Recombination between heterologous human acrocentric chromosomes

The short arms of the human acrocentric chromosomes 13, 14, 15, 21 and 22 (SAACs) share large homologous regions, including ribosomal DNA repeats and extended segmental duplications1,2. Although the resolution of these regions in the first complete assembly of a human genome—the Telomere-to-Telomere Consortium’s CHM13 assembly (T2T-CHM13)—provided a model of their homology3, it remained unclear whether these patterns were ancestral or maintained by ongoing recombination exchange. Here we show that acrocentric chromosomes contain pseudo-homologous regions (PHRs) indicative of recombination between non-homologous sequences. Utilizing an all-to-all comparison of the human pangenome from the Human Pangenome Reference Consortium4 (HPRC), we find that contigs from all of the SAACs form a community. A variation graph5 constructed from centromere-spanning acrocentric contigs indicates the presence of regions in which most contigs appear nearly identical between heterologous acrocentric chromosomes in T2T-CHM13. Except on chromosome 15, we observe faster decay of linkage disequilibrium in the pseudo-homologous regions than in the corresponding short and long arms, indicating higher rates of recombination6,7. The pseudo-homologous regions include sequences that have previously been shown to lie at the breakpoint of Robertsonian translocations8, and their arrangement is compatible with crossover in inverted duplications on chromosomes 13, 14 and 21. The ubiquity of signals of recombination between heterologous acrocentric chromosomes seen in the HPRC draft pangenome suggests that these shared sequences form the basis for recurrent Robertsonian translocations, providing sequence and population-based confirmation of hypotheses first developed from cytogenetic studies 50 years ago9.Our work depends on the HPRC draft human pangenome resource established in the accompanying Article4, and we thank the production and assembly groups for their efforts in establishing this resource. This work used the computational resources of the UTHSC Octopus cluster and NIH HPC Biowulf cluster. We acknowledge support in maintaining these systems that was critical to our analyses. The authors thank M. Miller for the development of a graphical synopsis of our study (Fig. 5); and R. Williams and N. Soranzo for support and guidance in the design and discussion of our work. This work was supported, in part, by National Institutes of Health/NIDA U01DA047638 (E.G.), National Institutes of Health/NIGMS R01GM123489 (E.G.), NSF PPoSS Award no. 2118709 (E.G. and C.F.), the Tennessee Governor’s Chairs programme (C.F. and E.G.), National Institutes of Health/NCI R01CA266339 (T.P., L.G.d.L. and J.L.G.), and the Intramural Research Program of the National Human Genome Research Institute, National Institutes of Health (A.R., S.K. and A.M.P.). We acknowledge support from Human Technopole (A.G.), Consiglio Nazionale delle Ricerche, Italy (S.B. and V.C.), and Stowers Institute for Medical Research (T.P., L.G.d.L., B.R. and J.L.G.).Peer Reviewed"Article signat per 13 autors/es: Andrea Guarracino, Silvia Buonaiuto, Leonardo Gomes de Lima, Tamara Potapova, Arang Rhie, Sergey Koren, Boris Rubinstein, Christian Fischer, Human Pangenome Reference Consortium, Jennifer L. Gerton, Adam M. Phillippy, Vincenza Colonna & Erik Garrison " Human Pangenome Reference Consortium: "Haley J. Abel, Lucinda L. Antonacci-Fulton, Mobin Asri, Gunjan Baid, Carl A. Baker, Anastasiya Belyaeva, Konstantinos Billis, Guillaume Bourque, Silvia Buonaiuto, Andrew Carroll, Mark J. P. Chaisson, Pi-Chuan Chang, Xian H. Chang, Haoyu Cheng, Justin Chu, Sarah Cody, Vincenza Colonna, Daniel E. Cook, Robert M. Cook-Deegan, Omar E. Cornejo, Mark Diekhans, Daniel Doerr, Peter Ebert, Jana Ebler, Evan E. Eichler, Jordan M. Eizenga, Susan Fairley, Olivier Fedrigo, Adam L. Felsenfeld, Xiaowen Feng, Christian Fischer, Paul Flicek, Giulio Formenti, Adam Frankish, Robert S. Fulton, Yan Gao, Shilpa Garg, Erik Garrison, Nanibaa’ A. Garrison, Carlos Garcia Giron, Richard E. Green, Cristian Groza, Andrea Guarracino, Leanne Haggerty, Ira Hall, William T. Harvey, Marina Haukness, David Haussler, Simon Heumos, Glenn Hickey, Kendra Hoekzema, Thibaut Hourlier, Kerstin Howe, Miten Jain, Erich D. Jarvis, Hanlee P. Ji, Eimear E. Kenny, Barbara A. Koenig, Alexey Kolesnikov, Jan O. Korbel, Jennifer Kordosky, Sergey Koren, HoJoon Lee, Alexandra P. Lewis, Heng Li, Wen-Wei Liao, Shuangjia Lu, Tsung-Yu Lu, Julian K. Lucas, Hugo Magalhães, Santiago Marco-Sola, Pierre Marijon, Charles Markello, Tobias Marschall, Fergal J. Martin, Ann McCartney, Jennifer McDaniel, Karen H. Miga, Matthew W. Mitchell, Jean Monlong, Jacquelyn Mountcastle, Katherine M. Munson, Moses Njagi Mwaniki, Maria Nattestad, Adam M. Novak, Sergey Nurk, Hugh E. Olsen, Nathan D. Olson, Benedict Paten, Trevor Pesout, Adam M. Phillippy, Alice B. Popejoy, David Porubsky, Pjotr Prins, Daniela Puiu, Mikko Rautiainen, Allison A. Regier, Arang Rhie, Samuel Sacco, Ashley D. Sanders, Valerie A. Schneider, Baergen I. Schultz, Kishwar Shafin, Jonas A. Sibbesen, Jouni Sirén, Michael W. Smith, Heidi J. Sofia, Ahmad N. Abou Tayoun, Françoise Thibaud-Nissen, Chad Tomlinson, Francesca Floriana Tricomi, Flavia Villani, Mitchell R. Vollger, Justin Wagner, Brian Walenz, Ting Wang, Jonathan M. D. Wood, Aleksey V. Zimin & Justin M. Zook"Postprint (published version

