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Journal articles on the topic 'Gene order rearrangements'

Author: Grafiati

Published: 2 June 2025

Last updated: 31 July 2025

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1

Zheng, Chen-Guang, Zheng Liu, Yan-Min Zhao, et al. "First Report on Mitochondrial Gene Rearrangement in Non-Biting Midges, Revealing a Synapomorphy in Stenochironomus Kieffer (Diptera: Chironomidae)." Insects 13, no. 2 (2022): 115. http://dx.doi.org/10.3390/insects13020115.

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(1) Background: Gene rearrangement of mitochondrial genome, especially those with phylogenetic signals, has long fascinated evolutionary biologists. The synapomorphic gene rearrangements have been identified across multiple orders and at many different taxonomic levels, supporting the monophyletic or systematic relationships of related lineages. However, mitochondrial gene rearrangement has never been observed in the non-biting midges (Diptera: Chironomidae); (2) methods: in this study, the complete mitogenomes of seven Stenochironomus species were sequenced and analyzed for the first time; (3

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2

Yuan, Siqi, Yun Xia, Yuchi Zheng, and Xiaomao Zeng. "Next-generation sequencing of mixed genomic DNA allows efficient assembly of rearranged mitochondrial genomes inAmolops chunganensisandQuasipaa boulengeri." PeerJ 4 (December 15, 2016): e2786. http://dx.doi.org/10.7717/peerj.2786.

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Recent improvements in next-generation sequencing (NGS) technologies can facilitate the obtainment of mitochondrial genomes. However, it is not clear whether NGS could be effectively used to reconstruct the mitogenome with high gene rearrangement. These high rearrangements would cause amplification failure, and/or assembly and alignment errors. Here, we choose two frogs with rearranged gene order,Amolops chunganensisandQuasipaa boulengeri, to test whether gene rearrangements affect the mitogenome assembly and alignment by using NGS. The mitogenomes with gene rearrangements are sequenced throug

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3

Piper, Hannah, Samuel Litwin, and Ramit Mehr. "Models for Antigen Receptor Gene Rearrangement. II. Multiple Rearrangement in the TCR: Allelic Exclusion or Inclusion?" Journal of Immunology 163, no. 4 (1999): 1799–808. http://dx.doi.org/10.4049/jimmunol.163.4.1799.

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Abstract This series of papers addresses the effects of continuous Ag receptor gene rearrangement in lymphocytes on allelic exclusion. The previous paper discussed light chain gene rearrangement and receptor editing in B cells, and showed that these processes are ordered on three different levels. This order, combined with the constraints imposed by a strong negative selection, was shown to lead to effective allelic exclusion. In the present paper, we discuss rearrangement of TCR genes. In the TCR α-chain, allelic inclusion may be the rule rather than the exception. Several previous models, wh

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4

Graninger, W. B., P. L. Goldman, C. C. Morton, S. J. O'Brien, and S. J. Korsmeyer. "The kappa-deleting element. Germline and rearranged, duplicated and dispersed forms." Journal of Experimental Medicine 167, no. 2 (1988): 488–501. http://dx.doi.org/10.1084/jem.167.2.488.

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Human light chain genes are used in a kappa before lambda order. Accompanying this hierarchy is the rearrangement of a kappa-deleting element (Kde) which eliminates the kappa locus before lambda gene rearrangement. In approximately 60% of rearrangements the Kde recombines at a conserved heptamer within the J kappa-C kappa intron. We demonstrated that aberrant V/J rearrangements possessing apparent "N" nucleotides existed 5' to the J kappa-Kde rearrangements. This suggests that the Kde may selectively eliminate nonfunctional V/J alleles. A kappa-producing cell that displayed the unusual finding

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5

Zhang, Yu, Lu Qi, Fengping Li, et al. "Mitogenomic Analysis of Pterioidea (Bivalvia: Pteriomorphia): Insights into the Evolution of the Gene Rearrangements." Fishes 8, no. 10 (2023): 528. http://dx.doi.org/10.3390/fishes8100528.

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The complete mitogenomes of Pinctada albina and Pinctada margaritifera were sequenced in this study, with sizes of 23,841 bp and 15,556 bp, respectively. The mitochondrial genome analysis of eight Pterioidea species indicated the existence of gene rearrangements within the superfamily. The ATP8 gene was not detected in the two new mitogenomes, and rrnS was found to be duplicated in P. albina’s mitogenome. The reconstructed phylogeny based on mitogenomes strongly supported the monophyly of Pterioidea and provided robust statistical evidence of the phylogenetic relationships within Pteriomorphia

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6

Swenson, Krister M., and Mathieu Blanchette. "Large-scale mammalian genome rearrangements coincide with chromatin interactions." Bioinformatics 35, no. 14 (2019): i117—i126. http://dx.doi.org/10.1093/bioinformatics/btz343.

