan, Ning Bi, Cai-Yuan Cheng, Fan Yang, Wei-Jun Yang, Jin-Shu Yang

Biochem J (2023) 480 (5): 385–401.

https://doi.org/10.1042/BCJ20220495

Published: 15 March 2023

View article titled, Identification and characterization of the Doublesex gene and its mRNA isoforms in the brine shrimp Artemia franciscana

Includes: Supplementary data

Articles

The NFkB activation domain is 14-amino-acid-long variant of the 9aaTAD

Josef Houser, Kristina Jendruchova, Andrea Knight, Martin Piskacek

Biochem J (2023) 480 (5): 297–306.

https://doi.org/10.1042/BCJ20220605

Published: 09 March 2023

View article titled, The NFkB activation domain is 14-amino-acid-long variant of the 9aaTAD

Includes: Supplementary data

Articles

GLI1 interaction with p300 modulates SDF1 expression in cancer-associated fibroblasts to promote pancreatic cancer cells migration

Renzo E. Vera, María J. Lamberti, Luciana L. Almada, Ezequiel J. Tolosa, Anne M. Vrabel, Ashley N. Sigafoos, Merih D. Toruner, Luis F. Flores, Viviana A. Rivarola, Natalia B. Rumie Vittar, Martín E. Fernández-Zapico

Biochem J (2023) 480 (3): 225–241.

https://doi.org/10.1042/BCJ20220521

Published: 14 February 2023

View article titled, GLI1 interaction with p300 modulates SDF1 expression in cancer-associated fibroblasts to promote pancreatic cancer cells migration

Includes: Supplementary data

Articles

Characterizing crosstalk in epigenetic signaling to understand disease physiology

In Collection

Cell signaling in the 21st century

Joanna K. Lempiäinen, Benjamin A. Garcia

Biochem J (2023) 480 (1): 57–85.

https://doi.org/10.1042/BCJ20220550

Published: 11 January 2023

View article titled, Characterizing crosstalk in epigenetic signaling to understand disease physiology

Articles

Structural and functional organization of germ plasm condensates

Austin Chiappetta, Jeffrey Liao, Siran Tian, Tatjana Trcek

Biochem J (2022) 479 (24): 2477–2495.

https://doi.org/10.1042/BCJ20210815

Published: 19 December 2022

View article titled, Structural and functional organization of germ plasm condensates

Articles

Regulation of B cell receptor signalling by Epstein–Barr virus nuclear antigens

Sarika Khasnis, Hildegonda Veenstra, Michael J. McClellan, Opeoluwa Ojeniyi, C. David Wood, Michelle J. West

Biochem J (2022) 479 (23): 2395–2417.

https://doi.org/10.1042/BCJ20220417

Published: 07 December 2022

View article titled, Regulation of B cell receptor signalling by Epstein–Barr virus nuclear antigens

Includes: Supplementary data

Articles

Poly-ADP ribosylation of p21 by tankyrases promotes p21 degradation and regulates cell cycle progression

Misun Jung, Wonyoung Kim, Jin Won Cho, Won Ho Yang, In Kwon Chung

Biochem J (2022) 479 (22): 2379–2394.

https://doi.org/10.1042/BCJ20220391

Published: 30 November 2022

View article titled, Poly-ADP ribosylation of p21 by tankyrases promotes p21 degradation and regulates cell cycle progression

Includes: Supplementary data

Articles

The C-terminal region of phytoene synthase is a key element to control carotenoid biosynthesis in the haloarchaeon Haloferax volcanii

Micaela Cerletti, Agustín Rabino, Roberto A. Paggi, Celeste Ferrari, Ansgar Poetsch, Harri Savilahti, Saija Kiljunen, Rosana E. De Castro

Biochem J (2022) 479 (22): 2365–2377.

https://doi.org/10.1042/BCJ20220403

Published: 23 November 2022

View article titled, The C-terminal region of phytoene synthase is a key element to control carotenoid biosynthesis in the haloarchaeon Haloferax volcanii

Includes: Supplementary data

Articles

Up-regulation of the PI3K/AKT and RHO/RAC/PAK signalling pathways in CHK1 inhibitor resistant Eµ-Myc lymphoma cells

Jill E. Hunter, Amy E. Campbell, Scott Kerridge, Callum Fraser, Nicola L. Hannaway, Saimir Luli, Iglika Ivanova, Philip J. Brownridge, Jonathan Coxhead, Leigh Taylor, Peter Leary, Megan S. R. Hasoon, Claire E. Eyers, Neil D. Perkins

