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Table of Contents

October 2020

Compared to European subspecies, honey bees adapted to the lowlands of southern and eastern Africa (Apis mellifera scutellata) preferentially forage for pollen over nectar and store little honey for winter. Foraging behavior is one of many divergently evolved traits that may contribute to a natural climatic range limit for scutellata-European hybrid honey bees, which spread rapidly out of Brazil in the 1950s and today dominate across tropical (but not temperate) regions in the Americas. See Calfee et al.

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Image Credit: Kathy Keatley Garvey

Editorial

By what name shall I call thee?

Gregory S. Barsh, Gregory P. Copenhaver

Research Articles

Phenotype-genotype comorbidity analysis of patients with rare disorders provides insight into their pathological and molecular bases

Elena Díaz-Santiago, Fernando M. Jabato, Elena Rojano, Pedro Seoane, Florencio Pazos, James R. Perkins, Juan A. G. Ranea

Disentangling the determinants of transposable elements dynamics in vertebrate genomes using empirical evidences and simulations

Yann Bourgeois, Robert P. Ruggiero, Imtiyaz Hariyani, Stéphane Boissinot

Selection for ancient periodic motifs that do not impart DNA bending

Aletheia Atzinger, Jeffrey G. Lawrence

Human ABCB1 with an ABCB11-like degenerate nucleotide binding site maintains transport activity by avoiding nucleotide occlusion

Katalin Goda, Yaprak Dönmez-Cakil, Szabolcs Tarapcsák, Gábor Szalóki, Dániel Szöllősi, Zahida Parveen, Dóra Türk, Gergely Szakács, Peter Chiba, Thomas Stockner

Diversified regulation of circadian clock gene expression following whole genome duplication

Alexander C. West, Marianne Iversen, Even H. Jørgensen, Simen R. Sandve, David G. Hazlerigg, Shona H. Wood

A cautionary note on the use of unsupervised machine learning algorithms to characterise malaria parasite population structure from genetic distance matrices

James A. Watson, Aimee R. Taylor, Elizabeth A. Ashley, Arjen Dondorp, Caroline O. Buckee, Nicholas J. White, Chris C. Holmes

Novel loci for childhood body mass index and shared heritability with adult cardiometabolic traits

Suzanne Vogelezang, Jonathan P. Bradfield, Tarunveer S. Ahluwalia, John A. Curtin, Timo A. Lakka, Niels Grarup, Markus Scholz, Peter J. van der Most, Claire Monnereau, Evie Stergiakouli, Anni Heiskala, Momoko Horikoshi, Iryna O. Fedko, Natalia Vilor-Tejedor, Diana L. Cousminer, Marie Standl, Carol A. Wang, Jorma Viikari, Frank Geller, Carmen Íñiguez, Niina Pitkänen, Alessandra Chesi, Jonas Bacelis, Loic Yengo, Maties Torrent, Ioanna Ntalla, Øyvind Helgeland, Saskia Selzam, Judith M. Vonk, Mohammed H. Zafarmand, Barbara Heude, Ismaa Sadaf Farooqi, Akram Alyass, Robin N. Beaumont, Christian T. Have, Peter Rzehak, Jose Ramon Bilbao, Theresia M. Schnurr, Inês Barroso, Klaus Bønnelykke, Lawrence J. Beilin, Lisbeth Carstensen, Marie-Aline Charles, Bo Chawes, Karine Clément, Ricardo Closa-Monasterolo, Adnan Custovic, Johan G. Eriksson, Joaquin Escribano, Maria Groen-Blokhuis, Veit Grote, Dariusz Gruszfeld, Hakon Hakonarson, Torben Hansen, Andrew T. Hattersley, Mette Hollensted, Jouke-Jan Hottenga, Elina Hyppönen, Stefan Johansson, Raimo Joro, Mika Kähönen, Ville Karhunen, Wieland Kiess, Bridget A. Knight, Berthold Koletzko, Andreas Kühnapfel, Kathrin Landgraf, Jean-Paul Langhendries, Terho Lehtimäki, Jaakko T. Leinonen, Aihuali Li, Virpi Lindi, Estelle Lowry, Mariona Bustamante, Carolina Medina-Gomez, Mads Melbye, Kim F. Michaelsen, Camilla S. Morgen, Trevor A. Mori, Tenna R. H. Nielsen, Harri Niinikoski, Albertine J. Oldehinkel, Katja Pahkala, Kalliope Panoutsopoulou, Oluf Pedersen, Craig E. Pennell, Christine Power, Sijmen A. Reijneveld, Fernando Rivadeneira, Angela Simpson, Peter D. Sly, Jakob Stokholm, Kook K. Teo, Elisabeth Thiering, Nicholas J. Timpson, André G. Uitterlinden, Catharina E. M. van Beijsterveldt, Barbera D. C. van Schaik, Marc Vaudel, Elvira Verduci, Rebecca K. Vinding, Mandy Vogel, Eleftheria Zeggini, Sylvain Sebert, Mads V. Lind, Christopher D. Brown, Loreto Santa-Marina, Eva Reischl, Christine Frithioff-Bøjsøe, David Meyre, Eleanor Wheeler, Ken Ong, Ellen A. Nohr, Tanja G. M. Vrijkotte, Gerard H. Koppelman, Robert Plomin, Pål R. Njølstad, George D. Dedoussis, Philippe Froguel, Thorkild I. A. Sørensen, Bo Jacobsson, Rachel M. Freathy, Babette S. Zemel, Olli Raitakari, Martine Vrijheid, Bjarke Feenstra, Leo-Pekka Lyytikäinen, Harold Snieder, Holger Kirsten, Patrick G. Holt, Joachim Heinrich, Elisabeth Widén, Jordi Sunyer, Dorret I. Boomsma, Marjo-Riitta Järvelin, Antje Körner, George Davey Smith, Jens-Christian Holm, Mustafa Atalay, Clare Murray, Hans Bisgaard, Mark I. McCarthy, Early Growth Genetics Consortium, Vincent W. V. Jaddoe, Struan F. A. Grant, Janine F. Felix