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Abstract Motivation Genome rearrangements drastically change gene order along great stretches of a chromosome. There has been initial evidence that these apparently non-local events in the 1D sense may have breakpoints that are close in the 3D sense. We harness the power of the Double Cut and Join model of genome rearrangement, along with Hi-C chromosome conformation capture data to test this hypothesis between human and mouse. Results We devise novel statistical tests that show that indeed, rearrangement scenarios that transform the human into the mouse gene order are enriched for pairs of br

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7

Cunha, Regina L., Katy R. Nicastro, Gerardo I. Zardi, et al. "Comparative mitogenomic analyses and gene rearrangements reject the alleged polyphyly of a bivalve genus." PeerJ 10 (September 26, 2022): e13953. http://dx.doi.org/10.7717/peerj.13953.

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Background The order and orientation of genes encoded by animal mitogenomes are typically conserved, although there is increasing evidence of multiple rearrangements among mollusks. The mitogenome from a Brazilian brown mussel (hereafter named B1) classified as Perna perna Linnaeus, 1758 and assembled from Illumina short-length reads revealed an unusual gene order very different from other congeneric species. Previous mitogenomic analyses based on the Brazilian specimen and other Mytilidae suggested the polyphyly of the genus Perna. Methods To confirm the proposed gene rearrangements, we seque

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Xing, Zhi-Ping, Xin Liang, Xu Wang, Hao-Yuan Hu, and Yi-Xin Huang. "Novel gene rearrangement pattern in mitochondrial genome of Ooencyrtus plautus Huang & Noyes, 1994: new gene order in Encyrtidae (Hymenoptera, Chalcidoidea)." ZooKeys 1124 (October 10, 2022): 1–21. https://doi.org/10.3897/zookeys.1124.83811.

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Studies of mitochondrial genomes have a wide range of applications in phylogeny, population genetics, and evolutionary biology. In this study, we sequenced and analyzed the mitochondrial genome of Ooencyrtus plautus Huang & Noyes, 1994 (Hymenoptera, Encyrtidae). The nearly complete mitogenome of O. plautus was 15,730 bp in size, including 13 PCGs (protein-coding genes), 22 tRNAs, 2 rRNAs, and a nearly complete control region. The nucleotide composition was significantly biased toward adenine and thymine, with an A + T content of 84.6%. We used the reference sequence of Chouioia cunea and c

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9

Dowton, M., L. R. Castro, and A. D. Austin. "Mitochondrial gene rearrangements as phylogenetic characters in the invertebrates: the examination of genome 'morphology'." Invertebrate Systematics 16, no. 3 (2002): 345. http://dx.doi.org/10.1071/is02003.

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Mitochondrial gene rearrangements are the latest tool in the arsenal of phylogeneticists for investigating historical relationships. They are complex molecular characters that may provide more reliable evidence of ancestry than comparative molecular data. Here we review the phylogenetic utility of mitochondrial gene rearrangements, and find that despite isolated incidences of convergence, derived gene order appears highly congruent with phylogenies produced from other sources of data. We calculate that the chance of two mitochondrial genomes sharing the same derived genome organisation is only

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10

Morley, Alexander A., Michael J. Brisco, Pamela J. Sykes, et al. "The Repertoire of Gene Rearrangements in Acute Lymphoblastic Leukemia." Blood 106, no. 11 (2005): 1464. http://dx.doi.org/10.1182/blood.v106.11.1464.1464.

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Abstract Rearrangements of the immunoglobulin and T-cell receptor genes provide molecular markers for clones in acute lymphoblastic leukemia (ALL). Determination of the repertoire of gene rearrangements in ALL aids in understanding the clonal biology of the disease and provides molecular markers which can be used to quantify minimal residual disease (MRD). We have developed a sensitive PCR-based method for analysing the repertoire of immunoglobulin heavy chain (IgH) rearrangements in ALL. Multiple parallel quantitative PCR’s are performed in microplates using different segment-specific primers

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11

Lee, N. E., and M. M. Davis. "T cell receptor beta-chain genes in BW5147 and other AKR tumors. Deletion order of murine V beta gene segments and possible 5' regulatory regions." Journal of Immunology 140, no. 5 (1988): 1665–75. http://dx.doi.org/10.4049/jimmunol.140.5.1665.

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Abstract The AKR thymoma BW5147 has rearranged both of its TCR beta-chain loci, using the same J beta region (J beta 2.5) in each, but with different V beta gene segments. Although the two rearrangements are expressed approximately equally in cytoplasmic RNA, the principle of allelic exclusion is maintained because only one rearrangement is in-frame and capable of encoding a functional protein. In hybridomas made with BW5147 as the fusion partner, this protein may combine with the alpha-chain protein derived from the normal cell to form new Ag/MHC specificities. An analysis of the sequences up

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12

Wu, Na, Jinlong Liu, Song Wang, and Xianguang Guo. "Comparative Analysis of Mitochondrial Genomes in Two Subspecies of the Sunwatcher Toad-Headed Agama (Phrynocephalus helioscopus): Prevalent Intraspecific Gene Rearrangements in Phrynocephalus." Genes 13, no. 2 (2022): 203. http://dx.doi.org/10.3390/genes13020203.