Biochem J (2022) 479 (19): 2131–2151.

https://doi.org/10.1042/BCJ20220103

Published: 14 October 2022

View article titled, Up-regulation of the PI3K/AKT and RHO/RAC/PAK signalling pathways in CHK1 inhibitor resistant Eµ-Myc lymphoma cells

Includes: Supplementary data

Articles

Carbidopa, an activator of aryl hydrocarbon receptor, suppresses IDO1 expression in pancreatic cancer and decreases tumor growth

Ksenija Korac, Devaraja Rajasekaran, Tyler Sniegowski, Bradley K. Schniers, Andrew F. Ibrahim, Yangzom D. Bhutia

Biochem J (2022) 479 (17): 1807–1824.

https://doi.org/10.1042/BCJ20210851

Published: 06 September 2022

View article titled, Carbidopa, an activator of aryl hydrocarbon receptor, suppresses IDO1 expression in pancreatic cancer and decreases tumor growth

Includes: Supplementary data

Articles

Characterization of functionally deficient SIM2 variants found in patients with neurological phenotypes

Emily L. Button, Joseph J. Rossi, Daniel P. McDougal, John B. Bruning, Daniel J. Peet, David C. Bersten, Jill A. Rosenfeld, Murray L. Whitelaw

Biochem J (2022) 479 (13): 1441–1454.

https://doi.org/10.1042/BCJ20220209

Published: 13 July 2022

View article titled, Characterization of functionally deficient SIM2 variants found in patients with neurological phenotypes

Includes: Supplementary data

Articles

Alphabetti kinase Spaghetti: the complex roles of IKKα and β in the canonical NF-κB pathway

In Collection

Cell death and survival

Neil D. Perkins

Biochem J (2022) 479 (11): 1121–1126.

https://doi.org/10.1042/BCJ20220023

Published: 01 June 2022

View article titled, Alphabetti kinase Spaghetti: the complex roles of IKKα and β in the canonical NF-κB pathway

Articles

The role of eIF2 phosphorylation in cell and organismal physiology: new roles for well-known actors

Xuemin Wang, Christopher G. Proud

Biochem J (2022) 479 (10): 1059–1082.

https://doi.org/10.1042/BCJ20220068

Published: 23 May 2022

View article titled, The role of eIF2 phosphorylation in cell and organismal physiology: new roles for well-known actors

Articles

No-nonsense: insights into the functional interplay of nonsense-mediated mRNA decay factors

Justine Mailliot, Mirella Vivoli-Vega, Christiane Schaffitzel

Biochem J (2022) 479 (9): 973–993.

https://doi.org/10.1042/BCJ20210556

Published: 12 May 2022

View article titled, No-nonsense: insights into the functional interplay of nonsense-mediated mRNA decay factors

Articles

Regulation of chromatin accessibility by hypoxia and HIF

In Collection

Towards systems biochemistry

Michael Batie, Julianty Frost, Dilem Shakir, Sonia Rocha

Biochem J (2022) 479 (6): 767–786.

https://doi.org/10.1042/BCJ20220008

Published: 28 March 2022

View article titled, Regulation of chromatin accessibility by hypoxia and HIF

Includes: Supplementary data

Articles

Adaptor protein 3BP2 regulates dectin-1-mediated cellular signalling to induce cytokine expression and NF-κB activation

Kazuyasu Chihara, Yuri Chihara, Kenji Takeuchi, Kiyonao Sada

Biochem J (2022) 479 (4): 503–523.

https://doi.org/10.1042/BCJ20210707

Published: 23 February 2022

View article titled, Adaptor protein 3BP2 regulates dectin-1-mediated cellular signalling to induce cytokine expression and NF-κB activation

Includes: Supplementary data

Articles

APLNR Regulates IFN-γ signaling via β-arrestin 1 mediated JAK-STAT1 pathway in melanoma cells

Yingying Liu, Xiaochuan Ma, Hui Yang, Xun Li, Yingli Ma, Brandon Ason, Suling Liu, Liaoyuan A. Hu

Biochem J (2022) 479 (3): 385–399.

https://doi.org/10.1042/BCJ20210813

Published: 11 February 2022

View article titled, APLNR Regulates IFN-γ signaling via β-arrestin 1 mediated JAK-STAT1 pathway in melanoma cells

