Article
Multidisciplinary Sciences
Austin B. Osmanski, Nicole S. Paulat, Jenny Korstian, Jenna R. Grimshaw, Michaela Halsey, Kevin A. M. Sullivan, Diana D. Moreno-Santillan, Claudia Crookshanks, Jacquelyn Roberts, Carlos Garcia, Matthew G. Johnson, Llewellyn D. Densmore, Richard D. Stevens, Jeb Rosen, Jessica M. Storer, Robert Hubley, Arian F. A. Smit, Liliana M. Davalos, Elinor K. Karlsson, Kerstin Lindblad-Toh, David A. Ray
Summary: We analyzed TE content in 248 placental mammal genomes and found substantial differences in recent TE accumulation among mammals. Young TEs, especially long interspersed elements, drive genome size increases, while DNA transposons are associated with smaller genomes. Mammals tend to accumulate only a few types of TEs at any given time, with one dominating TE type. We also found a correlation between dietary habit and the presence of DNA transposon invasions. These annotations will be useful for future comparative TE analyses in placental mammals.
Article
Cell Biology
Rene Massimiliano Marsano, Patrizio Dimitri
Summary: Transposable elements (TEs) are abundant components of constitutive heterochromatin and their accumulation in the genome may be influenced by reduced recombination and lack of functional genes. However, recent studies suggest that constitutive heterochromatin contains active genes and the accumulation of TEs may play a role in centromere and telomere structure.
Article
Multidisciplinary Sciences
Peter Ebert, Peter A. Audano, Qihui Zhu, Bernardo Rodriguez-Martin, David Porubsky, Marc Jan Bonder, Arvis Sulovari, Jana Ebler, Weichen Zhou, Rebecca Serra Mari, Feyza Yilmaz, Xuefang Zhao, PingHsun Hsieh, Joyce Lee, Sushant Kumar, Jiadong Lin, Tobias Rausch, Yu Chen, Jingwen Ren, Martin Santamarina, Wolfram Hops, Hufsah Ashraf, Nelson T. Chuang, Xiaofei Yang, Katherine M. Munson, Alexandra P. Lewis, Susan Fairley, Luke J. Tallon, Wayne E. Clarke, Anna O. Basile, Marta Byrska-Bishop, Andre Corvelo, Uday S. Evani, Tsung-Yu Lu, Mark J. P. Chaisson, Junjie Chen, Chong Li, Harrison Brand, Aaron M. Wenger, Maryam Ghareghani, William T. Harvey, Benjamin Raeder, Patrick Hasenfeld, Allison A. Regier, Haley J. Abel, Ira M. Hall, Paul Flicek, Oliver Stegle, Mark B. Gerstein, Jose M. C. Tubio, Zepeng Mu, Yang Li, Xinghua Shi, Alex R. Hastie, Kai Ye, Zechen Chong, Ashley D. Sanders, Michael C. Zody, Michael E. Talkowski, Ryan E. Mills, Scott E. Devine, Charles Lee, Jan O. Korbel, Tobias Marschall, Evan E. Eichler
Summary: Through the use of long-read and strand-specific sequencing technologies, this study has achieved the de novo assembly of high-quality haplotype-resolved human genomes without the need for parent-child trio data. The research identified various forms of genetic variation, including structural variants and SV hotspots, and revealed the mechanisms of SV formation while providing SV candidates for adaptive selection within the human population.
Review
Biology
Haeun Lee, Jun Won Min, Seyoung Mun, Kyudong Han
Summary: This review discusses the recently studied and utilized NGS technologies and effective computational approaches for discovering retrotransposons. NGS has provided new perspectives for detecting retrotransposon-mediated SVs and various computational methods have been developed for accurately detecting insertions and deletions in the human genome.