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Intraspecific rearrangements of mitochondrial genomes are rarely reported in reptiles, even in vertebrates. The sunwatcher toad-headed agama, Phryncoephalus helioscopus, can serve as an excellent model for investigating the dynamic mitogenome structure at intraspecific level. To date, seven subspecies of P. helioscopus are well recognized, but little is known about the mitogenomic evolution among different subspecies. In this study, complete mitogenomes of subspecies P. helioscopus varius II and P. helioscopus cameranoi were determined by next-generation sequencing, and another P. helioscopus

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13

Shapiro, A. M., M. S. Schlissel, D. Baltimore, and A. L. DeFranco. "Stimulation of kappa light-chain gene rearrangement by the immunoglobulin mu heavy chain in a pre-B-cell line." Molecular and Cellular Biology 13, no. 9 (1993): 5679–90. http://dx.doi.org/10.1128/mcb.13.9.5679-5690.1993.

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B-lymphocyte development exhibits a characteristic order of immunoglobulin gene rearrangements. Previous work has led to the hypothesis that expression of the immunoglobulin mu heavy chain induces rearrangement activity at the kappa light-chain locus. To examine this issue in more detail, we isolated five matched pairs of mu- and endogenously rearranged mu+ cell lines from the Abelson murine leukemia virus-transformed pro-B-cell line K.40. In four of the five mu+ cell lines, substantial expression of mu protein on the cell surface was observed, and this correlated with an enhanced frequency of

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14

Shapiro, A. M., M. S. Schlissel, D. Baltimore, and A. L. DeFranco. "Stimulation of kappa light-chain gene rearrangement by the immunoglobulin mu heavy chain in a pre-B-cell line." Molecular and Cellular Biology 13, no. 9 (1993): 5679–90. http://dx.doi.org/10.1128/mcb.13.9.5679.

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B-lymphocyte development exhibits a characteristic order of immunoglobulin gene rearrangements. Previous work has led to the hypothesis that expression of the immunoglobulin mu heavy chain induces rearrangement activity at the kappa light-chain locus. To examine this issue in more detail, we isolated five matched pairs of mu- and endogenously rearranged mu+ cell lines from the Abelson murine leukemia virus-transformed pro-B-cell line K.40. In four of the five mu+ cell lines, substantial expression of mu protein on the cell surface was observed, and this correlated with an enhanced frequency of

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15

Xing, Zhi-Ping, Xin Liang, Xu Wang, Hao-Yuan Hu, and Yi-Xin Huang. "Novel gene rearrangement pattern in mitochondrial genome of Ooencyrtus plautus Huang & Noyes, 1994: new gene order in Encyrtidae (Hymenoptera, Chalcidoidea)." ZooKeys 1124 (October 10, 2022): 1–21. http://dx.doi.org/10.3897/zookeys.1124.83811.

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Studies of mitochondrial genomes have a wide range of applications in phylogeny, population genetics, and evolutionary biology. In this study, we sequenced and analyzed the mitochondrial genome of Ooencyrtus plautus Huang & Noyes, 1994 (Hymenoptera, Encyrtidae). The nearly complete mitogenome of O. plautus was 15,730 bp in size, including 13 PCGs (protein-coding genes), 22 tRNAs, 2 rRNAs, and a nearly complete control region. The nucleotide composition was significantly biased toward adenine and thymine, with an A + T content of 84.6%. We used the reference sequence of Chouioia cunea and c

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16

Su, Xuechun, Deyuan Yang, Xiu Wu, Yanan Sun, Jian-Wen Qiu, and Yanjie Zhang. "Substantial mitochondrial gene order rearrangements and differential evolution rates within the family Capitellidae (Annelida)." Zoosystematics and Evolution 101, no. (3) (2025): 955–67. https://doi.org/10.3897/zse.101.144081.

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Capitellidae is a family of marine annelids commonly found in coastal to deep-sea sediments. These annelids are characterized by capillary chaetae at the anterior and long-handled hooks at the posterior part. Although mitochondrial genomes (mtgenomes) are widely used in phylogenetic analyses of invertebrates, their application is limited in many marine annelid families, particularly in Capitellidae. In this study, we obtained complete or nearly complete (except control region) mtgenomes through high-throughput sequencing of eight species across five genera of Capitellidae: <i>Barantolla</i> sp

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17

Davidyan, Yulya, Elena Parovichnikova, Vadim Surin, and Valeryi Savchenko. "Different Subclones of Adult Acute Lymphoblastic Leukemia Detected by Clonal Igh and TCR Markers Behave Differently during Remission and at Relapse." Blood 112, no. 11 (2008): 4860. http://dx.doi.org/10.1182/blood.v112.11.4860.4860.

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Abstract INTRODUCTION. Immunoglobulin (Ig) and T-cell receptor (TCR) gene rearrangements are excellent patient–specific targets for the detection of minimal residual disease (MRD) in acute lymphoblastic leukemia (ALL). However they might be unstable during the disease course. False-negative results due to clonal evolution are the major disadvantage of using Ig/TCR gene rearrangements as PCR targets for MRD detection. In order to minimize false-negative results, it is necessary to use more PCR targets for MRD monitoring. PATIENTS AND METHODS. Bone marrow samples of 34 ALL patients (27 B-ALL, 7

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Panzer-Grümayer, E. Renate, Karin Fasching, Simon Panzer, et al. "Nondisjunction of chromosomes leading to hyperdiploid childhood B-cell precursor acute lymphoblastic leukemia is an early event during leukemogenesis." Blood 100, no. 1 (2002): 347–49. http://dx.doi.org/10.1182/blood-2002-01-0144.

