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  1. The influence of prenatal alcohol exposure and maternal diet on offspring DNA methylation: a cross-species study

    This article has 15 authors:
    1. Mitchell Bestry
    2. Alexander N. Larcombe
    3. Nina Kresoje
    4. Emily K Chivers
    5. Chloe Bakker
    6. James P Fitzpatrick
    7. Elizabeth J Elliott
    8. Jeffrey M Craig
    9. Evelyne Muggli
    10. Jane Halliday
    11. Delyse Hutchinson
    12. Sam Buckberry
    13. Ryan Lister
    14. Martyn Symons
    15. David Martino
    This article has been curated by 1 group:
    • Curated by eLife

      eLife assessment

      This important study examines the effects of prenatal alcohol exposure and maternal diet on offspring DNA methylation, revealing that alcohol can alter epigenetic patterns and impact brain and organ development in the fetus, with some changes preventable by a diet rich in folate and choline. The work identifies several differentially methylated regions linked to adverse health outcomes from alcohol exposure, but the evidence is somewhat incomplete, as the paper currently lacks comprehensive methodological details and sensitivity analyses. Further analysis of the functional relevance of these DNA methylation changes, particularly addressing the current technical and statistical shortcomings, would increase the study's novelty and significance.

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    This article has 3 evaluationsAppears in 2 listsLatest version Latest activity
  2. Haplotype Function Score improves biological interpretation and cross-ancestry polygenic prediction of human complex traits

    This article has 3 authors:
    1. Weichen Song
    2. Yongyong Shi
    3. Guan Ning Lin
    This article has been curated by 1 group:
    • Curated by eLife

      eLife assessment

      This paper presents what could be a useful approach for association testing, using the output of neural networks that have been trained to predict functional changes from DNA sequences. The approach presented by the author is an interesting addition to statistical genetics. It is, however, unclear whether the method not only detects more associations but also whether the quality of these associations (i.e., the likelihood that they are causal associations) is as good or better than what one finds with conventional methods. The enrichment analyses are encouraging but without rigorous assessment of statistical power and a better understanding of the pitfalls of the method, the evidence for this being an advance that will find application in the field remains incomplete.

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    This article has 3 evaluationsAppears in 2 listsLatest version Latest activity
  3. Nucleosome conformation dictates the histone code

    This article has 16 authors:
    1. Matthew R. Marunde
    2. Harrison A. Fuchs
    3. Jonathan M. Burg
    4. Irina K. Popova
    5. Anup Vaidya
    6. Nathan W. Hall
    7. Matthew J. Meiners
    8. Rachel Watson
    9. Sarah A. Howard
    10. Katherine Novitzky
    11. Eileen McAnarney
    12. Marcus A. Cheek
    13. Zu-Wen Sun
    14. Bryan J. Venters
    15. Michael-C. Keogh
    16. Catherine A. Musselman
    This article has been curated by 1 group:
    • Curated by eLife

      eLife assessment

      The manuscript investigates how the tandem reader domains in BPTF co-recognize two types of modifications present on histone tails, H3K4me3 and H3 acetylation. The authors interpret their results in the context of the conformational restriction of histone tails due to interactions with nucleosomal DNA. The findings contribute new insights into how the nucleosomal context regulates the recognition of multiple histone modifications by tandem reader domains and should be of interest to the broader chromatin field.

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    This article has 3 evaluationsAppears in 2 listsLatest version Latest activity
  4. Yeast eIF2A has a minimal role in translation initiation and uORF-mediated translational control in vivo

    This article has 4 authors:
    1. Swati Gaikwad
    2. Fardin Ghobakhlou
    3. Hongen Zhang
    4. Alan G Hinnebusch
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    • Curated by eLife

      eLife assessment

      The authors used ribosome profiling in conjunction with standard biochemical approaches to investigate the role of eIF2A in translation initiation in yeast under optimal growth conditions or stress. The convincing data demonstrate that eIF2A does not play a substantial role in translation initiation in yeast. These important findings challenge the current view that eIF2A substitutes for eIF2 under stress and are thus anticipated to spur future investigation on the role(s) of eIF2A. Considering the broad scope of cellular functions attributed to eIF2A, this study should be of interest to a wide spectrum of biomedical researchers ranging from those studying fundamental mechanisms of translation regulation to virologists and cancer biologists.