Primary glia expressing the G93A-SOD1 mutation present a neuroinflammatory phenotype and provide a cellular system for studies of glial inflammation

Detailed study of glial inflammation has been hindered by lack of cell culture systems that spontaneously demonstrate the "neuroinflammatory phenotype". Mice expressing a glycine → alanine substitution in cytosolic Cu, Zn-superoxide dismutase (G93A-SOD1) associated with familial amyotrophic lateral sclerosis (ALS) demonstrate age-dependent neuroinflammation associated with broad-spectrum cytokine, eicosanoid and oxidant production. In order to more precisely study the cellular mechanisms underlying glial activation in the G93A-SOD1 mouse, primary astrocytes were cultured from 7 day mouse neonates. At this age, G93A-SOD1 mice demonstrated no in vivo hallmarks of neuroinflammation. Nonetheless astrocytes cultured from G93A-SOD1 (but not wild-type human SOD1-expressing) transgenic mouse pups demonstrated a significant elevation in either the basal or the tumor necrosis alpha (TNFα)-stimulated levels of proinflammatory eicosanoids prostaglandin E(2 )(PGE(2)) and leukotriene B(4 )(LTB(4)); inducible nitric oxide synthase (iNOS) and •NO (indexed by nitrite release into the culture medium); and protein carbonyl products. Specific cytokine- and TNFα death-receptor-associated components were similarly upregulated in cultured G93A-SOD1 cells as assessed by multiprobe ribonuclease protection assays (RPAs) for their mRNA transcripts. Thus, endogenous glial expression of G93A-SOD1 produces a metastable condition in which glia are more prone to enter an activated neuroinflammatory state associated with broad-spectrum increased production of paracrine-acting substances. These findings support a role for active glial involvement in ALS and may provide a useful cell culture tool for the study of glial inflammation

Expression of HPV16 E5 Produces Enlarged Nuclei and Polyploidy through Endoreplication

Anogenital cancers and head and neck cancers are causally-associated with infection by high-risk human papillomavirus (HPV). The mechanism by which high-risk HPVs contribute to oncogenesis is poorly understood. HPV16 encodes three genes (HPV16 E5, E6, and E7) that can transform cells when expressed independently. HPV16 E6 and E7 have well-described roles causing genomic instability and unregulated cell cycle progression. The role of HPV16 E5 in cell transformation remains to be elucidated. Expression of HPV16 E5 results in enlarged, polyploid nuclei that are dependent on the level and duration of HPV16 E5 expression. Live-cell imaging data indicate these changes do not arise from cell-cell fusion or failed cytokinesis. The increase in nuclear size is a continual process that requires DNA synthesis. We conclude HPV16 E5 produces polyploid cells by endoreplication. These findings provide insight into how HPV16 E5 can contribute to cell transformation

Comprehensive and Integrated Genomic Characterization of Adult Soft Tissue Sarcomas

Sarcomas are a broad family of mesenchymal malignancies exhibiting remarkable histologic diversity. We describe the multi-platform molecular landscape of 206 adult soft tissue sarcomas representing 6 major types. Along with novel insights into the biology of individual sarcoma types, we report three overarching findings: (1) unlike most epithelial malignancies, these sarcomas (excepting synovial sarcoma) are characterized predominantly by copy-number changes, with low mutational loads and only a few genes (, , ) highly recurrently mutated across sarcoma types; (2) within sarcoma types, genomic and regulomic diversity of driver pathways defines molecular subtypes associated with patient outcome; and (3) the immune microenvironment, inferred from DNA methylation and mRNA profiles, associates with outcome and may inform clinical trials of immune checkpoint inhibitors. Overall, this large-scale analysis reveals previously unappreciated sarcoma-type-specific changes in copy number, methylation, RNA, and protein, providing insights into refining sarcoma therapy and relationships to other cancer types