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Abstract A hyperdiploid karyotype is found in 30% of B-cell precursor acute lymphoblastic leukemias in childhood. The time of nondisjunction of chromosomes leading to hyperdiploidy during leukemogenesis is unknown. We used the 3 clonotypic immunoglobulin heavy chain (IgH) gene rearrangements as molecular markers for each of the 3 chromosomes 14 in a case with hyperdiploid acute lymphoblastic leukemia to define the order of events—namely, somatic recombination and nondisjunction of chromosomes—during leukemia development. A partial sequence homology of the incomplete DJH rearrangement with 1 of

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Mehr, Ramit, Michele Shannon, and Samuel Litwin. "Models for Antigen Receptor Gene Rearrangement. I. Biased Receptor Editing in B Cells: Implications for Allelic Exclusion." Journal of Immunology 163, no. 4 (1999): 1793–98. http://dx.doi.org/10.4049/jimmunol.163.4.1793.

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Abstract Recent evidence suggests that lymphocyte Ag receptor gene rearrangement does not always stop after the expression of the first productively rearranged receptor. Light chain gene rearrangement in B cells, and α-chain rearrangement in T cells can continue, which raises the question: how is allelic exclusion maintained, if at all, in the face of continued rearrangement? In this and the accompanying paper, we present comprehensive models of Ag receptor gene rearrangement and the interaction of this process with clonal selection. Our B cell model enables us to reconcile observations on the

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20

Roden, Anja C. "The Role of Gene Fusions in Thymic Epithelial Tumors." Cancers 15, no. 23 (2023): 5596. http://dx.doi.org/10.3390/cancers15235596.

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Thymic epithelial tumors (TET) are rare and large molecular studies are therefore difficult to perform. However, institutional case series and rare multi-institutional studies have identified a number of interesting molecular aberrations in TET, including gene fusions in a subset of these tumors. These gene fusions can aid in the diagnosis, shed light on the pathogenesis of a subset of tumors, and potentially may provide patients with the opportunity to undergo targeted therapy or participation in clinical trials. Gene fusions that have been identified in TET include MAML2 rearrangements in 50

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Tie, Li-Jun, Long-Jun Gu, and Li-Min Jiang. "Tandem Application of Flow Cytometry and Polymerase Chain Reaction for Choice Targets of Minimal Residual Disease in Childhood Acute Lymphoblastic Leukemia." Blood 106, no. 11 (2005): 4491. http://dx.doi.org/10.1182/blood.v106.11.4491.4491.

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Abstract Objective In order to allow monitoring virtually all patients with childhood acute lymphoblastic leukemia for minimal residual disease in resource-poor countries or patient population. Methods Choice targets of minimal residual disease using tandem application of multi-parameter flow cytometry with various combinations of monoclonal antibodies for leukemia-associated immunophenotypes and polymerase chain reaction (PCR) of clonal T-cell receptor or immunoglobulin gene rearrangements was performed in 122 patients with newly diagnosis acute lymphoblastic leukemia on protocol ALL-XH-99. R

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Minton, Russell L., Cruz Marco A. Martinez, Mark L. Farman, and Kathryn E. Perez. "Two complete mitochondrial genomes from Praticolella mexicana Perez, 2011 (Polygyridae) and gene order evolution in Helicoidea (Mollusca, Gastropoda)." ZooKeys 626 (October 25, 2016): 137–54. https://doi.org/10.3897/zookeys.626.9633.

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Helicoidea is a diverse group of land snails with a global distribution. While much is known regarding the relationships of helicoid taxa, comparatively little is known about the evolution of the mitochondrial genome in the superfamily. We sequenced two complete mitochondrial genomes from Praticolella mexicana Perez, 2011 representing the first such data from the helicoid family Polygyridae, and used them in an evolutionary analysis of mitogenomic gene order. We found the mitochondrial genome of P. mexicana to be 14,008 bp in size, possessing the typical 37 metazoan genes. Multiple alternate s

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Lebedeva, Svetlana, Elena Zerkalenkova, Olga Soldatkina, et al. "Novel KMT2A Partner Gene NUTM2A Revealed By Anchored Multiplex PCR in ALL." Blood 134, Supplement_1 (2019): 5203. http://dx.doi.org/10.1182/blood-2019-126602.

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Objectives Chromosomal rearrangements of the human MLL/KMT2A gene are associated with infant, pediatric and adult acute leukemias. Such rearrangements are more frequent in infants, in whom they are found in 60% - 80% of acute lymphoblastic leukemias (ALL). KMT2A-r group itself is genetically heterogeneous. KMT2A-r can occur with at least 94 partner genes previously described in «THE MLL RECOMBINOME <…> IN 2017». Detection of KMT2A-r is an essential part of AL initial diagnostics. Also, the accurate detection of all KMT2A-r types is crucial in order to perform minimal residual disease (MR

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Landsburg, Daniel J., Sunita Dwivedy Nasta, Jakub Svoboda, Jennifer JD Morrissette, and Stephen J. Schuster. "“Double-Hit” Cytogenetic Status Is Not Predicted By Baseline Clinicopathologic Characteristics and Is Highly Associated With Overall Survival In B Cell Lymphoma Patients." Blood 122, no. 21 (2013): 4338. http://dx.doi.org/10.1182/blood.v122.21.4338.4338.

