1
|
Gupta I, Shankrit S, Narta K, Ghazi M, Grover R, Pandey R, Kar HK, Menon SM, Gupta A, Yenamandra VK, Singh A, Mukerji M, Mukhopadhyay A, Rani R, Gokhale RS, Dash D, Natarajan VT. Whole-Exome Sequencing of Vitiligo Lesions Indicates Lower Burden of Somatic Variations: Implications in Risk for Nonmelanoma Skin Cancers. J Invest Dermatol 2022; 143:1111-1114.e8. [PMID: 36535361 DOI: 10.1016/j.jid.2022.11.018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 10/27/2022] [Accepted: 11/28/2022] [Indexed: 12/23/2022]
Affiliation(s)
- Iti Gupta
- Council for Scientific and Industrial Research (CSIR)-Institute of Genomics and Integrative Biology, New Delhi, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Shambhavi Shankrit
- Council for Scientific and Industrial Research (CSIR)-Institute of Genomics and Integrative Biology, New Delhi, India
| | - Kiran Narta
- Council for Scientific and Industrial Research (CSIR)-Institute of Genomics and Integrative Biology, New Delhi, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Madeeha Ghazi
- Council for Scientific and Industrial Research (CSIR)-Institute of Genomics and Integrative Biology, New Delhi, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Ritika Grover
- Council for Scientific and Industrial Research (CSIR)-Institute of Genomics and Integrative Biology, New Delhi, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Rajesh Pandey
- Council for Scientific and Industrial Research (CSIR)-Institute of Genomics and Integrative Biology, New Delhi, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Hemanta Kumar Kar
- Department of Dermatology, PGIMER Dr. Ram Manohar Lohia Hospital, New Delhi, India; Department of Dermatology, Kalinga Institute of Medical Sciences, Kalinga Institute of Industrial Technology, Bhubaneswar, Odisha
| | - Shruti M Menon
- Department of Dermatology, Dr. D.Y. Patil Medical College, Hospital & Research Centre, Dr. D.Y. Patil Vidyapeeth, Pune, India
| | - Aayush Gupta
- Department of Dermatology, Dr. D.Y. Patil Medical College, Hospital & Research Centre, Dr. D.Y. Patil Vidyapeeth, Pune, India
| | - Vamsi K Yenamandra
- Council for Scientific and Industrial Research (CSIR)-Institute of Genomics and Integrative Biology, New Delhi, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Archana Singh
- Council for Scientific and Industrial Research (CSIR)-Institute of Genomics and Integrative Biology, New Delhi, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Mitali Mukerji
- Department of Bioscience and Bioengineering, Indian Institute of Technology, Jodhpur, Rajasthan, India
| | - Arijit Mukhopadhyay
- Council for Scientific and Industrial Research (CSIR)-Institute of Genomics and Integrative Biology, New Delhi, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India; Translational Medicine Unit, Biomedical Research Centre, University of Salford, Manchester, United Kingdom
| | - Rajni Rani
- National Institute of Immunology, New Delhi, India
| | - Rajesh S Gokhale
- Council for Scientific and Industrial Research (CSIR)-Institute of Genomics and Integrative Biology, New Delhi, India; National Institute of Immunology, New Delhi, India
| | - Debasis Dash
- Council for Scientific and Industrial Research (CSIR)-Institute of Genomics and Integrative Biology, New Delhi, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Vivek T Natarajan
- Council for Scientific and Industrial Research (CSIR)-Institute of Genomics and Integrative Biology, New Delhi, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India.
| |
Collapse
|
2
|
Grover R, Burse SA, Shankrit S, Aggarwal A, Kirty K, Narta K, Srivastav R, Ray AK, Malik G, Vats A, Motiani RK, Thukral L, Roy SS, Bhattacharya S, Sharma R, Natarajan K, Mukerji M, Pandey R, Gokhale RS, Natarajan VT. Myg1 exonuclease couples the nuclear and mitochondrial translational programs through RNA processing. Nucleic Acids Res 2019; 47:5852-5866. [PMID: 31081026 PMCID: PMC6582341 DOI: 10.1093/nar/gkz371] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2018] [Revised: 04/12/2019] [Accepted: 04/30/2019] [Indexed: 01/25/2023] Open
Abstract
Semi-autonomous functioning of mitochondria in eukaryotic cell necessitates coordination with nucleus. Several RNA species fine-tune mitochondrial processes by synchronizing with the nuclear program, however the involved components remain enigmatic. In this study, we identify a widely conserved dually localized protein Myg1, and establish its role as a 3′-5′ RNA exonuclease. We employ mouse melanoma cells, and knockout of the Myg1 ortholog in Saccharomyces cerevisiae with complementation using human Myg1 to decipher the conserved role of Myg1 in selective RNA processing. Localization of Myg1 to nucleolus and mitochondrial matrix was studied through imaging and confirmed by sub-cellular fractionation studies. We developed Silexoseqencing, a methodology to map the RNAse trail at single-nucleotide resolution, and identified in situ cleavage by Myg1 on specific transcripts in the two organelles. In nucleolus, Myg1 processes pre-ribosomal RNA involved in ribosome assembly and alters cytoplasmic translation. In mitochondrial matrix, Myg1 processes 3′-termini of the mito-ribosomal and messenger RNAs and controls translation of mitochondrial proteins. We provide a molecular link to the possible involvement of Myg1 in chronic depigmenting disorder vitiligo. Our study identifies a key component involved in regulating spatially segregated organellar RNA processing and establishes the evolutionarily conserved ribonuclease as a coordinator of nucleo-mitochondrial crosstalk.
