Publications
2025
NF-κB is a Central Regulator of Hypoxia-Induced Gene Expression
2023
Oxygen-regulated post-translation modifications as master signalling pathway in cells.
Batie, M., Fasanya, T., Kenneth, N. S., & Rocha, S. (2023). Oxygen-regulated post-translation modifications as master signalling pathway in cells.. EMBO reports, e57849. doi:10.15252/embr.202357849
Fixed Cell Immunofluorescence for Quantification of Hypoxia-Induced Changes in Histone Methylation.
Shakir, D., Batie, M., & Rocha, S. (2023). Fixed Cell Immunofluorescence for Quantification of Hypoxia-Induced Changes in Histone Methylation.. Methods in molecular biology (Clifton, N.J.), 2675, 261-269. doi:10.1007/978-1-0716-3247-5_19
2022
Regulation of chromatin accessibility by hypoxia and HIF
Batie, M., Frost, J., Shakir, D., & Rocha, S. (2022). Regulation of chromatin accessibility by hypoxia and HIF. BIOCHEMICAL JOURNAL, 479(6), 767-786. doi:10.1042/BCJ20220008
Systems approaches to understand oxygen sensing: how multi-omics has driven advances in understanding oxygen-based signalling
Batie, M., Kenneth, N. S., & Rocha, S. (2022). Systems approaches to understand oxygen sensing: how multi-omics has driven advances in understanding oxygen-based signalling. The Biochemical journal, 479(3), 245-257. doi:10.1042/BCJ20210554
2021
Oxygen-dependent changes in binding partners and post-translational modifications regulate the abundance and activity of HIF-1 alpha/2 alpha
Daly, L. A., Brownridge, P. J., Batie, M., Rocha, S., See, V., & Eyers, C. E. (2021). Oxygen-dependent changes in binding partners and post-translational modifications regulate the abundance and activity of HIF-1 alpha/2 alpha. SCIENCE SIGNALING, 14(692). doi:10.1126/scisignal.abf6685
Use of ChIP-qPCR to Study the Crosstalk Between HIF and NF-kappa B Signaling in Hypoxia and Normoxia
Shakir, D., Batie, M., & Rocha, S. (2021). Use of ChIP-qPCR to Study the Crosstalk Between HIF and NF-kappa B Signaling in Hypoxia and Normoxia. NF-(KAPPA)B TRANSCRIPTION FACTORS, 2366, 255-265. doi:10.1007/978-1-0716-1669-7_15
PBRM1 Cooperates with YTHDF2 to Control HIF-1 alpha Protein Translation
Shmakova, A., Frost, M., Batie, M., Kenneth, N. S., & Rocha, S. (2021). PBRM1 Cooperates with YTHDF2 to Control HIF-1 alpha Protein Translation. CELLS, 10(6). doi:10.3390/cells10061425
Abstract IA-017: Chromatin and gene transcription in hypoxia
Batie, M., Frost, J., & Rocha, S. (2021). Abstract IA-017: Chromatin and gene transcription in hypoxia. Clinical Cancer Research, 27(8_Supplement). doi:10.1158/1557-3265.radsci21-ia-017
Roles of HIF and 2-Oxoglutarate-Dependent Dioxygenases in Controlling Gene Expression in Hypoxia
Frost, J., Frost, M., Batie, M., Jiang, H., & Rocha, S. (2021). Roles of HIF and 2-Oxoglutarate-Dependent Dioxygenases in Controlling Gene Expression in Hypoxia. CANCERS, 13(2). doi:10.3390/cancers13020350
Chromatin and gene transcription in hypoxia.