Includes: Supplementary data

Articles

Systems approaches to understand oxygen sensing: how multi-omics has driven advances in understanding oxygen-based signalling

In Collection

Towards systems biochemistry

Michael Batie, Niall S. Kenneth, Sonia Rocha

Biochem J (2022) 479 (3): 245–257.

https://doi.org/10.1042/BCJ20210554

Published: 04 February 2022

View article titled, Systems approaches to understand oxygen sensing: how multi-omics has driven advances in understanding oxygen-based signalling

Articles

Proteomic analysis identifies ZMYM2 as endogenous binding partner of TBX18 protein in 293 and A549 cells

Timo H.-W. Lüdtke, Marc-Jens Kleppa, Reginaldo Rivera-Reyes, Fairouz Qasrawi, Dervla M. Connaughton, Shirlee Shril, Friedhelm Hildebrandt, Andreas Kispert

Biochem J (2022) 479 (1): 91–109.

https://doi.org/10.1042/BCJ20210642

Published: 14 January 2022

View article titled, Proteomic analysis identifies ZMYM2 as endogenous binding partner of TBX18 protein in 293 and A549 cells

Includes: Supplementary data

Articles

An ERK5–KLF2 signalling module regulates early embryonic gene expression and telomere rejuvenation in stem cells

Helen A. Brown, Charles A.C. Williams, Houjiang Zhou, Diana Rios-Szwed, Rosalia Fernandez-Alonso, Saria Mansoor, Liam McMulkin, Rachel Toth, Robert Gourlay, Julien Peltier, Nora Dieguez-Martinez, Matthias Trost, Jose M. Lizcano, Marios P. Stavridis, Greg M. Findlay

Biochem J (2021) 478 (23): 4119–4136.

https://doi.org/10.1042/BCJ20210646

Published: 06 December 2021

View article titled, An ERK5–KLF2 signalling module regulates early embryonic gene expression and telomere rejuvenation in stem cells

Articles

Signalling dynamics in embryonic development

Katharina F. Sonnen, Claudia Y. Janda

Biochem J (2021) 478 (23): 4045–4070.

https://doi.org/10.1042/BCJ20210043

Published: 06 December 2021

View article titled, Signalling dynamics in embryonic development

Articles

BACH1, the master regulator of oxidative stress, has a dual effect on CFTR expression

Monali NandyMazumdar, Alekh Paranjapye, James Browne, Shiyi Yin, Shih-Hsing Leir, Ann Harris

Biochem J (2021) 478 (20): 3741–3756.

https://doi.org/10.1042/BCJ20210252

Published: 21 October 2021

View article titled, BACH1, the master regulator of oxidative stress, has a dual effect on CFTR expression

Includes: Supplementary data

Articles

SREBP-1c and lipogenesis in the liver: an update

In Collection

Celebrating 100 years of insulin research

Pascal Ferré, Franck Phan, Fabienne Foufelle

Biochem J (2021) 478 (20): 3723–3739.

https://doi.org/10.1042/BCJ20210071

Published: 21 October 2021

View article titled, SREBP-1c and lipogenesis in the liver: an update

Articles

The many ways that nature has exploited the unusual structural and chemical properties of phosphohistidine for use in proteins

Rajasree Kalagiri, Tony Hunter

Biochem J (2021) 478 (19): 3575–3596.

https://doi.org/10.1042/BCJ20210533

Published: 08 October 2021

View article titled, The many ways that nature has exploited the unusual structural and chemical properties of phosphohistidine for use in proteins

Includes: Supplementary data

Articles

The roles of epigenetics in cancer progression and metastasis

Jocelyn F. Chen, Qin Yan

Biochem J (2021) 478 (17): 3373–3393.

https://doi.org/10.1042/BCJ20210084

Published: 14 September 2021

View article titled, The roles of epigenetics in cancer progression and metastasis

Articles

TFEB phosphorylation on Serine 211 is induced by autophagy in human synovial fibroblasts and by p62/SQSTM1 overexpression in HEK293 cells

Biserka Relic, Celine Deroyer, Olivier Malaise, Zelda Plener, Philippe Gillet, Dominique de Seny, Michel G. Malaise

Biochem J (2021) 478 (16): 3145–3155.

https://doi.org/10.1042/BCJ20210174

Published: 27 August 2021

View article titled, TFEB phosphorylation on Serine 211 is induced by autophagy in human synovial fibroblasts and by p62/SQSTM1 overexpression in HEK293 cells

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