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    This article has 4 evaluationsAppears in 2 listsLatest version Latest activity
  5. Regulation of Chromatin Architecture by Transcription Factor Binding

    This article has 4 authors:
    1. Stephanie Portillo-Ledesma
    2. Suckwoo Chung
    3. Jill Hoffman
    4. Tamar Schlick
    This article has been curated by 1 group:
    • Curated by eLife

      eLife assessment

      In this important study, chromatin is simulated as a polymer at the scale of genes and 3D organization is analyzed at nucleosome resolution. There is convincing evidence for the emergence of microdomains due to the action of transcription factors, based on the simulation incorporating well-known biophysical properties of DNA, of nucleosomes, of linker histones, and of the transcription factor pair Myc:Max, as well as the 3D organization resulting from bending and looping of DNA. The work improves our knowledge of how the joint action of transcription factors and chromatin features affects chromatin structure and accessibility, which is of interest to anyone studying gene regulation.

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    This article has 3 evaluationsAppears in 2 listsLatest version Latest activity
  6. Single cell ‘omic profiles of human aortic endothelial cells in vitro and human atherosclerotic lesions ex vivo reveals heterogeneity of endothelial subtype and response to activating perturbations

    This article has 9 authors:
    1. Maria L. Adelus
    2. Jiacheng Ding
    3. Binh T. Tran
    4. Austin C. Conklin
    5. Anna K. Golebiewski
    6. Lindsey K. Stolze
    7. Michael B. Whalen
    8. Darren A. Cusanovich
    9. Casey E. Romanoski
    This article has been curated by 1 group:
    • Curated by eLife

      eLife assessment

      This is a fundamental resource of snRNA-seq and and chromatin accessibility data from human aortic endothelial cells (ECs), treated with relevant perturbations such as IL1b, TGFB2, or si-EGR. The authors show that ECs can be categorized by distinct subpopulations of differing plasticity. The support for the existence of these subpopulations is compelling, supported also by three publicly available scRNA-seq datasets, and differential enrichment of coronary artery disease associated SNPs in open chromatin in these subpopulations. Inter alia, clarifications of controls and variability among EC responses would strengthen the interpretations of the study.

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    This article has 3 evaluationsAppears in 2 listsLatest version Latest activity
  7. Uncharacterized yeast gene YBR238C, an effector of TORC1 signaling in a mitochondrial feedback loop, accelerates cellular aging via HAP4 - and RMD9 -dependent mechanisms

    This article has 10 authors:
    1. Mohammad Alfatah
    2. Jolyn Jia Jia Lim
    3. Yizhong Zhang
    4. Arshia Naaz
    5. Trishia Yi Ning Cheng
    6. Sonia Yogasundaram
    7. Nashrul Afiq Faidzinn
    8. Jovian Jing Lin
    9. Birgit Eisenhaber
    10. Frank Eisenhaber
    This article has been curated by 1 group:
    • Curated by eLife

      eLife assessment

      This valuable study identifies an uncharacterized yeast gene regulating chronological lifespan in a mitochondrial-dependent pathway. The approach to identify and characterise this new gene is compelling, but the evidence is incomplete in supporting the major conclusions. With a stronger focus on the relevance of replicative in addition to chronological lifespan, and stronger data linking to mitochondrial function, this paper would be interesting to the yeast biologists working in metabolism and aging.