Collapse
Affiliation(s)
- Ritika Grover
- CSIR-Institute of Genomics and Integrative Biology, Mathura Road, New Delhi, India.,Academy of Scientific and Innovative Research, Rafi Marg, New Delhi, India
| | - Shaunak A Burse
- CSIR-Institute of Genomics and Integrative Biology, Mathura Road, New Delhi, India.,Academy of Scientific and Innovative Research, Rafi Marg, New Delhi, India
| | - Shambhavi Shankrit
- CSIR-Institute of Genomics and Integrative Biology, Mathura Road, New Delhi, India
| | - Ayush Aggarwal
- CSIR-Institute of Genomics and Integrative Biology, Mathura Road, New Delhi, India.,Academy of Scientific and Innovative Research, Rafi Marg, New Delhi, India
| | - Kritika Kirty
- School of Life Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Kiran Narta
- CSIR-Institute of Genomics and Integrative Biology, Mathura Road, New Delhi, India
| | - Rajpal Srivastav
- CSIR-Institute of Genomics and Integrative Biology, Mathura Road, New Delhi, India
| | - Ashwini Kumar Ray
- School of environmental Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Garima Malik
- CSIR-Institute of Genomics and Integrative Biology, Mathura Road, New Delhi, India
| | - Archana Vats
- CSIR-Institute of Genomics and Integrative Biology, Mathura Road, New Delhi, India
| | - Rajender K Motiani
- CSIR-Institute of Genomics and Integrative Biology, Mathura Road, New Delhi, India
| | - Lipi Thukral
- CSIR-Institute of Genomics and Integrative Biology, Mathura Road, New Delhi, India
| | - Soumya Sinha Roy
- CSIR-Institute of Genomics and Integrative Biology, Mathura Road, New Delhi, India
| | - Sudha Bhattacharya
- School of environmental Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Rakesh Sharma
- CSIR-Institute of Genomics and Integrative Biology, Mathura Road, New Delhi, India
| | | | - Mitali Mukerji
- CSIR-Institute of Genomics and Integrative Biology, Mathura Road, New Delhi, India
| | - Rajesh Pandey
- CSIR-Institute of Genomics and Integrative Biology, Mathura Road, New Delhi, India
| | - Rajesh S Gokhale
- CSIR-Institute of Genomics and Integrative Biology, Mathura Road, New Delhi, India.,National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi, India
| | - Vivek T Natarajan
- CSIR-Institute of Genomics and Integrative Biology, Mathura Road, New Delhi, India.,Academy of Scientific and Innovative Research, Rafi Marg, New Delhi, India
| |
Collapse
|
3
|
Gandy LM, Gumm J, Fertig B, Thessen A, Kennish MJ, Chavan S, Marchionni L, Xia X, Shankrit S, Fertig EJ. Synthesizer: Expediting synthesis studies from context-free data with information retrieval techniques. PLoS One 2017; 12:e0175860. [PMID: 28437440 PMCID: PMC5402950 DOI: 10.1371/journal.pone.0175860] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2016] [Accepted: 03/31/2017] [Indexed: 11/18/2022] Open
Abstract
Scientists have unprecedented access to a wide variety of high-quality datasets. These datasets, which are often independently curated, commonly use unstructured spreadsheets to store their data. Standardized annotations are essential to perform synthesis studies across investigators, but are often not used in practice. Therefore, accurately combining records in spreadsheets from differing studies requires tedious and error-prone human curation. These efforts result in a significant time and cost barrier to synthesis research. We propose an information retrieval inspired algorithm, Synthesize, that merges unstructured data automatically based on both column labels and values. Application of the Synthesize algorithm to cancer and ecological datasets had high accuracy (on the order of 85-100%). We further implement Synthesize in an open source web application, Synthesizer (https://github.com/lisagandy/synthesizer). The software accepts input as spreadsheets in comma separated value (CSV) format, visualizes the merged data, and outputs the results as a new spreadsheet. Synthesizer includes an easy to use graphical user interface, which enables the user to finish combining data and obtain perfect accuracy. Future work will allow detection of units to automatically merge continuous data and application of the algorithm to other data formats, including databases.
Collapse
Affiliation(s)
- Lisa M. Gandy
- Department of Computer Science, Central Michigan University, Mt Pleasant, MI, United States of America
- * E-mail: (LMG); (EJF)
| | - Jordan Gumm
- Department of Computer Science, Central Michigan University, Mt Pleasant, MI, United States of America
| | - Benjamin Fertig
- Ronin Institute for Independent Scholarship, Montclair, NJ, United States of America
| | - Anne Thessen
- Ronin Institute for Independent Scholarship, Montclair, NJ, United States of America
| | - Michael J. Kennish
- Department of Marine and Coastal Sciences, Rutgers University, New Brunswick, NJ, United States of America
| | - Sameer Chavan
- Colorado Center for Personalized Medicine, University of Colorado Denver, Denver, CO, United States of America
| | - Luigi Marchionni
- Department of Oncology, Johns Hopkins University, Baltimore, MD, United States of America
| | - Xiaoxin Xia
- Department of Oncology, Johns Hopkins University, Baltimore, MD, United States of America
| | - Shambhavi Shankrit
- Department of Oncology, Johns Hopkins University, Baltimore, MD, United States of America
| | - Elana J. Fertig
- Department of Oncology, Johns Hopkins University, Baltimore, MD, United States of America
- * E-mail: (LMG); (EJF)
| |
Collapse
|