The DNA methylome of human sperm is distinct from blood with little evidence for tissue-consistent obesity associations

Fredrika Åsenius, Tyler J. Gorrie-Stone, Ama Brew, Yasmin Panchbhaya, Elizabeth Williamson, Leonard C. Schalkwyk, Vardhman K. Rakyan, Michelle L. Holland, Sarah J. Marzi, David J. Williams

Quantitative analysis questions the role of MeCP2 as a global regulator of alternative splicing

Kashyap Chhatbar, Justyna Cholewa-Waclaw, Ruth Shah, Adrian Bird, Guido Sanguinetti

Chromosome number evolves at equal rates in holocentric and monocentric clades

Sarah N. Ruckman, Michelle M. Jonika, Claudio Casola, Heath Blackmon

Comparing DNA replication programs reveals large timing shifts at centromeres of endocycling cells in maize roots

Emily E. Wear, Jawon Song, Gregory J. Zynda, Leigh Mickelson-Young, Chantal LeBlanc, Tae-Jin Lee, David O. Deppong, George C. Allen, Robert A. Martienssen, Matthew W. Vaughn, Linda Hanley-Bowdoin, William F. Thompson

A high-throughput CRISPR interference screen for dissecting functional regulators of GPCR/cAMP signaling

Khairunnisa Mentari Semesta, Ruilin Tian, Martin Kampmann, Mark von Zastrow, Nikoleta G. Tsvetanova

A single Ho-induced double-strand break at the MAT locus is lethal in Candida glabrata

Laetitia Maroc, Youfang Zhou-Li, Stéphanie Boisnard, Cécile Fairhead

A Rad51-independent pathway promotes single-strand template repair in gene editing

Danielle N. Gallagher, Nhung Pham, Annie M. Tsai, Abigail N. Janto, Jihyun Choi, Grzegorz Ira, James E. Haber

Mesenchyme-derived IGF2 is a major paracrine regulator of pancreatic growth and function

Constanze M. Hammerle, Ionel Sandovici, Gemma V. Brierley, Nicola M. Smith, Warren E. Zimmer, Ilona Zvetkova, Haydn M. Prosser, Yoichi Sekita, Brian Y. H. Lam, Marcella Ma, Wendy N. Cooper, Antonio Vidal-Puig, Susan E. Ozanne, Gema Medina-Gómez, Miguel Constância

Mutation of NEKL-4/NEK10 and TTLL genes suppress neuronal ciliary degeneration caused by loss of CCPP-1 deglutamylase function

Kade M. Power, Jyothi S. Akella, Amanda Gu, Jonathon D. Walsh, Sebastian Bellotti, Margaret Morash, Winnie Zhang, Yasmin H. Ramadan, Nicole Ross, Andy Golden, Harold E. Smith, Maureen M. Barr, Robert O’Hagan

The Ccr4-Not complex regulates TORC1 signaling and mitochondrial metabolism by promoting vacuole V-ATPase activity