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    This article has 4 evaluationsAppears in 2 listsLatest version Latest activity
  8. Ethanol stress induces transient restructuring of the yeast genome yet stable formation of Hsf1 transcriptional condensates

    This article has 3 authors:
    1. Linda S. Rubio
    2. Suman Mohajan
    3. David S. Gross
    This article has been curated by 1 group:
    • Curated by eLife

      eLife assessment

      This is a useful contribution to our understanding of how different cell stressors (ethanol or heat-shock) might elicit unique responses at the genomic and topographical level under the regulation of yeast transcription factor Hsf1, and of the temporal coupling (or lack thereof) between Hsf1 aggregation and long-range communication among co-regulated heat-shock loci versus chromatin remodeling and transcriptional activation. A particular strength is the combination of genomic and imaging-based experimental approaches applied to genetically engineered in vivo systems. While much of the data is convincing, the work is incomplete in not providing strong evidence supporting (i) a similar rate and extent of proteotoxic stress under the two chosen stress conditions, (ii) relatively greater bulk chromatin compaction elicited by ethanol, (iii) reproducible levels of interactions between chromosomal loci, and (iv) phase-separated condensates versus other types of Hsf1 clusters.

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    This article has 4 evaluationsAppears in 2 listsLatest version Latest activity
  9. Identification of CFAP52 as a novel diagnostic target of male infertility with defects of sperm head-tail connection and flagella development

    This article has 7 authors:
    1. Hui-Juan Jin
    2. Tie-Chao Ruan
    3. Si-Yu Dai
    4. Xin-Yan Geng
    5. Yi-Hong Yang
    6. Ying Shen
    7. Su-Ren Chen
    This article has been curated by 1 group:
    • Curated by eLife

      eLife assessment

      This study provides useful information on the function of a ciliary and flagellar-associated protein, CFAP52, in the assembly of sperm head-tail connecting apparatus (HTCA) and tail formation in humans and mice. The significance is to identify CFAP52 as a genetic factor for asthenoteratozoospermia with a mixed acephalic spermatozoa syndrome (ASS) and multiple morphological abnormalities of the sperm flagella (MMAF) phenotype. The strength of the study is that the experimental evidence using CFAP52 loss-of-function in mice is solid to support that CFAP52 is essential for sperm motility and male fertility by contributing to HTCA and 9+2 axoneme, corroborating the sperm phenotypes of human patients with compound heterozygous mutations in CFAP52.

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    This article has 5 evaluationsAppears in 2 listsLatest version Latest activity
  10. Regulation of Nuclear Transcription by Mitochondrial RNA

    This article has 18 authors:
    1. Kiran Sriram
    2. Zhijie Qi
    3. Dongqiang Yuan
    4. Naseeb K. Malhi
    5. Xuejing Liu
    6. Riccardo Calandrelli
    7. Yingjun Luo
    8. Shengyan Jin
    9. Ji Shi
    10. Martha Salas
    11. Runrui Dang
    12. Brian Armstrong
    13. Saul J. Priceman
    14. Ping Wang
    15. Jiayu Liao
    16. Rama Natarajan
    17. Sheng Zhong
    18. Zhen B. Chen
    This article has been curated by 1 group:
    • Curated by eLife

      eLife assessment

      This work is fundamental in providing compelling evidence of mitochondria-encoded RNAs playing a role in controlling nuclear gene expression. How mitochondria and the nucleus communicates is an important but yet not well-appreciated area of biology. Using the iMARI (in situ mapping of RNA-Genome Interactions) technology developed by this team, the authors found that mitochondria-encoded RNAs play an unexpected role in regulating nuclear gene expressions in endothelial cells and intriguingly, depletion or overexpression of a specific mt-caRNA altered stress-induced transcription of nuclear genes encoding for innate inflammation and endothelial activation. Overall, these findings are interesting and supported by experimental confirmation, bulk-RNA-seq, and snRNA and scRNA-seq data and will be of interest to the field studying RNA regulation, gene expression and cell biology.

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    This article has 3 evaluationsAppears in 2 listsLatest version Latest activity
  11. Genetic basis of Arabidopsis thaliana responses to infection by naive and adapted isolates of turnip mosaic virus

    This article has 6 authors:
    1. Anamarija Butkovic
    2. Thomas J Ellis
    3. Ruben Gonzalez
    4. Benjamin Jaegle
    5. Magnus Nordborg
    6. Santiago F. Elena
    This article has been curated by 1 group:
    • Curated by eLife

      eLife assessment

      This manuscript presents valuable findings that inform our understanding of the genetic underpinnings of the model plant Arabidopsis' resistance to turnip mosaic virus (TuMV). The strength of the evidence in the manuscript is convincing, with very large sample sizes, careful controls, multiple follow-up experiments, and broadening to the evolutionary context. There is very good support for each of the manuscript's conclusions and the work could pave the way for functional studies.