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Abstract Background “Double-Hit” (DH) lymphomas are most commonly defined as B cell lymphomas demonstrating a MYC gene rearrangement and additional rearrangement(s) involving BCL2 and/or BCL6. DH lymphomas respond poorly to standard immunochemotherapy regimens, often prompting the use of more intensive treatments. DH gene rearrangements can be identified through metaphase cytogenetic testing or more sensitive fluorescence in situ hybridization (FISH) on diagnostic tissue specimens, although these studies are not routinely performed. Here, we analyze a cohort of B cell lymphoma patients to dete

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Donaldson, Brendan, Daniel A. F. Villagomez, and W. Allan King. "Classical, Molecular, and Genomic Cytogenetics of the Pig, a Clinical Perspective." Animals 11, no. 5 (2021): 1257. http://dx.doi.org/10.3390/ani11051257.

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The chromosomes of the domestic pig (Sus scrofa domesticus) are known to be prone to reciprocal chromosome translocations and other balanced chromosome rearrangements with concomitant fertility impairment of carriers. In response to the remarkable prevalence of chromosome rearrangements in swine herds, clinical cytogenetics laboratories have been established in several countries in order to screen young boars for chromosome rearrangements prior to service. At present, clinical cytogenetics laboratories typically apply classical cytogenetics techniques such as giemsa-trypsin (GTG)-banding to pr

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Kong, Xiaoyu, Xiaoli Dong, Yanchun Zhang, Wei Shi, Zhongming Wang, and Ziniu Yu. "A novel rearrangement in the mitochondrial genome of tongue sole, Cynoglossus semilaevis: control region translocation and a tRNA gene inversion." Genome 52, no. 12 (2009): 975–84. http://dx.doi.org/10.1139/g09-069.

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The organization of fish mitochondrial genomes (mitogenomes) is quite conserved, usually with the heavy strand encoding 12 of 13 protein-coding genes and 14 of 22 tRNA genes, and the light strand encoding ND6 and the remaining 8 tRNA genes. Currently, there are only a few reports on gene reorganization of fish mitogenomes, with only two types of rearrangements (shuffling and translocation) observed. No gene inversion has been detected in approximately 420 complete fish mitogenomes available so far. Here we report a novel rearrangement in the mitogenome of Cynoglossus semilaevis (Cynoglossinae,

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Shaskolskiy, Boris, Dmitry Kravtsov, Ilya Kandinov, Ekaterina Dementieva, and Dmitry Gryadunov. "Genomic Diversity and Chromosomal Rearrangements in Neisseria gonorrhoeae and Neisseria meningitidis." International Journal of Molecular Sciences 23, no. 24 (2022): 15644. http://dx.doi.org/10.3390/ijms232415644.

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Chromosomal rearrangements in N. gonorrhoeae and N. meningitidis were studied with the determination of mobile elements and their role in rearrangements. The results of whole-genome sequencing and de novo genome assembly for 50 N. gonorrhoeae isolates collected in Russia were compared with 96 genomes of N. gonorrhoeae and 138 genomes of N. meningitidis from the databases. Rearrangement events with the determination of the coordinates of syntenic blocks were analyzed using the SibeliaZ software v.1.2.5, the minimum number of events that allow one genome to pass into another was calculated using

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Bochkareva, Olga O., Natalia O. Dranenko, Elena S. Ocheredko, et al. "Genome rearrangements and phylogeny reconstruction in Yersinia pestis." PeerJ 6 (March 27, 2018): e4545. http://dx.doi.org/10.7717/peerj.4545.

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Genome rearrangements have played an important role in the evolution of Yersinia pestis from its progenitor Yersinia pseudotuberculosis. Traditional phylogenetic trees for Y. pestis based on sequence comparison have short internal branches and low bootstrap supports as only a small number of nucleotide substitutions have occurred. On the other hand, even a small number of genome rearrangements may resolve topological ambiguities in a phylogenetic tree. We reconstructed phylogenetic trees based on genome rearrangements using several popular approaches such as Maximum likelihood for Gene Order a

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Chen, Jianshu, Wei Chen, and Yudong Li. "Conservation of gene order in human microRNA-neighboring regions." Genome 55, no. 09 (2012): 701–4. http://dx.doi.org/10.1139/g2012-055.

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The biological function and evolution of microRNAs (miRNAs), an important class of noncoding regulatory genes, have attracted wide interest. However, their evolutionary impact on gene order rearrangements remains unknown. We examined the gene-order stability of miRNA-neighboring regions by a comparative human–mouse genomic analysis and found that the neighboring genes of human miRNAs tend to have a conserved gene order. This observation cannot be attributed to the functional bias of neighboring genes, and is a unique characteristic of miRNAs but not other noncoding RNAs. Our findings suggest t

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Gubb, D., M. Ashburner, J. Roote, and T. Davis. "A novel transvection phenomenon affecting the white gene of Drosophila melanogaster." Genetics 126, no. 1 (1990): 167–76. http://dx.doi.org/10.1093/genetics/126.1.167.

