Article
Multidisciplinary Sciences
Nikolay Postika, Paul Schedl, Pavel Georgiev, Olga Kyrchanova
Summary: The autonomy of segment-specific regulatory domains in the Bithorax complex is conferred by boundary elements and associated Polycomb response elements (PREs). The role of HS1 and HS2 in boundary function suggests that the boundary function of Fab-6 HS1 must be bolstered by a second element that has PRE activity.
SCIENTIFIC REPORTS
(2021)
Article
Genetics & Heredity
Miki Fujioka, Anastasiya Nezdyur, James B. Jaynes
Summary: Chromatin insulators are regulatory DNA elements that separate genes along chromosomes into functional units. Deleting an insulator can lead to the activation of a flanking promoter and transcriptional read-through, causing repression of the target gene. This study highlights the importance of transcriptional read-through in understanding the effects of insulators on gene expression.
Article
Multidisciplinary Sciences
Osama Brosh, Daniel K. Fabian, Rodrigo Cogni, Ignacio Tolosana, Jonathan P. Day, Francesca Olivieri, Manon Merckx, Nazli Akilli, Piotr Szkuta, Francis M. Jiggins
Summary: Researchers have identified a polymorphic transposable element insertion in fruit flies that greatly reduces viral titers and allows the flies to escape the harmful effects of infection. The insertion occurs in the protein-coding sequence of the gene Veneno and creates a gene encoding a novel resistance factor.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Genetics & Heredity
Shreekant Verma, Rashmi U. Pathak, Rakesh K. Mishra
Summary: The study revealed the regulatory mechanisms maintaining the unique expression pattern of the eyeless gene in Drosophila, involving boundary elements ME and EB, as well as a newly identified element ey-PRE. These findings suggest a general regulatory mechanism for the maintenance of genes in functionally independent chromatin domains.
G3-GENES GENOMES GENETICS
(2021)
Article
Genetics & Heredity
Shreekant Verma, Rashmi U. Pathak, Rakesh K. Mishra
Summary: The study reveals distinct spatial and temporal expression patterns of the eyeless gene in Drosophila compared to its flanking genes, maintained through boundary elements ME and EB. The functional autonomy and insulation of the ey locus from neighboring regions is suggested. Additionally, a new Polycomb Response Element, ey-PRE, is identified to help maintain the expression state of the ey gene during early development.
G3-GENES GENOMES GENETICS
(2021)
Article
Genetics & Heredity
Marat Sabirov, Olga Kyrchanova, Galina V. Pokholkova, Artem Bonchuk, Natalia Klimenko, Elena Belova, Igor F. Zhimulev, Oksana Maksimenko, Pavel Georgiev
Summary: Our results demonstrate the critical role of the CP190 protein in insulation and suggest that regulatory elements are composed of combinations of binding sites that interact with multiple architectural proteins. Unexpectedly, we found that CP190 remained associated with most genome regions bound by the mutant Pita protein, indicating that other architectural proteins were still recruiting CP190 to these regions.
EPIGENETICS & CHROMATIN
(2021)
Article
Thermodynamics
Theodore V. Gortsas, Stephanos V. Tsinopoulos
Summary: This paper presents a numerical method, called Local Domain Boundary Element Method (LD-BEM), for solving the convection-diffusion-reaction (CDR) equation. The method divides the domain of interest into small subdomains and considers the integral representation of the solution separately for each subdomain. By eliminating the fluxes at the subdomain interfaces, the proposed LD-BEM leads to sparse linear system coefficient matrices and reduced degrees of freedom.
INTERNATIONAL JOURNAL OF HEAT AND MASS TRANSFER
(2022)
Article
Biology
Marissa M. Gaskill, Tyler J. Gibson, Elizabeth D. Larson, Melissa M. Harrison
Summary: In Drosophila, besides Zelda, another pioneer factor GAF plays a crucial role in development during the maternal-to-zygotic transition. By activating widespread zygotic transcription and remodeling the chromatin accessibility landscape, GAF and Zelda together drive the development through this critical period.
Article
Biochemistry & Molecular Biology
Gabriel N. Aughey, Elhana Forsberg, Krista Grimes, Shen Zhang, Tony D. Southall
Summary: During neuronal development, chromatin states change extensively to regulate gene expression. The molecular factors involved in repressing non-neuronal genes in differentiated neurons are not well understood. The Mi2/NuRD complex is a multiprotein complex that can remodel nucleosomes and remove acetyl groups from histones. In this study, we found that Mi-2 activity is essential for preventing the abnormal expression of germline genes in neurons, and components of NuRD, including Mi-2, regulate neural gene expression for proper development of the larval nervous system. We also observed that Mi-2 binding in the genome is dynamic during neuronal maturation, and its repression of ectopic gene expression is limited to the early stages of neuronal development, suggesting its role in establishing stable neuronal transcriptomes.