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    This article has 4 evaluationsAppears in 2 listsLatest version Latest activity
  12. Plasma Growth Hormone Pulses Induce Male-biased Pulsatile Chromatin Opening and Epigenetic Regulation in Adult Mouse Liver

    This article has 3 authors:
    1. Andy Rampersaud
    2. Jeannette Connerney
    3. David J. Waxman
    This article has been curated by 1 group:
    • Curated by eLife

      eLife assessment

      This important study offers new and convincing support for the idea that about a third of mouse liver DNAse hypersensitivity sites (DHS) showing male-biased chromatin opening are sex-biased because of the male-specific cyclic action of growth hormone pulses to alter chromatin accessibility, as compared to the relative ineffectiveness of the more static pattern of growth hormone secretion in females. Supporting evidence is found in the impact of hypophysectomy and growth hormone treatment on chromatin accessibility, and the binding of specific transcription factors and epigenetic marks at STAT5-sensitive sites. This work uncovers mechanisms underlying sex differences in liver function and will be of broad interest to endocrinologists and hepatologists.

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    This article has 7 evaluationsAppears in 2 listsLatest version Latest activity
  13. ZC3H11A mutations cause high myopia by triggering PI3K-AKT and NF-κB mediated inflammatory reactions in humans and mice

    This article has 9 authors:
    1. Chong Chen
    2. Qian Liu
    3. Yu Rong
    4. Cheng Tang
    5. Xinyi Zhao
    6. Dandan Li
    7. Fan Lu
    8. Jia Qu
    9. Xinting Liu
    This article has been curated by 1 group:
    • Curated by eLife

      eLife assessment

      This useful study reports an investigation of ZC3H11A as a cause of high myopia through the analysis of human data and experiments with genetic knockout of Zc3h11a in mice, providing a model of myopia. The evidence supporting the conclusions is currently incomplete. It could be strengthened by a more thorough genetic analysis, fuller presentation of human phenotypic data, and more explanation for the reasons why there was no increased axial length in mice with myopia. The work will be of interest to ophthalmologists and researchers working on myopia.

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    This article has 4 evaluationsAppears in 2 listsLatest version Latest activity
  14. Cis -regulatory modes of Ultrabithorax inactivation in butterfly forewings

    This article has 7 authors:
    1. Amruta Tendolkar
    2. Anyi Mazo-Vargas
    3. Luca Livraghi
    4. Joseph J. Hanly
    5. Kelsey C. Van Horne
    6. Lawrence E. Gilbert
    7. Arnaud Martin
    This article has been curated by 1 group:
    • Curated by eLife

      eLife assessment

      This valuable paper examines the Bithorax complex in several butterfly species, in which the complex is contiguous and not split, as it is in the well-studied fruit fly Drosophila. Based on genetic screens and genetic manipulations of a boundary element involved in segment-specific regulation of Ubx, the authors provide solid evidence for their conclusions, which could be further strengthened by additional data and analyses. The data presented are relevant for those interested in the evolution and function of Hox genes and of gene regulation in general.

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    This article has 3 evaluationsAppears in 2 listsLatest version Latest activity
  15. Elimination of subtelomeric repeat sequences exerts little effect on telomere functions in Saccharomyces cerevisiae

    This article has 7 authors:
    1. Can Hu
    2. Xue-Ting Zhu
    3. Ming-Hong He
    4. Yangyang Shao
    5. Zhongjun Qin
    6. Zhi-Jing Wu
    7. Jin-Qiu Zhou
    This article has been curated by 1 group:
    • Curated by eLife

      eLife assessment

      This important study advances our understanding of the biological significance of the DNA sequence adjacent to telomeres. The data presented convincingly demonstrates that subtelomeric repeats are non-essential and have a minimal, if any, role in maintaining telomere integrity of budding yeast. The work will be of interest to telomere community specifically and the genome integrity community more broadly.