Batie, M., Frost, J., & Rocha, S. (2021). Chromatin and gene transcription in hypoxia.. In CLINICAL CANCER RESEARCH Vol. 27. Retrieved from https://www.webofscience.com/
2020
Roles Of HIF and 2-Oxoglutarate Dependent Enzymes in Controlling Gene Expression In Hypoxia
Frost, J., Frost, M., Batie, M., Jiang, H., & Rocha, S. (2020). Roles Of HIF and 2-Oxoglutarate Dependent Enzymes in Controlling Gene Expression In Hypoxia. doi:10.20944/preprints202011.0651.v1
Oxygen-sensing mechanisms in cells
Wilson, J. W., Shakir, D., Batie, M., Frost, M., & Rocha, S. (2020). Oxygen-sensing mechanisms in cells. FEBS JOURNAL, 287(18), 3888-3906. doi:10.1111/febs.15374
Gene transcription and chromatin regulation in hypoxia
Batie, M., & Rocha, S. (2020). Gene transcription and chromatin regulation in hypoxia. Biochemical Society transactions, 48(3), 1121-1128. doi:10.1042/bst20191106
HIF-1beta Positively Regulates NF-kappaB Activity via Direct Control of TRAF6
D'Ignazio, L., Shakir, D., Batie, M., Muller, H. A., & Rocha, S. (2020). HIF-1beta Positively Regulates NF-kappaB Activity via Direct Control of TRAF6. International Journal of Molecular Sciences, 21(8). doi:10.20944/preprints202003.0168.v1
HIF-1β Positively Regulates NF-κB Activity via Direct Control of TRAF6
D'Ignazio, L., Shakir, D., Batie, M., Muller, H. A., & Rocha, S. (2020). HIF-1β Positively Regulates NF-κB Activity via Direct Control of TRAF6. INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES, 21(8). doi:10.3390/ijms21083000
2019
JmjC histone demethylases act as chromatin oxygen sensors
Batie, M., & Rocha, S. (2019). JmjC histone demethylases act as chromatin oxygen sensors. Molecular and Cellular Oncology. doi:10.1080/23723556.2019.1608501
Hypoxia Induces Rapid Changes to Histone Methylation and Reprograms Chromatin
Batie, M., Frost, J., Frost, M., Wilson, J. W., Schofield, P., & Rocha, S. (2019). Hypoxia Induces Rapid Changes to Histone Methylation and Reprograms Chromatin. Science, 363(6432), 1222-1226. doi:10.1126/science.aau5870
Hypoxia induces rapid changes to histone methylation reprogramming chromatin for the cellular response: Supplementary material
Batie, M., Frost, J., Frost, M., Wilson, J., Schofield, P., & Rocha, S. (2019). Hypoxia induces rapid changes to histone methylation reprogramming chromatin for the cellular response: Supplementary material. doi:10.1101/513069
2018
TNFSF14/LIGHT, a Non-Canonical NF-κB Stimulus, Induces the HIF Pathway
D'Ignazio, L., Batie, M., & Rocha, S. (2018). TNFSF14/LIGHT, a Non-Canonical NF-κB Stimulus, Induces the HIF Pathway. CELLS, 7(8). doi:10.3390/cells7080102
TNFSF14/LIGHT, a Non-Canonical NF-kB Stimulus, Induces the HIF Pathway
D'Ignazio, L., Batie, M., & Rocha, S. (2018). TNFSF14/LIGHT, a Non-Canonical NF-kB Stimulus, Induces the HIF Pathway. doi:10.20944/preprints201807.0007.v1
SINHCAF/FAM60A and SIN3A specifically repress HIF-2α expression
Biddlestone, J., Batie, M., Bandarra, D., Munoz, I., & Rocha, S. (2018). SINHCAF/FAM60A and SIN3A specifically repress HIF-2α expression. BIOCHEMICAL JOURNAL, 475, 2073-2090. doi:10.1042/BCJ20170945
Hypoxia and Chromatin: A Focus on Transcriptional Repression Mechanisms
Batie, M., del Peso, L., & Rocha, S. (2018). Hypoxia and Chromatin: A Focus on Transcriptional Repression Mechanisms. BIOMEDICINES, 6(2). doi:10.3390/biomedicines6020047
Hypoxia and Chromatin, a Focus on Transcriptional Repression Mechanisms
Batie, M., del Peso, L., & Rocha, S. (2018). Hypoxia and Chromatin, a Focus on Transcriptional Repression Mechanisms. doi:10.20944/preprints201803.0004.v1
2017
SINHCAF/FAM60A links SIN3A function to the hypoxia response and its levels are predictive of cancer patient survival
Hypoxia and Inflammation in Cancer, Focus on HIF and NF-κB.
D'Ignazio, L., Batie, M., & Rocha, S. (2017). Hypoxia and Inflammation in Cancer, Focus on HIF and NF-κB.. Biomedicines, 5(2), E21. doi:10.3390/biomedicines5020021
Hypoxia and Inflammation in Cancer, Focus on HIF and NF-кB
D'Ignazio, L., Batie, M., & Rocha, S. (2017). Hypoxia and Inflammation in Cancer, Focus on HIF and NF-кB. doi:10.20944/preprints201703.0240.v1
KDM2 Family Members are Regulated by HIF-1 in Hypoxia
Batie, M., Druker, J., D'Ignazio, L., & Rocha, S. (2017). KDM2 Family Members are Regulated by HIF-1 in Hypoxia. CELLS, 6(1). doi:10.3390/cells6010008
2014
PITX1, a specificity determinant in the HIF-1α-mediated transcriptional response to hypoxia
Mudie, S., Bandarra, D., Batie, M., Biddlestone, J., Moniz, S., Ortmann, B., . . . Rocha, S. (2014). PITX1, a specificity determinant in the HIF-1α-mediated transcriptional response to hypoxia. CELL CYCLE, 13(24), 3878-3891. doi:10.4161/15384101.2014.972889
Chromatin and oxygen sensing in the context of JmjC histone demethylases
Shmakova, A., Batie, M., Druker, J., & Rocha, S. (2014). Chromatin and oxygen sensing in the context of JmjC histone demethylases. BIOCHEMICAL JOURNAL, 462, 385-395. doi:10.1042/BJ20140754