Testis Specific Histone 2B Is Associated with Sperm Chromatin Dynamics and Bull Fertility-A Pilot Study Naseer A
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Gene Regulation and Speciation in House Mice
Downloaded from genome.cshlp.org on September 26, 2021 - Published by Cold Spring Harbor Laboratory Press Research Gene regulation and speciation in house mice Katya L. Mack,1 Polly Campbell,2 and Michael W. Nachman1 1Museum of Vertebrate Zoology and Department of Integrative Biology, University of California, Berkeley, California 94720-3160, USA; 2Department of Integrative Biology, Oklahoma State University, Stillwater, Oklahoma 74078, USA One approach to understanding the process of speciation is to characterize the genetic architecture of post-zygotic isolation. As gene regulation requires interactions between loci, negative epistatic interactions between divergent regulatory elements might underlie hybrid incompatibilities and contribute to reproductive isolation. Here, we take advantage of a cross between house mouse subspecies, where hybrid dysfunction is largely unidirectional, to test several key predictions about regulatory divergence and reproductive isolation. Regulatory divergence between Mus musculus musculus and M. m. domesticus was charac- terized by studying allele-specific expression in fertile hybrid males using mRNA-sequencing of whole testes. We found ex- tensive regulatory divergence between M. m. musculus and M. m. domesticus, largely attributable to cis-regulatory changes. When both cis and trans changes occurred, they were observed in opposition much more often than expected under a neutral model, providing strong evidence of widespread compensatory evolution. We also found evidence for lineage-specific positive se- lection on a subset of genes related to transcriptional regulation. Comparisons of fertile and sterile hybrid males identified a set of genes that were uniquely misexpressed in sterile individuals. Lastly, we discovered a nonrandom association between these genes and genes showing evidence of compensatory evolution, consistent with the idea that regulatory interactions might contribute to Dobzhansky-Muller incompatibilities and be important in speciation. -
Androgen Receptor Function Is Required in Sertoli Cells for the Terminal Differentiation of Haploid Spermatids Robert W
Research article 459 Androgen receptor function is required in Sertoli cells for the terminal differentiation of haploid spermatids Robert W. Holdcraft and Robert E. Braun* University of Washington School of Medicine, Department of Genome Sciences, Seattle, WA 98195, USA *Author for correspondence (e-mail: [email protected]) Accepted 20 October 2003 Development 131, 459-467 Published by The Company of Biologists 2004 doi:10.1242/dev.00957 Summary Androgen receptor function is required for male embryonic and their release from the seminiferous epithelium is AR sexual differentiation, pubertal development and the dependent and maximally sensitive to AR depletion within regulation of spermatogenesis in mammals. During the testis. Cell-specific disruption of Ar in Sertoli cells of spermatogenesis, this requirement is thought to be hypomorphic animals further shows that progression of mediated by Sertoli cells and its genetic and late-round spermatids to elongating steps is sensitive to loss pharmacological disruption is manifested in spermatocytes of Sertoli cell AR function, but that progression through as meiotic arrest. Through studies of a hypomorphic and meiosis and early-round spermatid differentiation are conditional allele of the androgen receptor (Ar) gene, we surprisingly unaffected. have uncovered a dual post-meiotic requirement for androgen receptor activity during male germ cell Supplemental data available online differentiation. Observations in Ar hypomorphic animals demonstrate that terminal differentiation of spermatids Key words: Androgen receptor, Sertoli, Spermatogenesis, Mouse Introduction function from that resulting from the abdominal positioning Androgen receptor (AR) function is essential in males for of the testes. Mice homozygous for a mutation in the proper sexual differentiation and for the maintenance of normal gonadotrophin releasing hormone gene (Gnrh), which have spermatogenesis. -
Entropy Based Analysis of Vertebrate Sperm Protamines Sequences: Evidence of Potential Dityrosine and Cysteine-Tyrosine Cross-Linking in Sperm Protamines Christian D