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    This article has 4 evaluationsAppears in 2 listsLatest version Latest activity
  16. Stable population structure in Europe since the Iron Age, despite high mobility

    This article has 97 authors:
    1. Margaret L. Antonio
    2. Clemens L. Weiß
    3. Ziyue Gao
    4. Susanna Sawyer
    5. Victoria Oberreiter
    6. Hannah M. Moots
    7. Jeffrey P. Spence
    8. Olivia Cheronet
    9. Brina Zagorc
    10. Elisa Praxmarer
    11. Kadir Toykan Özdoğan
    12. Lea Demetz
    13. Pere Gelabert
    14. Daniel Fernandes
    15. Michaela Lucci
    16. Timka Alihodžić
    17. Selma Amrani
    18. Pavel Avetisyan
    19. Christèle Baillif-Ducros
    20. Željka Bedić
    21. Audrey Bertrand
    22. Maja Bilić
    23. Luca Bondioli
    24. Paulina Borówka
    25. Emmanuel Botte
    26. Josip Burmaz
    27. Domagoj Bužanić
    28. Francesca Candilio
    29. Mirna Cvetko
    30. Daniela De Angelis
    31. Ivan Drnić
    32. Kristián Elschek
    33. Mounir Fantar
    34. Andrej Gaspari
    35. Gabriella Gasperetti
    36. Francesco Genchi
    37. Snežana Golubović
    38. Zuzana Hukeľová
    39. Rimantas Jankauskas
    40. Kristina Jelinčić Vučković
    41. Gordana Jeremić
    42. Iva Kaić
    43. Kevin Kazek
    44. Hamazasp Khachatryan
    45. Anahit Khudaverdyan
    46. Sylvia Kirchengast
    47. Miomir Korać
    48. Valérie Kozlowski
    49. Mária Krošláková
    50. Dora Kušan Špalj
    51. Francesco La Pastina
    52. Marie Laguardia
    53. Sandra Legrand
    54. Tino Leleković
    55. Tamara Leskovar
    56. Wiesław Lorkiewicz
    57. Dženi Los
    58. Ana Maria Silva
    59. Rene Masaryk
    60. Vinka Matijević
    61. Yahia Mehdi Seddik Cherifi
    62. Nicholas Meyer
    63. Ilija Mikić
    64. Nataša Miladinović-Radmilović
    65. Branka Milošević Zakić
    66. Lina Nacouzi
    67. Magdalena Natuniewicz-Sekuła
    68. Alessia Nava
    69. Christine Neugebauer-Maresch
    70. Jan Nováček
    71. Anna Osterholtz
    72. Julianne Paige
    73. Lujana Paraman
    74. Dominique Pieri
    75. Karol Pieta
    76. Stefan Pop-Lazić
    77. Matej Ruttkay
    78. Mirjana Sanader
    79. Arkadiusz Sołtysiak
    80. Alessandra Sperduti
    81. Tijana Stankovic Pesterac
    82. Maria Teschler-Nicola
    83. Iwona Teul
    84. Domagoj Tončinić
    85. Julien Trapp
    86. Dragana Vulović
    87. Tomasz Waliszewski
    88. Diethard Walter
    89. Milos Zivanovic
    90. Mohamed el Mostefa Filah
    91. Morana Čaušević-Bully
    92. Mario Šlaus
    93. Dusan Boric
    94. Mario Novak
    95. Alfredo Coppa
    96. Ron Pinhasi
    97. Jonathan K. Pritchard
    This article has been curated by 1 group:
    • Curated by eLife

      eLife assessment

      This paper will be of considerable interest to population geneticists and other scholars in the field of paleogenomics. The study provides an impressive dataset containing 200+ novel human ancient genome sequences and a very creative, robust, and novel approach for studying human migration across time using ancient DNA. The authors find that the population structure in Europe has been remarkably stable over time. The conclusions are well supported by the data and the methods used are thoughtful and rigorous.