Article
Biology
Kei Fukuda, Chikako Shimura, Hisashi Miura, Akie Tanigawa, Takehiro Suzuki, Naoshi Dohmae, Ichiro Hiratani, Yoichi Shinkai
Summary: The study reveals that H3K9me2 in mouse embryonic stem cells is regulated by multiple MTases, with different MTases controlling H3K9me2 and transcription in the A and B compartments. Additionally, decreased H3K9me2 is associated with a more active compartmental state and transcriptional activation, contributing to the setting of inactive compartments. This suggests that H3K9 methyltransferases play a crucial role in maintaining genome organization in transcriptionally inactive compartments.
COMMUNICATIONS BIOLOGY
(2021)
Article
Multidisciplinary Sciences
Maria Isabel Navarro-Mendoza, Carlos Perez-Arques, Joseph Heitman
Summary: Chromatin modifications, specifically H3K9 methylation, play a crucial role in repressing transcription in early-diverging fungi. RNA interference (RNAi) and heterochromatin formation are independent regulatory mechanisms in Mucor, contributing to genome stability and defense.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
Article
Biotechnology & Applied Microbiology
Isaac Adeyemi Babarinde, Andrew Paul Hutchins
Summary: This study systematically investigated the impact of sequencing depth on the accuracy of assembled transcripts. The results show that the effect of sequencing depth varies based on cell or tissue type, read type, and the nature and expression levels of the transcripts. Increasing long-read sequencing depth specifically benefits transcripts containing transposable elements. Additionally, the study demonstrates how transcripts assembled from bulk long-read samples can guide single-cell RNA-seq and reveals that noncoding transcripts are expressed at similar levels to coding transcripts but in fewer cells.
Article
Plant Sciences
Carlos de Tomas, Amelie Bardil, Raul Castanera, Josep M. Casacuberta, Carlos M. Vicient
Summary: The fusion of two parental genomes in the peach x almond hybrid did not result in significant changes in DNA methylation or transcription, challenging the expectation of genomic shock. This finding suggests the possibility of using interspecific peach x almond crosses for peach improvement.
HORTICULTURE RESEARCH
(2022)
Review
Plant Sciences
Alexander V. Vershinin, Evgeny A. Elisafenko, Elena V. Evtushenko
Summary: Fifty years ago, Susumu Ohno proposed the C-value paradox, which states that there is no correlation between genome size and organism complexity, and emphasized on genome redundancy. The concept of junk DNA, referring to DNA that does not have a positive effect on organism fitness, remains controversial. Rye is used as a subject to test the validity and scientific significance of this concept. The review analyzes the structural organization of rye chromosomes and discusses the molecular mechanisms and DNA sequences involved in genome size increase during evolution.
Review
Biology
Xingyu Liao, Wufei Zhu, Juexiao Zhou, Haoyang Li, Xiaopeng Xu, Bin Zhang, Xin Gao
Summary: This review explores the characteristics of DNA repeats, their functional impacts, and available tools for their analysis.
COMMUNICATIONS BIOLOGY
(2023)
Article
Genetics & Heredity
Isa Schon, Fernando Rodriguez, Matthew Dunn, Koen Martens, Michael Shribak, Irina R. Arkhipova
Summary: The study investigated the TE load and diversity in the ancient asexual ostracod Darwinula stevensoni, finding higher TE content and diversity compared to other putatively ancient asexual species. There was a high prevalence of diverse transposon families, predominantly DNA transposons, indicating recent activity, and TEs were mainly located outside of introns with very few found in exons. The study provides valuable insights into TE dynamics in ancient asexual ostracods, although further verification with high quality draft genomes is necessary.
Article
Multidisciplinary Sciences
Li He, Huan Huang, Mariem Bradai, Cheng Zhao, Yin You, Jun Ma, Lun Zhao, Rosa Lozano-Duran, Jian-Kang Zhu
Summary: DNA methylation plays a crucial role in plant development and gene regulation, and is essential for multiple biological processes.