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Abstract The zeste mutation of Drosophila melanogaster suppresses the expression of white genes in the eye. This suppression is normally dependent on there being two copies of w+ located close to each other in the genome--they may either be in cis (as in a tandem duplication of w+) or in trans, i.e. on homologous chromosomes. Duplicated w+ genes carried by a giant transposing element, TE146(Z), are suppressed by z whether they are in direct (tandem) or inverted order. The tandem form of the TE is very sensitive to a rearrangement on the homologous chromosome--many rearrangements with breakpoin

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Kwon, Mi, Ismael Buño, Javier Anguita, et al. "Correlation between Flow Cytometry Immunophenotyping, Chimerism Quantification and IGH Gene Rearrangement Analysis in Disease Associated Leukocyte Lineages after Stem Cell Transplantation in an ALL Patient." Blood 108, no. 11 (2006): 4437. http://dx.doi.org/10.1182/blood.v108.11.4437.4437.

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Abstract INTRODUCTION: Oligocloanality is a phenomenon shown in up to 40% of patients with childhood B-lineage acute lymphoblastic leukemia (ALL), and it might be associated with a poorer prognosis. OBJECTIVE: To present a case of oligoclonality based on the detection of IGH gene rearrangements in a patient with ALL and the correlation of the results with those of flow cytometry immunophenotyping and chimerism quantification. PATIENT AND METHODS: 26 years old female, pre-B ALL diagnosed in her childhood, in relapse after autologous and allogeneic HLA-identical unrelated stem cell transplantati

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Carico, Zachary Mark, Baojun Zhang, Kingshuk Choudhury, Yuan Zhuang, and Michael S. Krangel. "Mechanisms that diversify an otherwise intrinsically processive Trav-Traj recombination program." Journal of Immunology 198, no. 1_Supplement (2017): 202.12. http://dx.doi.org/10.4049/jimmunol.198.supp.202.12.

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Abstract In DP thymocytes, the Tcra locus undergoes multiple rounds of V-J rearrangement in order to generate a functional TCRα chain. While Traj segment usage is strictly ordered from 5′ to 3′ as rearrangement proceeds, it is unclear to what degree Trav usage is also ordered. To test this, we assessed the Trav-Traj combinatorial repertoire in murine DP thymocytes using 5′ RACE followed by paired end sequencing. In 129Sv/J WT thymocytes, we found a clear bias toward proximal-proximal and distal-distal joins, but Trav-Traj pairings were highly diverse, even in primary V-J rearrangement. However

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Sirotinina, E., E. Romanova, and D. Sherbakov. "Dynamics of gene order rearrangements in mitochondrial genomes of Baikalian amphipods." Limnology and Freshwater Biology, no. 4 (2020): 818–19. http://dx.doi.org/10.31951/2658-3518-2020-a-4-818.

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Sinkora, Marek, Katerina Stepanova, and Jana Sinkorova. "Consequences of the different order of immunoglobulin gene rearrangements in swine." Developmental & Comparative Immunology 126 (January 2022): 104196. http://dx.doi.org/10.1016/j.dci.2021.104196.

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Brito, Klairton Lima, Géraldine Jean, Guillaume Fertin, Andre Rodrigues Oliveira, Ulisses Dias, and Zanoni Dias. "Sorting by Genome Rearrangements on Both Gene Order and Intergenic Sizes." Journal of Computational Biology 27, no. 2 (2020): 156–74. http://dx.doi.org/10.1089/cmb.2019.0293.

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36

Suyama, Mikita, and Peer Bork. "Evolution of prokaryotic gene order: genome rearrangements in closely related species." Trends in Genetics 17, no. 1 (2001): 10–13. http://dx.doi.org/10.1016/s0168-9525(00)02159-4.

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Persiani, D. M., J. Durdik, and E. Selsing. "Active lambda and kappa antibody gene rearrangement in Abelson murine leukemia virus-transformed pre-B cell lines." Journal of Experimental Medicine 165, no. 6 (1987): 1655–74. http://dx.doi.org/10.1084/jem.165.6.1655.

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The two Abelson murine leukemia virus (A-MuLV)-transformed cell lines, BM18-4 and ABC-1, undergo immunoglobulin L-chain gene recombination during passage in tissue culture. BM18-4 cells are capable of kappa gene recombination, whereas ABC-1 cells are capable of both kappa and lambda gene recombination. The expression of H chains is apparently not necessary for continuing L chain gene recombination in either of these cells, although H-chain expression may have been involved in the initiation of L-chain gene recombination. All ABC-1 cells that have lambda gene rearrangements also display recombi

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Vaughan, Andrew T., Rebecca Wright, and Katrina Slemmons. "Estradiol Induces Gene Proximity and MLL-MLLT3 Fusion In An AICDA-Mediated Pathway." Blood 122, no. 21 (2013): 806. http://dx.doi.org/10.1182/blood.v122.21.806.806.