Classic mitosis in a vertebrate cell

Presents a video showing classic mitosis in a Xenopus laevis cell S3 stably expressing GFP alpha-tubulin to visualize dynamics of the microtubule network. It illustrates a complete sequence of mitotic events starting from late G2 with disassembly of nucleoli. Subsequently in prophase, the spindle poles separate, the chromosomes condense and the nuclear envelope breaks down. Later during prometaphase and metaphase, the cell contracts, the mitotic spindle forms, and chromosomes align at the metaphase plate. At the onset of anaphase, the chromatids segregate to opposite poles of the spindle and the cleavage furrow separates the cell in two daughter cells connected by the midbody. In the subsequent telophase cells undergo exit from mitosis, illustrated by chromosome decondensation, formation of nuclear envelope and nucleoli, establishment of the interphase array of microtubules and expansion of the cell cytoplasm on the substrate. In the end, the two daughter cells are in G1 and remain connected by the midbodyComponente Curricular::Educação Superior::Ciências Biológicas::Biologia Gera

Back in mitosis

Presents video that shows a Xenopus laevis S3 cell reversing cytokinesis and exit from mitosis. The cell is stably expressing GFP alpha-tubulin to visualize dynamics of the microtubule network. This cell was blocked in metaphase with high levels of cyclin B and Cdk1 activity by the addition of the proteasome inhibitor, MG132. Upon treatment with the reversible Cdk inhibitor, Flavopiridol, the cell undergoes cytokinesis without chromosome separation and exits mitosis. Mitotic exit is accompanied by anaphase-like changes in the microtubule network, chromosome decondensation, assembly of the nuclear envelope and formation of a midbody. When the Cdk inhibitor is removed, the midbody recedes and the cleavage furrow re-opens. The mitotic spindle re-forms. The nuclear envelope disassembles. The chromosomes condense and re-align at the metaphase plateComponente Curricular::Educação Superior::Ciências Biológicas::Biologia Gera

Back in mitosis: waltz of the microtubules

Presents video that shows the microtubule network of a Xenopus laevis S3 cell during induction and reversal of mitotic exit. This cell, stably expressing GFP alpha-tubulin, was blocked at metaphase with high levels of cyclin B and Cdk1 activity by the addition of the proteasome inhibitor, MG132. The metaphase-arrested cell demonstrates the characteristic mitotic spindle. Upon treatment with the reversible Cdk inhibitor, Flavopiridol, the cell undergoes cytokinesis and mitotic exit. This is accompanied by anaphase-like changes in microtubule network. When the Cdk inhibitor is removed, the mitotic spindle re-formsComponente Curricular::Educação Superior::Ciências Biológicas::Biologia Gera

The Consequences of Chromosome Segregation Errors in Mitosis and Meiosis

Mistakes during cell division frequently generate changes in chromosome content, producing aneuploid or polyploid progeny cells. Polyploid cells may then undergo abnormal division to generate aneuploid cells. Chromosome segregation errors may also involve fragments of whole chromosomes. A major consequence of segregation defects is change in the relative dosage of products from genes located on the missegregated chromosomes. Abnormal expression of transcriptional regulators can also impact genes on the properly segregated chromosomes. The consequences of these perturbations in gene expression depend on the specific chromosomes affected and on the interplay of the aneuploid phenotype with the environment. Most often, these novel chromosome distributions are detrimental to the health and survival of the organism. However, in a changed environment, alterations in gene copy number may generate a more highly adapted phenotype. Chromosome segregation errors also have important implications in human health. They may promote drug resistance in pathogenic microorganisms. In cancer cells, they are a source for genetic and phenotypic variability that may select for populations with increased malignance and resistance to therapy. Lastly, chromosome segregation errors during gamete formation in meiosis are a primary cause of human birth defects and infertility. This review describes the consequences of mitotic and meiotic errors focusing on novel concepts and human health

Back in mitosis

Presents video that shows a Xenopus laevis S3 cell reversing cytokinesis and exit from mitosis. The cell is stably expressing GFP alpha-tubulin to visualize dynamics of the microtubule network. This cell was blocked in metaphase with high levels of cyclin B and Cdk1 activity by the addition of the proteasome inhibitor, MG132. Upon treatment with the reversible Cdk inhibitor, Flavopiridol, the cell undergoes cytokinesis without chromosome separation and exits mitosis. Mitotic exit is accompanied by anaphase-like changes in the microtubule network, chromosome decondensation, assembly of the nuclear envelope and formation of a midbody. When the Cdk inhibitor is removed, the midbody recedes and the cleavage furrow re-opens. The mitotic spindle re-forms. The nuclear envelope disassembles. The chromosomes condense and re-align at the metaphase plateComponente Curricular::Educação Superior::Ciências Biológicas::Biologia Gera