Powell et al. BMC Genomics (2020) 21:277 https://doi.org/10.1186/s12864-020-6681-2 RESEARCH ARTICLE Open Access Entropy based analysis of vertebrate sperm protamines sequences: evidence of potential dityrosine and cysteine-tyrosine cross-linking in sperm protamines Christian D. Powell1,2,DanielC.Kirchoff1, Jason E. DeRouchey1 and Hunter N. B. Moseley2,3,4* Abstract Background: Spermatogenesis is the process by which germ cells develop into spermatozoa in the testis. Sperm protamines are small, arginine-rich nuclear proteins which replace somatic histones during spermatogenesis, allowing a hypercondensed DNA state that leads to a smaller nucleus and facilitating sperm head formation. In eutherian mammals, the protamine-DNA complex is achieved through a combination of intra- and intermolecular cysteine cross-linking and possibly histidine-cysteine zinc ion binding. Most metatherian sperm protamines lack cysteine but perform the same function. This lack of dicysteine cross-linking has made the mechanism behind metatherian protamines folding unclear. Results: Protamine sequences from UniProt’s databases were pulled down and sorted into homologous groups. Multiple sequence alignments were then generated and a gap weighted relative entropy score calculated for each position. For the eutherian alignments, the cysteine containing positions were the most highly conserved. For the metatherian alignment, the tyrosine containing positions were the most highly conserved and corresponded to the cysteine positions in the eutherian alignment. Conclusions: High conservation indicates likely functionally/structurally important residues at these positions in the metatherian protamines and the correspondence with cysteine positions within the eutherian alignment implies a similarity in function. One possible explanation is that the metatherian protamine structure relies upon dityrosine cross-linking between these highly conserved tyrosines. -
Relating Sequence Encoded Information to Form and Function of Intrinsically Disordered Proteins
Available online at www.sciencedirect.com ScienceDirect Relating sequence encoded information to form and function of intrinsically disordered proteins Rahul K Das, Kiersten M Ruff and Rohit V Pappu Intrinsically disordered proteins (IDPs) showcase the of archetypal IDPs. CCRs enable the assignments of importance of conformational plasticity and heterogeneity in conformational descriptors and inferences regarding the protein function. We summarize recent advances that connect amplitudes of conformational fluctuations of IDPs. These information encoded in IDP sequences to their conformational insights are relevant because amino acid compositions are properties and functions. We focus on insights obtained often well conserved among orthologs of IDPs even if their through a combination of atomistic simulations and biophysical sequences are poorly conserved [42,43]. measurements that are synthesized into a coherent framework using polymer physics theories. Compositional classes of IDPs Address Amino acid compositions of IDPs are characterized by Department of Biomedical Engineering and Center for Biological distinct biases [5]. They are deficient in canonical hydro- Systems Engineering, Washington University in St. Louis, One Brookings phobic residues and enriched in polar and charged resi- Drive, Campus Box 1097, St. Louis, MO 63130, USA dues. Accordingly, IDPs fall into three distinct compositional classes that reflect the fraction of charged Corresponding author: Pappu, Rohit V ([email protected]) versus polar residues. The distinct classes are polar tracts, polyampholytes, and polyelectrolytes [41] (see Figure 1). Polar Current Opinion in Structural Biology 2015, 32:102–112 tracts are deficient in charged, hydrophobic, and proline residues. They are enriched in polar amino acids such as This review comes from a themed issue on Sequences and topology Asn, Gly, Gln, His, Ser, and Thr. -
Identification of Reproduction-Related Gene Polymorphisms Using Whole
INVESTIGATION Identification of Reproduction-Related Gene Polymorphisms Using Whole Transcriptome Sequencing in the Large White Pig Population Daniel Fischer,* Asta Laiho,† Attila Gyenesei,‡ and Anu Sironen*,1 *Natural Resources Institute Finland (Luke), Green Technology, Animal and Plant Genomics and Breeding, FI-31600 Jokioinen, Finland, †The Finnish Microarray and Sequencing Centre, Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, Tykistökatu 6, FI-20520 Turku, Finland, and ‡Campus Science Support Facilities, Vienna Biocenter, A-1030 Vienna, Austria ORCID ID: 0000-0003-2064-6960 (D.F.) ABSTRACT Recent developments in high-throughput sequencing techniques have enabled large-scale KEYWORDS analysis of genetic variations and gene expression in different tissues and species, but gene expression oviduct patterns and genetic variations in livestock are not well-characterized. In this