Article
Cell Biology
Elizabeth A. Brija, Zhuo Guan, Suresh K. Jetti, Troy Littleton
Summary: This study demonstrates that RNA editing of the C-terminus of Cpx modifies its control ability for SNARE-mediated fusion and alters presynaptic output. The RNA editing of Cpx in single neurons is random and can fine tune neurotransmitter release by altering subcellular localization and clamping properties of the protein.
Article
Multidisciplinary Sciences
Naihua N. Gong, Leela Chakravarti Dilley, Charlette E. Williams, Emilia H. Moscato, Milan Szuperak, Qin Wang, Matthew Jensen, Santhosh Girirajan, Tiong Yang Tan, Matthew A. Deardorff, Dong Li, Yuanquan Song, Matthew S. Kayser
Summary: The chromatin remodeler ISWI is essential for adult fly sleep and its loss leads to disrupted circadian rhythms, memory, and social behavior. Expressing human ISWI homologs in flies can rescue adult phenotypes to different extents, highlighting the importance of chromatin remodeling machinery for sleep circuit formation in neurodevelopmental disorders.
Article
Multidisciplinary Sciences
Qiu Sun, Alan Perez-Rathke, Daniel M. Czajkowsky, Zhifeng Shao, Jie Liang
Summary: This study presents a computational method for reconstructing a large 3D-ensemble of single-cell chromatin conformations from population Hi-C data, applied to study embryogenesis in Drosophila. The modeling of chromatin conformations quantifies chromatin heterogeneity and reveals significant changes during embryogenesis. The findings highlight the importance of high-resolution 3D-ensembles of single-cell chromatin conformations for interpreting population Hi-C data and understanding genome organization.
NATURE COMMUNICATIONS
(2021)
Article
Biochemical Research Methods
Ankush Sharma, Akshay Akshay, Marie Rogne, Ragnhild Eskeland
Summary: The developed ShinyArchR.UiO application facilitates better understanding of gene regulatory mechanisms and sharing of massive chromatin accessibility data, improving data accessibility. Additionally, it also streamlines collaborative efforts among researchers.
Article
Multidisciplinary Sciences
Harmony R. Salzler, Vasudha Vandadi, Benjamin D. McMichael, John C. Brown, Sally A. Boerma, Mary P. Leatham-Jensen, Kirsten M. Adams, Michael P. Meers, Jeremy M. Simon, Robert J. Duronio, Daniel J. McKay, A. Gregory Matera
Summary: Polycomb complexes regulate cell type-specific gene expression programs through heritable silencing. H3K27me3 is essential for this process, while disruption of H3K36 interferes with H3K27me3. Mutants of Drosophila replication-dependent or replication-independent histone H3 genes maintain Polycomb silencing and reach later stages of development, but combined mutants display widespread Hox gene misexpression and fail to develop past the first larval stage. Chromatin profiling revealed that the H3.2K36R mutation disrupts H3K27me3 levels broadly, while H3.3K36R animals are mostly unaffected. Analysis of H3.3 distributions showed the enrichment of H3.3 at presumptive Polycomb response elements located outside of silenced domains.
Article
Multidisciplinary Sciences
Claudia Isabelle Keller Valsecchi, M. Felicia Basilicata, Plamen Georgiev, Aline Gaub, Janine Seyfferth, Tanvi Kulkarni, Amol Panhale, Giuseppe Semplicio, Vinitha Manjunath, Herbert Holz, Pouria Dasmeh, Asifa Akhtar
Summary: This study reveals that dosage compensation of the X chromosome in Drosophila involves nucleation by MSL2 and the non-coding RNA roX, with the crucial interactions between the C-terminal domain of MSL2 and roX playing a key role in this process. Additionally, the condensing nature of the roX-MSL2(CTD) complex is identified as the primary determinant for the specific compartmentalization of the X chromosome in Drosophila.
Article
Andrology
Shilpa Bisht, Sofia Banu, Surabhi Srivastava, Rashmi U. Pathak, Rajeev Kumar, Rima Dada, Rakesh K. Mishra
Article
Biology
Arumugam Srinivasan, Rakesh K. Mishra
JOURNAL OF BIOSCIENCES
(2020)
Article
Biology
Avinash Srivastava, Rakesh K. Mishra
JOURNAL OF BIOSCIENCES
(2020)
Article
Genetics & Heredity
Shagufta Khan, Divya Tej Sowpati, Arumugam Srinivasan, Mamilla Soujanya, Rakesh K. Mishra
G3-GENES GENOMES GENETICS
(2020)
Article
Substance Abuse
Sofia Banu, Surabhi Srivastava, Arif Mohammed, Gopal Kushawah, Divya Tej Sowpati, Rakesh K. Mishra
Summary: Alcohol exposure can lead to systemic disorders by causing transcriptional changes in zebrafish. This study found that the brain transcriptome in zebrafish recovers better than the liver after chronic alcohol exposure. Genes can be categorized into those that recover their pre-alcohol expression profile and those that retain altered expression after withdrawal from alcohol. Gender-specific responses to alcohol exposure show that male zebrafish have a higher percentage of perturbed genes, while female fish recover better upon withdrawal.