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Abstract Translocation breakpoints involving the MLL gene linked to Infant Acute Leukemia (IAL) and therapy related acute leukemia (tAL) are tightly clustered between MLL exons 8 and 12. Exon 12 also marks the location of a well-described cleavage hotspot that is synchronous with a sharp decline in total MLL fusions observed in clinical samples. Though multiple MLL fusion partners have been identified, fusions to MLLT3 (AF9) and AFF1 (AF4) comprise 56% of all clinical rearrangements so far assayed. Epidemiological data has linked maternal exposure to birth control formulations with an increase

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39

Raghavachar, A., E. Thiel, and CR Bartram. "Analyses of phenotype and genotype in acute lymphoblastic leukemias at first presentation and in relapse." Blood 70, no. 4 (1987): 1079–83. http://dx.doi.org/10.1182/blood.v70.4.1079.1079.

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Abstract As a clue to the cellular origin of leukemic populations in relapse we analyzed 11 cases of acute lymphoblastic leukemia (ALL) by immunological and molecular genetic approaches. Blast cells obtained from both initial diagnosis and relapse were immunophenotyped using a variety of monoclonal antibodies; simultaneously we hybridized Southern blots of respective cell samples to immunoglobulin (Ig) heavy and light chain as well as to T-cell receptor beta-chain (T beta) sequences. While similar phenotypes were observed in both states of nine cases, comparison of Ig gene rearrangements revea

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40

Raghavachar, A., E. Thiel, and CR Bartram. "Analyses of phenotype and genotype in acute lymphoblastic leukemias at first presentation and in relapse." Blood 70, no. 4 (1987): 1079–83. http://dx.doi.org/10.1182/blood.v70.4.1079.bloodjournal7041079.

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As a clue to the cellular origin of leukemic populations in relapse we analyzed 11 cases of acute lymphoblastic leukemia (ALL) by immunological and molecular genetic approaches. Blast cells obtained from both initial diagnosis and relapse were immunophenotyped using a variety of monoclonal antibodies; simultaneously we hybridized Southern blots of respective cell samples to immunoglobulin (Ig) heavy and light chain as well as to T-cell receptor beta-chain (T beta) sequences. While similar phenotypes were observed in both states of nine cases, comparison of Ig gene rearrangements revealed clona

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41

Biggerstaff, Julie A. Sanford, Weihui Liu, Caron D. Glotzbach, and Lisa G. Shaffer. "Development and Clinical Validation of a “Home-Brew” Dual-Color FISH Probe Assay To Differentiate between ELL and ENL Gene Rearrangements in Leukemia." Blood 106, no. 11 (2005): 3268. http://dx.doi.org/10.1182/blood.v106.11.3268.3268.

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Abstract Patients with t(11;19) leukemias have one of two different translocations resulting in gene rearrangement with the MLL gene on 11q23. The ELL (eleven-nineteen lysine-rich leukemia) gene at 19p13.1, is rearranged in individuals with t(11;19) and acute myeloid leukemia, while the ENL (eleven-nineteen leukemia) gene at 19p13.3, is rearranged most frequently in those patients with t(11;19) and B-cell acute lymphoid leukemia. However, AML and rare T-cell ALL patients have been reported with the ENL gene rearrangement. At the cytogenetic level of resolution, it is not always possible to dis

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Unger, Kristian, Johannes Wienberg, Andrew Riches, et al. "Novel gene rearrangements in transformed breast cells identified by high-resolution breakpoint analysis of chromosomal aberrations." Endocrine-Related Cancer 17, no. 1 (2010): 87–98. http://dx.doi.org/10.1677/erc-09-0065.

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Chromosomal copy number alterations and chromosomal rearrangements are frequent mutations in human cancer. Unlike copy number alterations, little is known about the role and occurrence of chromosomal rearrangements in breast cancer. This may be due to the fact that chromosome-based breakpoint analysis is widely restricted to cultured cells. In order to identify gene rearrangements in breast cancer, we studied the chromosomal breakpoints in radiation-transformed epithelial breast cell lines using a high-resolution array-based approach using 1 Mb bacterial artificial chromosome (BAC) arrays. The

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Lennon, G. G., and R. P. Perry. "The temporal order of appearance of transcripts from unrearranged and rearranged Ig genes in murine fetal liver." Journal of Immunology 144, no. 5 (1990): 1983–87. http://dx.doi.org/10.4049/jimmunol.144.5.1983.

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Abstract The developmental time course of RNA transcribed from unrearranged (germ-line) and rearranged Ig genes in murine fetal liver was determined by a quantitative Northern blot analysis. Sterile Cmu transcripts and germ-line VH transcripts are detectable as early as day 14, whereas significant amounts of rearranged VDJCmu H chain transcripts do not appear until days 16 to 17. The sterile Cmu transcripts continuously increase in abundance throughout fetal development, in contrast to the germ-line VH transcripts, which decrease abruptly after day 16. Transcripts of germ-line and rearranged C

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Nagy, Naya, and Paul Hodor. "Chromosomal gene order defines several structural classes of Staphylococcus epidermidis genomes." PLOS ONE 19, no. 10 (2024): e0311520. http://dx.doi.org/10.1371/journal.pone.0311520.