NATURE COMMUNICATIONS
(2022)
Review
Genetics & Heredity
Eva Satovic-Vuksic, Miroslav Plohl
Summary: According to the classical view, satellite DNAs are abundant non-coding DNA sequences repeated in tandem located in heterochromatin. Recent studies have shown that satellite DNAs and their organizational forms exhibit more diversity and complexity than previously thought in different animal and plant species. Differences are observed in their distribution, length, interspersion patterns, association with transposable elements, and localization in heterochromatin and/or euchromatin. This review compares the organizational features of satellite DNAs and satellitomes across species to summarize the evolutionary processes leading to the diversity of satellitomes and reevaluate the basic notions of repetitive DNA landscapes in genomes.
Article
Biology
Job van Riet, Chinmoy Saha, Nikolaos Strepis, Rutger W. W. Brouwer, Elena S. Martens-Uzunova, Wesley S. van de Geer, Sigrid M. A. Swagemakers, Andrew Stubbs, Yassir Halimi, Sanne Voogd, Arif Mohammad Tanmoy, Malgorzata A. Komor, Youri Hoogstrate, Bart Janssen, Remond J. A. Fijneman, Yashar S. Niknafs, Arul M. Chinnaiyan, Wilfred F. J. van IJcken, Peter J. van der Spek, Guido Jenster, Rogier Louwen
Summary: Clustered Regularly Interspaced Short Palindromic Repeats (CRISPRs) have been discovered in the human genome, termed hCRISPRs, which are expressed as small non-coding RNAs (sncRNAs) and can distinguish normal from malignant tissues. These findings suggest the potential use of hCRISPRs as diagnostic biomarkers for cancer and the development of point-of-care tests based on their differential expression.
COMMUNICATIONS BIOLOGY
(2022)
Review
Plant Sciences
Muthusamy Ramakrishnan, Pradeep K. Papolu, Sileesh Mullasseri, Mingbing Zhou, Anket Sharma, Zishan Ahmad, Viswanathan Satheesh, Ruslan Kalendar, Qiang Wei
Summary: This article briefly discusses the potential and challenges of using LTR retrotransposons as a tool for plant genetic engineering, and the opportunity provided by their similarity to retroviruses. While recent research has advanced our understanding of LTR retrotransposons, controlling and directing their integration into the genome remains unclear. Utilizing existing intragenic elements for desired genome composition is a better approach than artificial constructs, but how to precisely control the process is yet to be resolved. However, if the activity of LTR retrotransposons can be controlled through specific epigenetic mechanisms, they could be a powerful tool for plant genetic engineering.
PLANT CELL REPORTS
(2023)
Article
Food Science & Technology
Igor Rzhepakovsky, Shahida Anusha Siddiqui, Svetlana Avanesyan, Mehmet Benlidayi, Kunaal Dhingra, Alexander Dolgalev, Natella Enukashvily, Tilman Fritsch, Volker Heinz, Stanislav Kochergin, Andrey Nagdalian, Marina Sizonenko, Lyudmila Timchenko, Marko Vukovic, Sergey Piskov, Wolf-Dieter Grimm
Summary: The study shows that the chicken embryo tissue hydrolyzate has therapeutic effects on chronic arthritis and may serve as a potential nutraceutical agent for treating rheumatoid arthritis.
FOOD SCIENCE & NUTRITION
(2021)
Article
Biochemistry & Molecular Biology
Anastasia Kotova, Arseniy A. Lobov, Julia A. Dombrovskaya, Valentina Y. Sannikova, Nadezhda A. Ryumina, Polina Klausen, Alexey L. Shavarda, Anna B. Malashicheva, Natella Enukashvily
Summary: Dental stem cells, derived from neural crest stem cells, exhibit differences in functional and biological properties, including neural markers, cell morphology, proliferation rate, and osteogenic differentiation capabilities. Dental pulp stem cells and periodontal ligament stem cells show distinctions in neural markers, nuclear protein expression, proliferation rate, etc.
