1
|
Benedetti R, Bajardi F, Capozziello S, Carafa V, Conte M, Del Sorbo MR, Nebbioso A, Singh M, Stunnenberg HG, Valadan M, Altucci L, Altucci C. Different Approaches to Unveil Biomolecule Configurations and Their Mutual Interactions. ANAL LETT 2021. [DOI: 10.1080/00032719.2020.1716241] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Affiliation(s)
- R. Benedetti
- Dipartimento di Biochimica, Biofisica e Patologia Generale, Università degli Studi della Campania “L. Vanvitelli”, Napoli, Italy
| | - F. Bajardi
- Dipartimento di Fisica “Ettore Pancini”, Università degli Studi di Napoli “Federico II”, Napoli, Italy
- Istituto Nazionale di Fisica Nucleare (INFN), Sez. di Napoli, Napoli, Italy
| | - S. Capozziello
- Dipartimento di Fisica “Ettore Pancini”, Università degli Studi di Napoli “Federico II”, Napoli, Italy
- Istituto Nazionale di Fisica Nucleare (INFN), Sez. di Napoli, Napoli, Italy
- Gran Sasso Science Institute, L’Aquila, Italy
| | - V. Carafa
- Dipartimento di Biochimica, Biofisica e Patologia Generale, Università degli Studi della Campania “L. Vanvitelli”, Napoli, Italy
| | - M. Conte
- Dipartimento di Biochimica, Biofisica e Patologia Generale, Università degli Studi della Campania “L. Vanvitelli”, Napoli, Italy
| | - M. R. Del Sorbo
- Istituto Statale d’Istruzione Superiore “Leonardo da Vinci”, Poggiomarino, NA, Italy
| | - A. Nebbioso
- Dipartimento di Biochimica, Biofisica e Patologia Generale, Università degli Studi della Campania “L. Vanvitelli”, Napoli, Italy
| | - M. Singh
- Dipartimento di Fisica “Ettore Pancini”, Università degli Studi di Napoli “Federico II”, Napoli, Italy
| | - H. G. Stunnenberg
- Department of Molecular Biology, NCMLS, Radboud University, Nijmegen, the Netherlands
| | - M. Valadan
- Dipartimento di Fisica “Ettore Pancini”, Università degli Studi di Napoli “Federico II”, Napoli, Italy
- Istituto Nazionale di Fisica Nucleare (INFN), Sez. di Napoli, Napoli, Italy
| | - L. Altucci
- Dipartimento di Biochimica, Biofisica e Patologia Generale, Università degli Studi della Campania “L. Vanvitelli”, Napoli, Italy
| | - C. Altucci
- Dipartimento di Fisica “Ettore Pancini”, Università degli Studi di Napoli “Federico II”, Napoli, Italy
- Istituto Nazionale di Fisica Nucleare (INFN), Sez. di Napoli, Napoli, Italy
| |
Collapse
|
2
|
Time-resolved analysis of DNA-protein interactions in living cells by UV laser pulses. Sci Rep 2017; 7:11725. [PMID: 28916762 PMCID: PMC5601431 DOI: 10.1038/s41598-017-12010-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2017] [Accepted: 08/30/2017] [Indexed: 11/08/2022] Open
Abstract
Interactions between DNA and proteins are mainly studied through chemical procedures involving bi-functional reagents, mostly formaldehyde. Chromatin immunoprecipitation is used to identify the binding between transcription factors (TFs) and chromatin, and to evaluate the occurrence and impact of histone/DNA modifications. The current bottleneck in probing DNA-protein interactions using these approaches is caused by the fact that chemical crosslinkers do not discriminate direct and indirect bindings or short-lived chromatin occupancy. Here, we describe a novel application of UV laser-induced (L-) crosslinking and demonstrate that a combination of chemical and L-crosslinking is able to distinguish between direct and indirect DNA-protein interactions in a small number of living cells. The spatial and temporal dynamics of TF bindings to chromatin and their role in gene expression regulation may thus be assessed. The combination of chemical and L-crosslinking offers an exciting and unprecedented tool for biomedical applications.
Collapse
|
3
|
Kaspi A, Ziemann M, Keating ST, Khurana I, Connor T, Spolding B, Cooper A, Lazarus R, Walder K, Zimmet P, El-Osta A. Non-referenced genome assembly from epigenomic short-read data. Epigenetics 2015; 9:1329-38. [PMID: 25437048 DOI: 10.4161/15592294.2014.969610] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Current computational methods used to analyze changes in DNA methylation and chromatin modification rely on sequenced genomes. Here we describe a pipeline for the detection of these changes from short-read sequence data that does not require a reference genome. Open source software packages were used for sequence assembly, alignment, and measurement of differential enrichment. The method was evaluated by comparing results with reference-based results showing a strong correlation between chromatin modification and gene expression. We then used our de novo sequence assembly to build the DNA methylation profile for the non-referenced Psammomys obesus genome. The pipeline described uses open source software for fast annotation and visualization of unreferenced genomic regions from short-read data.
Collapse
Affiliation(s)
- Antony Kaspi
- a Epigenetics in Human Health and Disease Laboratory ; Baker IDI Heart and Diabetes Institute ; The Alfred Medical Research and Education Precinct ; Melbourne , Victoria , Australia
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|