study, we have used high- testis throughput transcriptomic sequencing of the Finnish Large White to identify gene expression patterns and gene expression coding polymorphisms within the breed in the testis and oviduct. The main objective of this study was to polymorphism identify polymorphisms within genes that are highly and specifically expressed in male and/or female SNP reproductive organs. The differential expression (DE) analysis underlined 1234 genes highly expressed in pig the testis and 1501 in the oviduct. Furthermore, we used a novel in-house R-package hoardeR for the transcriptome identification of novel genes and their orthologs, which underlined 55 additional DE genes based on RNAseq orthologs in the human, cow, and sheep. Identification of polymorphisms in the dataset resulted in a total of reproduction 29,973 variants, of which 10,704 were known coding variants. -
The Chromatin Remodeling Factor CHD5 Is a Transcriptional Repressor of WEE1
The Chromatin Remodeling Factor CHD5 Is a Transcriptional Repressor of WEE1 The Harvard community has made this article openly available. Please share how this access benefits you. Your story matters Citation Quan, Jinhua, Guillaume Adelmant, Jarrod A. Marto, A. Thomas Look, and Timur Yusufzai. 2014. “The Chromatin Remodeling Factor CHD5 Is a Transcriptional Repressor of WEE1.” PLoS ONE 9 (9): e108066. doi:10.1371/journal.pone.0108066. http:// dx.doi.org/10.1371/journal.pone.0108066. Published Version doi:10.1371/journal.pone.0108066 Citable link http://nrs.harvard.edu/urn-3:HUL.InstRepos:13347631 Terms of Use This article was downloaded from Harvard University’s DASH repository, and is made available under the terms and conditions applicable to Other Posted Material, as set forth at http:// nrs.harvard.edu/urn-3:HUL.InstRepos:dash.current.terms-of- use#LAA The Chromatin Remodeling Factor CHD5 Is a Transcriptional Repressor of WEE1 Jinhua Quan1,2, Guillaume Adelmant2,3, Jarrod A. Marto2,3, A. Thomas Look4, Timur Yusufzai1,2* 1 Department of Radiation Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, United States of America, 2 Department of Biological Chemistry & Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts, United States of America, 3 Blais Proteomics Center, Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts, United States of America, 4 Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, United States of America Abstract Loss of the chromatin remodeling ATPase CHD5 has been linked to the progression of neuroblastoma tumors, yet the underlying mechanisms behind the tumor suppressor role of CHD5 are unknown. -
Definition and Characterization of a Region of 1P36.3 Consistently
Oncogene (2005) 24, 2684–2694 & 2005 Nature Publishing Group All rights reserved 0950-9232/05 $30.00 www.nature.com/onc Definition and characterization of a region of 1p36.3 consistently deleted in neuroblastoma Peter S White*,1,2, Patricia M Thompson1, Takahiro Gotoh1, Erin R Okawa1, Jun Igarashi1, Marleen Kok1, Cynthia Winter1, Simon G Gregory3, MichaelD Hogarty 1,2, John M Maris1,2,4 and Garrett M Brodeur1,2 1Division of Oncology, The Children’s Hospital of Philadelphia, 3516 Civic Center Blvd, Philadelphia, PA 19104, USA; 2Department of Pediatrics, University of Pennsylvania School of Medicine, Philadelphia, PA 19104, USA; 3Center for Human Genetics, Duke University School of Medicine, Durham, NC 27710, USA; 4Abramson Family Cancer Research Institute, University of Pennsylvania School of Medicine, Philadelphia, PA 19104, USA Substantial genomic and functional evidence from primary Introduction tumors and cell lines indicates that a consistent region of distal chromosome 1p is deleted in a sizable proportion of Neuroblastoma is a common pediatric malignancy of human neuroblastomas, suggesting that this region contains the peripheralsympathetic nervous system. Despite one or more tumor suppressor genes. To determine system- recent advances in therapy, a large proportion of atically and precisely the location and extent of 1p deletion neuroblastoma patients succumb to the disease. Thus, in neuroblastomas, we performed allelic loss studies of 737 identification and characterization of the genetic events primary neuroblastomas and genotype analysis of 46 underlying neuroblastoma tumorigenesis and progres- neuroblastoma cell lines. Together, the results defined a sion are important priorities for management of this single region within 1p36.3 that was consistently deleted in malignancy. -
A Genomic Atlas of Human Adrenal and Gonad Development [Version 2; Referees: 4 Approved] Ignacio Del Valle1, Federica Buonocore1, Andrew J