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    This article has 4 evaluationsAppears in 2 listsLatest version Latest activity
  17. Activity of MukBEF for chromosome management in E. coli and its inhibition by MatP

    This article has 3 authors:
    1. Mohammed Seba
    2. Frédéric Boccard
    3. Stéphane Duigou
    This article has been curated by 1 group:
    • Curated by eLife

      eLife assessment

      This paper presents important new data related to the non-canonical SMC complex MukBEF in E. coli, which remains less well understood compared to more canonical SMC complexes in many other bacteria. The authors use a combination of Hi-C and ChIP-seq to demonstrate that MukBEF loads at multiple locations along the chromosome, preferentially in newly replicated DNA, with the MatP/matS system antagonizing MukBEF activity and localizing in terminus proximal regions. Most of the data to support these findings are compelling, with modest concerns raised about the effect sizes of the ChIP-seq data, which could be bolstered with some additional controls.

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    This article has 4 evaluationsAppears in 2 listsLatest version Latest activity
  18. Association of genetic variation in COL11A1 with adolescent idiopathic scoliosis

    This article has 25 authors:
    1. Hao Yu
    2. Anas M. Khanshour
    3. Aki Ushiki
    4. Nao Otomo
    5. Yoshinao Koike
    6. Elisabet Einarsdottir
    7. Yanhui Fan
    8. Lilian Antunes
    9. Yared H. Kidane
    10. Reuel Cornelia
    11. Rory Sheng
    12. Yichi Zhang
    13. Jimin Pei
    14. Nick V. Grishin
    15. Bret M. Evers
    16. Jason Pui Yin Cheung
    17. John A. Herring
    18. Chikashi Terao
    19. You-Qiang Song
    20. Christina A. Gurnett
    21. Paul Gerdhem
    22. Shiro Ikegawa
    23. Jonathan J. Rios
    24. Nadav Ahituv
    25. Carol A. Wise
    This article has been curated by 1 group:
    • Curated by eLife

      eLife assessment

      This valuable study analyzes a large cohort of Adolescent Idiopathic Scoliosis (AIS) patients, identifying an association with a variant in COL11A1 (Pro1335Leu). Experimental testing of this potentially pathogenic variant in vitro suggests a connection between Pax1, Col11a1, Mmp3, and estrogen signaling, thus providing solid support for the proposed link between hormonal and matrix components in the development of AIS.

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    This article has 8 evaluationsAppears in 2 listsLatest version Latest activity
  19. Enhancing CRISPR prime editing by reducing misfolded pegRNA interactions

    This article has 7 authors:
    1. Weiting Zhang
    2. Karl Petri
    3. Junyan Ma
    4. Hyunho Lee
    5. Chia-Lun Tsai
    6. J. Keith Joung
    7. Jing-Ruey Joanna Yeh
    This article has been curated by 1 group:
    • Curated by eLife

      eLife assessment

      This useful paper reports on two simple methods for improving the efficiency of prime editing, a prominent gene editing technique. In combination with published modifications, the strategies described in this study may lead to significant improvements in editing efficiencies. The data are solid, and the methods will be of broad interest to anyone using gene editing.

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    This article has 4 evaluationsAppears in 2 listsLatest version Latest activity
  20. Control of meiotic entry by dual inhibition of a key mitotic transcription factor

    This article has 3 authors:
    1. Amanda J. Su
    2. Siri C. Yendluri
    3. Elçin Ünal
    This article has been curated by 1 group:
    • Curated by eLife

      eLife assessment

      This study identifies several modes of regulation or pathways that are valuable for understanding the entry or progression into meiosis, which implies both the repression of some mitotic cell cycle regulators and the expression of meiotic functions. Convincing approaches identify several of the involved genes, although some were known before. How these modes of regulation and genes cooperate remains to be understood.

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    This article has 4 evaluationsAppears in 2 listsLatest version Latest activity