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The original methodology for describing the pangenome of a prokaryotic species is based on modeling genomes as unordered sets of genes. More recent findings have underlined the importance of considering the ordering of genes along the genetic material as well, when making comparisons among genomes. To further investigate the benefits of gene order when describing genomes of a given species, we applied two distance metrics on a dataset of 84 genomes of Staphylococcus epidermidis. The first metric, GeLev, depends on the order of genes and is a derivative of the Levenshtein distance. The second,

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Ye, Fei, Hu Li, and Qiang Xie. "Mitochondrial Genomes from Two Specialized Subfamilies of Reduviidae (Insecta: Hemiptera) Reveal Novel Gene Rearrangements of True Bugs." Genes 12, no. 8 (2021): 1134. http://dx.doi.org/10.3390/genes12081134.

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Reduviidae, a hyper-diverse family, comprise 25 subfamilies with nearly 7000 species and include many natural enemies of crop pests and vectors of human disease. To date, 75 mitochondrial genomes (mitogenomes) of assassin bugs from only 11 subfamilies have been reported. The limited sampling of mitogenome at higher categories hinders a deep understanding of mitogenome evolution and reduviid phylogeny. In this study, the first mitogenomes of Holoptilinae (Ptilocnemus lemur) and Emesinae (Ischnobaenella hainana) were sequenced. Two novel gene orders were detected in the newly sequenced mitogenom

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Veltroni, Marinella, Maddalena Paganin, Chiara Frasson, et al. "Clonal Profile Analysis of Leukemic Progenitors and Diagnosis Blast Cells in Pediatric B-Cell Precursor Acute Lymphoblastic Leukemia." Blood 112, no. 11 (2008): 4879. http://dx.doi.org/10.1182/blood.v112.11.4879.4879.

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Abstract Recent studies suggest that the majority of malignant cells found in B-cell precursor acute lymphoblastic leukemia (BCP-ALL) arise from a rare population of leukemic progenitors. Little information is available on the presence of clonal rearrangements in cells at the stage of early precursor. To address this issue we analyzed clonality profile of early leukemic precursors sorted by flow-cytometry. Leukemic cells were obtained from bone marrow samples collected at diagnosis from 6 patients with childhood BCP-ALL. Furthermore, bone marrow cells were collected from 3 healthy children who

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Liu, Qiaoqiao, Jia He, Fan Song, Li Tian, Wanzhi Cai, and Hu Li. "Positive Correlation of the Gene Rearrangements and Evolutionary Rates in the Mitochondrial Genomes of Thrips (Insecta: Thysanoptera)." Insects 13, no. 7 (2022): 585. http://dx.doi.org/10.3390/insects13070585.

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Extensive gene rearrangement is characteristic in the mitogenomes of thrips (Thysanoptera), but the historical process giving rise to the contemporary gene rearrangement pattern remains unclear. To better understand the evolutionary processes of gene rearrangement in the mitogenomes of thrips, we sequenced the mitogenome of the banded thrip species Aeolothrips xinjiangensis. First, we found a novel mitochondrial gene order in this species. This mitogenome is 16,947 bp in length and encodes the typical 37 coding genes (13 protein-coding genes, 22 tRNA genes, and two rRNA genes) of insects. The

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48

Walter, M. A., H. M. Dosch, and D. W. Cox. "A deletion map of the human immunoglobulin heavy chain variable region." Journal of Experimental Medicine 174, no. 2 (1991): 335–49. http://dx.doi.org/10.1084/jem.174.2.335.

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Analysis of VH gene segments deleted in the process of immunoglobulin heavy chain (IGH) variable region assembly in three series of monoclonal B cell lines has been used to determine the human VH region organization. A deletion map of the relative positions of 21 different VH gene segments has been determined. The characterization of B cell lines from three unrelated adults of two racial groups yielded the same relative VH gene segment order, suggesting that the overall order of VH genes in the normal population is constant. This VH gene segment order was consistent with what we had previously

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49

Pereira, Sérgio Luiz. "Mitochondrial genome organization and vertebrate phylogenetics." Genetics and Molecular Biology 23, no. 4 (2000): 745–52. http://dx.doi.org/10.1590/s1415-47572000000400008.

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With the advent of DNA sequencing techniques the organization of the vertebrate mitochondrial genome shows variation between higher taxonomic levels. The most conserved gene order is found in placental mammals, turtles, fishes, some lizards and Xenopus. Birds, other species of lizards, crocodilians, marsupial mammals, snakes, tuatara, lamprey, and some other amphibians and one species of fish have gene orders that are less conserved. The most probable mechanism for new gene rearrangements seems to be tandem duplication and multiple deletion events, always associated with tRNA sequences. Some n

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Martín-Jiménez, Patricia, Miguel Alcoceba, Maria E. Sarasquete, et al. "Molecular Characterization in Hairy Cell Leukemia (HCL): Rearrangement Analysis of Heavy Chain in Immunoglobulin Genes (IgH)." Blood 104, no. 11 (2004): 4798. http://dx.doi.org/10.1182/blood.v104.11.4798.4798.

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Abstract Introduction: Currently, the origin of the HCL tumor clone is believed to be marginal zone B-cell that has previously contacted the antigen, and has therefore undergone somatic hypermutation (SHM). However, the low frequency of HCL has hamper the investigation of IgH rearrangements in large series of patients and whether preferential uses of specific VDJ segments or non-functional rearrangements exist. Aims: To characterize IgH gene rearrangements in 25 HCL patients in order to ascertain the frequency and characteristics of both incomplete DJH and complete VDJH rearrangements and to d

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