Wellcome Open Research 2017, 2:25 Last updated: 08 NOV 2017 RESEARCH ARTICLE A genomic atlas of human adrenal and gonad development [version 2; referees: 4 approved] Ignacio del Valle1, Federica Buonocore1, Andrew J. Duncan1, Lin Lin1, Martino Barenco2, Rahul Parnaik1, Sonia Shah3,4, Mike Hubank5, Dianne Gerrelli2, John C. Achermann 1 1Genetics and Genomic Medicine, UCL Great Ormond Street Institute of Child Health, London, UK 2Developmental Biology and Cancer, UCL Great Ormond Street Institute of Child Health, London, UK 3Institute for Molecular Bioscience, University of Queensland, Brisbane, Australia 4Institute of Cardiovascular Science, University College London, London, UK 5The Centre for Molecular Pathology, Royal Marsden Hospital, Sutton, UK v2 First published: 07 Apr 2017, 2:25 (doi: 10.12688/wellcomeopenres.11253.1) Open Peer Review Latest published: 23 Oct 2017, 2:25 (doi: 10.12688/wellcomeopenres.11253.2) Referee Status: Abstract Background: In humans, the adrenal glands and gonads undergo distinct biological events between 6-10 weeks post conception (wpc), such as testis Invited Referees determination, the onset of steroidogenesis and primordial germ cell 1 2 3 4 development. However, relatively little is currently known about the genetic mechanisms underlying these processes. We therefore aimed to generate a detailed genomic atlas of adrenal and gonad development across these critical version 2 report report stages of human embryonic and fetal development. published Methods: RNA was extracted from 53 tissue samples between 6-10 wpc 23 Oct 2017 (adrenal, testis, ovary and control). Affymetrix array analysis was performed and differential gene expression was analysed using Bioconductor. A version 1 mathematical model was constructed to investigate time-series changes across published report report report report 07 Apr 2017 the dataset. -
Genome-Wide DNA Methylation Analysis Reveals Molecular Subtypes of Pancreatic Cancer
www.impactjournals.com/oncotarget/ Oncotarget, 2017, Vol. 8, (No. 17), pp: 28990-29012 Research Paper Genome-wide DNA methylation analysis reveals molecular subtypes of pancreatic cancer Nitish Kumar Mishra1 and Chittibabu Guda1,2,3,4 1Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, NE, 68198, USA 2Bioinformatics and Systems Biology Core, University of Nebraska Medical Center, Omaha, NE, 68198, USA 3Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, NE, 68198, USA 4Fred and Pamela Buffet Cancer Center, University of Nebraska Medical Center, Omaha, NE, 68198, USA Correspondence to: Chittibabu Guda, email: [email protected] Keywords: TCGA, pancreatic cancer, differential methylation, integrative analysis, molecular subtypes Received: October 20, 2016 Accepted: February 12, 2017 Published: March 07, 2017 Copyright: Mishra et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC-BY), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. ABSTRACT Pancreatic cancer (PC) is the fourth leading cause of cancer deaths in the United States with a five-year patient survival rate of only 6%. Early detection and treatment of this disease is hampered due to lack of reliable diagnostic and prognostic markers. Recent studies have shown that dynamic changes in the global DNA methylation and gene expression patterns play key roles in the PC development; hence, provide valuable insights for better understanding the initiation and progression of PC. In the current study, we used DNA methylation, gene expression, copy number, mutational and clinical data from pancreatic patients. -
Defining the Transcriptomic Landscape of the Developing Enteric Nervous System and Its Cellular Environment Sweta Roy-Carson Iowa State University, [email protected]
Genetics, Development and Cell Biology Genetics, Development and Cell Biology Publications 2017 Defining the transcriptomic landscape of the developing enteric nervous system and its cellular environment Sweta Roy-Carson Iowa State University, [email protected] Kevin Natukunda Iowa State University, [email protected] Hsien-chao Chou Iowa State University Narinder Pal Iowa State University Caitlin Farris Iowa State University Follow this and additional works at: https://lib.dr.iastate.edu/gdcb_las_pubs See next page for additional authors Part of the Cell and Developmental Biology Commons, and the Molecular Genetics Commons The ompc lete bibliographic information for this item can be found at https://lib.dr.iastate.edu/ gdcb_las_pubs/202. For information on how to cite this item, please visit http://lib.dr.iastate.edu/ howtocite.html. This Article is brought to you for free and open access by the Genetics, Development and Cell Biology at Iowa State University Digital Repository. It has been accepted for inclusion