Article
Biochemistry & Molecular Biology
Natella Enukashvily, Natalia Semenova, Anna Chubar, Dmitry Ostromyshenskii, Ekaterina A. Gushcha, Sergei Gritsaev, Stanislav S. Bessmeltsev, Viktor Rugal, Egor M. Prikhodko, Ivan Kostroma, Anastasia Zherniakova, Anastasia Kotova, Liubov A. Belik, Alexander Shumeev, Irina I. Maslennikova, Dmitry I. Ivolgin
Summary: This study aimed to investigate the functional properties, including transcription profile of non-coding DNA, of mesenchymal stromal cells (MSC) from the hematopoietic niche of treated multiple myeloma (MM) patients. The results demonstrated that the cancer-associated phenotype of the hematopoietic niche is retained after treatment. Transcription of pericentromeric non-coding DNA is associated with the cancer-associated phenotype in patients with ineffective or partially effective MM treatment.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Developmental Biology
M. A. Dobrynin, N. M. Korchagina, N. V. Ponomartsev, O. I. Podgornaya, N. I. Enukashvily
Summary: Tandemly repeated pericentromeric noncoding DNA (TR DNA) makes up approximately 10% of the human genome. In this study, the researchers aimed to develop a method for inactivating HS2/HS3 transcripts and assess its effect on DDX4-containing RNPs. The results showed a significant decrease in the total HS2/HS3 RNA signal and an increase in the number of DDX4-positive inclusions upon inactivation of HS2/HS3 transcription.
RUSSIAN JOURNAL OF DEVELOPMENTAL BIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Ilya Borisenko, Maria Daugavet, Alexander Ereskovsky, Andrey Lavrov, Olga Podgornaya
Summary: Sponges are early-branching animals with a simple body plan but a complex genetic repertoire. The continuity between larval cells and adult tissues is still not well understood. This study identified a novel protein, ilborin, which is present in multiple species and may be involved in calcium-mediated regulation of energy metabolism.
Article
Biochemistry & Molecular Biology
Nadezhda G. Ivanova, Irina Kartavtseva, Vera N. Stefanova, Dmitrii Ostromyshenskii, Olga Podgornaya
Summary: The aim of this study was to investigate the distribution of tandem repeat sequences (TR) on the chromosomes of the Chinese hamster and striped hamster. The results showed that the Chinese and striped hamsters are separate species due to the differences in TR distribution between them. The observed variation in TR within the striped hamster chromosomes is attributed to the lack of inbreeding in natural populations.
Article
Cell Biology
Daria Kostina, Arseniy Lobov, Polina Klausen, Vitaly Karelkin, Rashid Tikhilov, Svetlana Bozhkova, Andrey Sereda, Nadezhda Ryumina, Natella Enukashvily, Anna Malashicheva
Summary: The present study shares a workflow for efficiently isolating and culturing osteoblasts from human bones, and provides characteristics and phenotype detection methods of these cells. This is of great importance for bone biology and related research fields.
Article
Cell Biology
Natella I. I. Enukashvily, Nikita V. V. Ponomartsev, Avanee Ketkar, Roman Suezov, Anna V. V. Chubar, Andrey D. D. Prjibelski, Daria D. D. Shafranskaya, Sabrina Elmshaeuser, Corinna U. U. Keber, Vera N. N. Stefanova, Andrey L. L. Akopov, Ursula Klingmueller, Petra I. I. Pfefferle, Thorsten Stiewe, Matthias Lauth, Anna I. I. Brichkina
Summary: The abnormal tumor microenvironment significantly influences the response of cancer to chemo- and immuno-therapy. This study demonstrates the induction of pericentromeric satellite DNA (satDNA) transcription in cancer-associated fibroblasts (CAFs) of lung adenocarcinoma. The findings suggest that satellite long non-coding (lnc) RNAs in CAFs regulate inflammatory gene expression and can be secreted, potentially playing a role in cell-cell communication in the tumor microenvironment.