Article
Biochemical Research Methods
Rahul Sureka, Rakesh Mishra
Summary: By studying the developing embryos of Drosophila melanogaster and Danio rerio, 362 core NuMat proteins conserved between the two organisms were identified. Comparisons with publicly available Mus musculus NuMat dataset and Homo sapiens cellular localization dataset revealed 252 core homologous NuMat proteins, with 86 protein groups originating from preexisting proteins in prokaryotes. Thirty-six were conserved across all eukaryotic supergroups, 14 evolved before the last eukaryotic common ancestor, and these 50 proteins out of the 252 core conserved NuMat proteins have been conserved across all eukaryotes for over 1.5 billion years, indicating their crucial role in nuclear function.
JOURNAL OF PROTEOME RESEARCH
(2021)
Review
Biology
Surabhi Srivastava, Sofia Banu, Priya Singh, Divya Tej Sowpati, Rakesh K. Mishra
Summary: COVID-19 emerged as a global pandemic since late 2019, affecting countries including India. Mutations in the viral genome during host transmission have implications for disease surveillance and management, vaccine development, and reinfections. Therefore, continued sequencing-based surveillance is crucial in India for tracking and understanding the evolution of the virus.
JOURNAL OF BIOSCIENCES
(2021)
Review
Cell Biology
Rashmi Upadhyay Pathak, Mamilla Soujanya, Rakesh Kumar Mishra
Summary: The metazoan nucleus is a highly structured organelle that can undergo abnormalities in morphology and architecture in aged cells. Computational image analysis of nuclear features offers a promising tool to evaluate physiological age of a cell and can be used to examine progression of age-related diseases and therapies.
AGEING RESEARCH REVIEWS
(2021)
Article
Biotechnology & Applied Microbiology
Harishankar Kopperi, Athmakuri Tharak, Manupati Hemalatha, Uday Kiran, C. G. Gokulan, Rakesh K. Mishra, S. Venkata Mohan
Summary: Since the outbreak of COVID-19, wastewater-based epidemiology (WBE) studies have gained increasing interest as a surveillance system for early warning signals and effective disease management strategies. This study establishes a structured protocol for conducting WBE studies, revealing the dynamic spread of viral RNA in different time points and sampling methods, providing important insights for monitoring the spread of the pandemic.
ENVIRONMENTAL TECHNOLOGY & INNOVATION
(2021)
Article
Biology
C. G. Gokulan, Uday Kiran, Santosh Kumar Kuncha, Rakesh K. Mishra
Summary: This study demonstrates the temporal stability and performance of dry swab viral detection method under two different temperatures, showing that the method is as efficient as VTM-RNA-based method within 48 hours with better sensitivity. The results suggest that dry swab samples are stable at room temperature for 24 hours and detection of SARS-CoV-2 RNA by RT-PCR is comparable to VTM-RNA. This extraction-free, direct RT-PCR method holds significant potential in current life-threatening circumstances caused by SARS-CoV-2.
JOURNAL OF BIOSCIENCES
(2021)
Article
Infectious Diseases
Vinithra Iyer, Sheetal Tushir, Shreekant Verma, Sudeshna Majumdar, Srimonta Gayen, Rakesh Mishra, Utpal Tatu
Summary: The study reveals the split nature of the Hsp90 gene in G. lamblia, with two ORFs separated on chromosome 5 and connected through a unique trans-splicing reaction. The presence of canonical nucleotide elements in independent pre-mRNAs suggests the involvement of spliceosomes in trans-splicing of Hsp90. Research also shows that an RNA helicase interacts with HspN pre-mRNA, and the trans-spliced genes of Giardia are spatially close in the nucleus.
PLOS NEGLECTED TROPICAL DISEASES
(2021)
Article
Environmental Sciences
Athmakuri Tharak, Harishankar Kopperi, Manupati Hemalatha, Uday Kiran, Gokulan C. G., Shivranjani Moharir, Rakesh K. K. Mishra, S. Venkata Mohan
Summary: Wastewater-based epidemiology is an emerging approach to study the infection dynamics of SARS-CoV-2 at a community level. Periodic sewage surveillance can predict early surges of the pandemic, understand infection dynamics, and facilitate proper healthcare management.
INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH
(2022)
Article
Cell Biology
Rashmi U. Pathak, Rahul Sureka, Ashish Bihani, Parul Varma, Rakesh K. Mishra
Summary: This study provides a new method for preparing nuclear matrix in intact Drosophila melanogaster embryos and dissecting its components of nuclear architecture. The protocol does not require nucleus isolation, therefore maintaining the three-dimensional environment of an intact embryo, which is more biologically relevant. The protocol has been extended to larval tissues with little modification, making it possible to carry out studies in parallel to genetic experiments.
Article
Biochemical Research Methods
Rashmi U. Pathak, Ashish Bihani, Rahul Sureka, Rakesh K. Mishra
Summary: This article presents a method to isolate and visualize the nuclear matrix (NuMat) and its applications. By removing chromatin, the underlying nuclear architectural components can be revealed. This protocol combines the power of Drosophila genetics with cell biological observation of the nuclear architecture.