in Genetics, Development and Cell Biology Publications by an authorized administrator of Iowa State University Digital Repository. For more information, please contact [email protected]. Defining the transcriptomic landscape of the developing enteric nervous system and its cellular environment Abstract Background: Motility and the coordination of moving food through the gastrointestinal tract rely on a complex network of neurons known as the enteric nervous system (ENS). Despite its critical function, many of the molecular mechanisms that direct the development of the ENS and the elaboration of neural network connections remain unknown. The og al of this study was to transcriptionally identify molecular pathways and candidate genes that drive specification, differentiation and the neural circuitry of specific neural progenitors, the phox2b expressing ENS cell lineage, during normal enteric nervous system development. -
A Rare CHD5 Haplotype and Its Interactions with Environmental
Xiao et al. BMC Cancer (2018) 18:658 https://doi.org/10.1186/s12885-018-4551-y RESEARCHARTICLE Open Access ArareCHD5 haplotype and its interactions with environmental factors predicting hepatocellular carcinoma risk Qin Xiao1,2†, Lianzhou Chen3†, Haiqing Luo1,4†, Hongmei Li1,5†, Qingming Kong6, Fei Jiao7, Shifeng Pang1, Ming Zhang8, Feifei Lan9, Wenguo Fan10, Hui Luo1*, Tao Tao8* and Xiao Zhu1* Abstract Background: CHD5 is a conventional tumour-suppressing gene in many tumours. The aim of this study was to determine whether CHD5 variants contribute to the risk of hepatocellular carcinoma (HCC). Methods: Gene variants were identified using next-generation sequencing targeted on referenced mutations followed by TaqMan genotyping in two case-control studies. Results: We discovered a rare variant (haplotype AG) in CHD5 (rs12564469-rs9434711) that was markedly associated with the risk of HCC in a Chinese population. A logistical regression model and permutation test confirmed the association. Indeed, the association quality increased in a gene dose-dependent manner as the number of samples increased. In the stratified analysis, this haplotype risk effect was statistically significant in a subgroup of alcohol drinkers. The false-positive report probability and multifactor dimensionality reduction further supported the finding. Conclusions: Our results suggest that the rare CHD5 gene haplotype and alcohol intake contribute to the risk of HCC. Our findings can be valuable to researchers of cancer precision medicine looking to improve diagnosis and treatment of HCC. Keywords: CHD5, Gene haplotype, Hepatocellular carcinoma, Alcohol intake, Risk Background is one of the nine members of the CHD-binding en- Hepatocellular carcinoma (HCC) is the most common zymes and belongs to the snf2 DNA helicase/methylase primary liver cancer and has the worst prognoses of all superfamily [2]. -
CHD5 Is Required for Neurogenesis and Has a Dual Role in Facilitating Gene Expression and Polycomb Gene Repression
Developmental Cell Article CHD5 Is Required for Neurogenesis and Has a Dual Role in Facilitating Gene Expression and Polycomb Gene Repression Chris M. Egan,1,9 Ulrika Nyman,7,9 Julie Skotte,3 Gundula Streubel,1 Siobha´ n Turner,1 David J. O’Connell,6 Vilma Rraklli,7 Michael J. Dolan,1 Naomi Chadderton,1 Klaus Hansen,3 Gwyneth Jane Farrar,1 Kristian Helin,3,4,5 Johan Holmberg,7,8,10,* and Adrian P. Bracken1,2,10,* 1The Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland 2The Adelaide and Meath Hospital, Incorporating the National Children’s Hospital, Dublin 16, Ireland 3Biotech Research and Innovation Centre (BRIC) 4Centre for Epigenetics 5The Danish Stem Cell Center (DanStem) University of Copenhagen, 2200 Copenhagen, Denmark 6The Conway Institute, University College Dublin, Dublin 4, Ireland 7Ludwig Institute for Cancer Research 8Department of Cell and Molecular Biology Karolinska Institutet, Stockholm S-171 77, Sweden 9These authors contributed equally to this work 10These authors contributed equally to this work *Correspondence: [email protected] (J.H.), [email protected] (A.P.B.) http://dx.doi.org/10.1016/j.devcel.2013.07.008 SUMMARY alternative lineages are silenced. Furthermore, the precise roles of chromatin regulators during neuronal lineage specification The chromatin remodeler CHD5 is expressed in neu- remain largely unexplored. ral tissue and is frequently deleted in aggressive Chromatin regulators are generally considered to act as facili- neuroblastoma. Very little is known about the function tators of lineage specification, rather than actually directing the of CHD5 in the nervous system or its mechanism of process (Holmberg and Perlmann, 2012).