CELL DEATH & DISEASE
(2023)
Article
Genetics & Heredity
Natella I. I. Enukashvily, Liubov. A. Belik, Natalia Yu. Semenova, Ivan I. I. Kostroma, Ekaterina V. V. Motyko, Sergey V. V. Gritsaev, Stanislav S. S. Bessmeltsev, Sergey V. V. Sidorkevich, Irina S. S. Martynkevich
Summary: Mesenchymal stromal cells (MSCs) are important for bone tissue remodeling, but they lose their osteogenic potential in multiple myeloma (MM) patients. The WNT pathway, which maintains the balance of osteoblasts and osteoclasts, functions abnormally in MM. This study compared the transcription levels of WNT genes in bone marrow MSCs of healthy donors and MM patients before and after therapy.
Article
Cell & Tissue Engineering
Arseniy Lobov, Polina Kuchur, Aigul Khizhina, Anastasia Kotova, Andrei Ivashkin, Daria Kostina, Polina Klausen, Evgeniia Khokhlova, Egor Repkin, Kseniia Postnikova, Daria Perepletchikova, Evgeny Denisov, Tatiana Gerashchenko, Rashid Tikhilov, Svetlana Bozhkova, Andrey Sereda, Vitaliy Karelkin, Natella Enukashvily, Anna Malashicheva
Summary: In this study, we conducted a comparative analysis of mesenchymal cell primary cultures from various sources and found differences in their ability to undergo osteogenic differentiation and produce extracellular matrix. Based on the analysis of secretome, proteome, and transcriptome, we classified them into dental stem cells, mesenchymal stem cells, and fetal stem cells. Although they have differences, mesenchymal cells from all sources secreted core bone extracellular matrix-associated proteins. These findings shed light on the distinctive characteristics of mesenchymal stem cells and provide insights into their potential applications in regenerative medicine and the inherent diversity of mesenchymal cells in vivo.
Meeting Abstract
Oncology
Anna N. Kirienko, Ekaterina V. Motyko, Daria V. Kustova, Elizaveta V. Efremova, Elena V. Morozova, Dzhariyat I. Shikhbabaeva, Olga Yu Vinogradova, Natalya Yu Semenova, Natella I. Enukashvily, Vasilii A. Shuvaev, Sergey V. Voloshin, Sergey V. Sidorkevich, Irina S. Martynkevich
CLINICAL LYMPHOMA MYELOMA & LEUKEMIA
(2022)
Meeting Abstract
Oncology
Daria Kustova, Ekaterina Motyko, Anna Kirienko, Marina Bakay, Elizaveta Efremova, Natalya Semenova, Natella Enukashvily, Sergei Voloshin, Vasily Shuvaev, Sergei Sidorkevich, Irina Martynkevich
CLINICAL LYMPHOMA MYELOMA & LEUKEMIA
(2022)
Review
Developmental Biology
Mikhail A. A. Dobrynin, Ekaterina O. O. Bashendjieva, Natella I. I. Enukashvily
Summary: Biocondensates play crucial roles in eukaryotic cells, including determining cell fate in germ cells and regulating protein activity through transposon inactivation in other animals.
JOURNAL OF DEVELOPMENTAL BIOLOGY
(2022)
Article
Biotechnology & Applied Microbiology
Natella I. Enukashvily, Julia A. Dombrovskaya, Anastasia V. Kotova, Natalia Semenova, Irina Karabak, Roman E. Banashkov, Dmitry Baram, Tatiana Paderina, Stanislav S. Bilyk, Wolf-Dieter Grimm, Anton N. Kovalenko, Dmitry Ivolgin, Egor M. Prikhodko, Alexey V. Silin
Summary: This study aimed to develop a technology for creating cell-seeded fibrin gel implants matching the size and shape of bone defects. Through experiments with fibrin gel implants, it was found that cell-seeded gel implants can promote bone tissue repair and remodeling process, with better results than cell-free implants.
BIOENGINEERING-BASEL
(2021)
Meeting Abstract
Cell & Tissue Engineering
L. Belik, E. Prikhodko, A. Chubar, N. Semenova, S. Bessmeltsev, S. Gritsaev, I. Kostroma, A. Zhernyakova, A. Kotova, I. I. Maslennikova, D. Ivolgin, N. Enukashvily