Hongfeng Chen, P. Winston Miller, Daniel L. Johnson, R. Nicholas Laribee

Selection and hybridization shaped the rapid spread of African honey bee ancestry in the Americas

Erin Calfee, Marcelo Nicolás Agra, María Alejandra Palacio, Santiago R. Ramírez, Graham Coop

Predominance of positive epistasis among drug resistance-associated mutations in HIV-1 protease

Tian-hao Zhang, Lei Dai, John P. Barton, Yushen Du, Yuxiang Tan, Wenwen Pang, Arup K. Chakraborty, James O. Lloyd-Smith, Ren Sun

Evaluation of both exonic and intronic variants for effects on RNA splicing allows for accurate assessment of the effectiveness of precision therapies

Anya T. Joynt, Taylor A. Evans, Matthew J. Pellicore, Emily F. Davis-Marcisak, Melis A. Aksit, Alice C. Eastman, Shivani U. Patel, Kathleen C. Paul, Derek L. Osorio, Alyssa D. Bowling, Calvin U. Cotton, Karen S. Raraigh, Natalie E. West, Christian A. Merlo, Garry R. Cutting, Neeraj Sharma

A new domestic cat genome assembly based on long sequence reads empowers feline genomic medicine and identifies a novel gene for dwarfism

Reuben M. Buckley, Brian W. Davis, Wesley A. Brashear, Fabiana H. G. Farias, Kei Kuroki, Tina Graves, LaDeana W. Hillier, Milinn Kremitzki, Gang Li, Rondo P. Middleton, Patrick Minx, Chad Tomlinson, Leslie A. Lyons, William J. Murphy, Wesley C. Warren

Related Articles

Genetically predicted telomere length is associated with clonal somatic copy number alterations in peripheral leukocytes

Derek W. Brown, Shu-Hong Lin, Po-Ru Loh, Stephen J. Chanock, Sharon A. Savage, Mitchell J. Machiela

Effect of H2A.Z deletion is rescued by compensatory mutations in Fusarium graminearum

Zhenhui Chen, Enric Zehraoui, Anna K. Atanasoff-Kardjalieff, Joseph Strauss, Lena Studt, Nadia Ponts

A fast and scalable framework for large-scale and ultrahigh-dimensional sparse regression with application to the UK Biobank

Junyang Qian, Yosuke Tanigawa, Wenfei Du, Matthew Aguirre, Chris Chang, Robert Tibshirani, Manuel A. Rivas, Trevor Hastie

Modeling epistasis in mice and yeast using the proportion of two or more distinct genetic backgrounds: Evidence for “polygenic epistasis”

Christoph D. Rau, Natalia M. Gonzales, Joshua S. Bloom, Danny Park, Julien Ayroles, Abraham A. Palmer, Aldons J. Lusis, Noah Zaitlen

Tissue-specific isoforms of the single C. elegans Ryanodine receptor gene unc-68 control specific functions

Filipe Marques, Saurabh Thapliyal, Avelino Javer, Priyanka Shrestha, André E. X. Brown, Dominique A. Glauser

Estimating indirect parental genetic effects on offspring phenotypes using virtual parental genotypes derived from sibling and half sibling pairs

Liang-Dar Hwang, Justin D. Tubbs, Justin Luong, Mischa Lundberg, Gunn-Helen Moen, Geng Wang, Nicole M. Warrington, Pak C. Sham, Gabriel Cuellar-Partida, David M. Evans

Insulin signaling represents a gating mechanism between different memory phases in Drosophila larvae

Melanie Eschment, Hanna R. Franz, Nazlı Güllü, Luis G. Hölscher, Ko-Eun Huh, Annekathrin Widmann

DOT-1.1-dependent H3K79 methylation promotes normal meiotic progression and meiotic checkpoint function in C. elegans

Laura I. Lascarez-Lagunas, Esther Herruzo, Alla Grishok, Pedro A. San-Segundo, Mónica P. Colaiácovo

Dual function of perivascular fibroblasts in vascular stabilization in zebrafish

Arsheen M. Rajan, Roger C. Ma, Katrinka M. Kocha, Dan J. Zhang, Peng Huang

Function of multiple sclerosis-protective HLA class I alleles revealed by genome-wide protein-quantitative trait loci mapping of interferon signalling

Christian Lundtoft, Pascal Pucholt, Juliana Imgenberg-Kreuz, Jonas Carlsson-Almlöf, Maija-Leena Eloranta, Ann-Christine Syvänen, Gunnel Nordmark, Johanna K. Sandling, Ingrid Kockum, Tomas Olsson, Lars Rönnblom, Niklas Hagberg

Auxin apical dominance governed by the OsAsp1-OsTIF1 complex determines distinctive rice caryopses development on different branches

Shu Chang, Yixing Chen, Shenghua Jia, Yihao Li, Kun Liu, Zhouhua Lin, Hanmeng Wang, Zhilin Chu, Jin Liu, Chao Xi, Heping Zhao, Shengcheng Han, Yingdian Wang

Developmental constraint shaped genome evolution and erythrocyte loss in Antarctic fishes following paleoclimate change

Jacob M. Daane, Juliette Auvinet, Alicia Stoebenau, Donald Yergeau, Matthew P. Harris, H. William Detrich III

Major role of iron uptake systems in the intrinsic extra-intestinal virulence of the genus Escherichia revealed by a genome-wide association study

Marco Galardini, Olivier Clermont, Alexandra Baron, Bede Busby, Sara Dion, Sören Schubert, Pedro Beltrao, Erick Denamur

Extensive trimming of short single-stranded DNA oligonucleotides during replication-coupled gene editing in mammalian cells

Thomas W. van Ravesteyn, Marcos Arranz Dols, Wietske Pieters, Marleen Dekker, Hein te Riele

Evolution of linkage and genome expansion in protocells: The origin of chromosomes

András Szilágyi, Viktor Péter Kovács, Eörs Szathmáry, Mauro Santos

CenH3 distribution reveals extended centromeres in the model beetle Tribolium castaneum

Tena Gržan, Evelin Despot-Slade, Nevenka Meštrović, Miroslav Plohl, Brankica Mravinac

Transcriptome and epigenome diversity and plasticity of muscle stem cells following transplantation

Brendan Evano, Diljeet Gill, Irene Hernando-Herraez, Glenda Comai, Thomas M. Stubbs, Pierre-Henri Commere, Wolf Reik, Shahragim Tajbakhsh

Corrections

Correction: Molecular predictors of brain metastasis-related microRNAs in lung adenocarcinoma

Guogui Sun, Xiao Ding, Nan Bi, Zhiwu Wang, Lihong Wu, Wei Zhou, Zitong Zhao, Jingbo Wang, Weimin Zhang, Jing Fan, WenJue Zhang, Xin Dong, Ning Lv, Yongmei Song, Qimin Zhan, LuHua Wang

Related Articles

Correction: Architecture of the Escherichia coli nucleoid

Subhash C. Verma, Zhong Qian, Sankar L. Adhya

Related Articles

Correction: The Airn lncRNA does not require any DNA elements within its locus to silence distant imprinted genes

Daniel Andergassen, Markus Muckenhuber, Philipp C. Bammer, Tomasz M. Kulinski, Hans-Christian Theussl, Takahiko Shimizu, Josef M. Penninger, Florian M. Pauler, Quanah J. Hudson

Related Articles

Correction: Telomere length-dependent transcription and epigenetic modifications in promoters remote from telomere ends

Ananda Kishore Mukherjee, Shalu Sharma, Suman Sengupta, Dhurjhoti Saha, Pankaj Kumar, Tabish Hussain, Vivek Srivastava, Sumitabho Deb Roy, Jerry W. Shay, Shantanu Chowdhury

Related Articles

Correction: Leveraging correlations between variants in polygenic risk scores to detect heterogeneity in GWAS cohorts

Jie Yuan, Hengrui Xing, Alexandre Louis Lamy, The Schizophrenia Working Group of the Psychiatric Genomics Consortium, Todd Lencz, Itsik Pe’er

Related Articles

Correction: yippee like 3 (ypel3) is a novel gene required for myelinating and perineurial glia development

Bernardo Blanco-Sánchez, Aurélie Clément, Sarah J. Stednitz, Jennifer Kyle, Judy L. Peirce, Marcie McFadden, Jeremy Wegner, Jennifer B. Phillips, Ellen Macnamara, Yan Huang, David R. Adams, Camilo Toro, William A. Gahl, May Christine V. Malicdan, Cynthia J. Tifft, Erika M. Zink, Kent J. Bloodsworth, Kelly G. Stratton, Undiagnosed Diseases Network, David M. Koeller, Thomas O. Metz, Philip Washbourne, Monte Westerfield

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Topic Page

RNA-directed DNA Methylation

Robert M. Erdmann, Colette L. Picard