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Research: Somatic retrotransposition in the developing rhesus macaque brain
- Victor Billon,
- Francisco J. Sanchez-Luque,
- Jay Rasmussen,
- Gabriela O. Bodea,
- Daniel J. Gerhardt,
- Patricia Gerdes,
- Seth W. Cheetham,
- Stephanie N. Schauer,
- Prabha Ajjikuttira,
- Thomas J. Meyer,
- Cora E. Layman,
- Kimberly A. Nevonen,
- Natasha Jansz,
- Jose L. Garcia-Perez,
- Sandra R. Richardson,
- Adam D. Ewing,
- Lucia Carbone,
- and Geoffrey J. Faulkner
Genome Res. July 2022 32: 1298-1314; Published in Advance June 21, 2022, doi:10.1101/gr.276451.121
...lineage cells (Brouha et al. 2003; Muotri et al. 2005; Coufal et al. 2009; Beck et al. 2010; Evrony et al. 2015; Erwin et al. 2016; Faulkner and Garcia-Perez 2017; Macia et al. 2017; Sanchez-Luque et al. 2019). To retrotranspose, L1 generates a bicistronic mRNA encoding two proteins (ORF1p and ORF2p) that...
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Resource: An atlas of chromatin accessibility in the adult human brain
- John F. Fullard,
- Mads E. Hauberg,
- Jaroslav Bendl,
- Gabor Egervari,
- Maria-Daniela Cirnaru,
- Sarah M. Reach,
- Jan Motl,
- Michelle E. Ehrlich,
- Yasmin L. Hurd,
- and Panos Roussos
Genome Res. August 2018 28: 1243-1252; Published in Advance June 26, 2018, doi:10.1101/gr.232488.117
...human iPSCs and differentiated cells. Genome Res 28: 122–131. ↵Brené S, Lindefors N, Ehrlich M, Taubes T, Horiuchi A, Kopp J, Hall H, Sedvall G, Greengard P, Persson H. 1994. Expression of mRNAs encoding ARPP-16/19, ARPP-21, and DARPP-32 in human brain tissue. J Neurosci 14: 985–998. ↵Buenrostro JD...
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Research: Analysis of alternative splicing associated with aging and neurodegeneration in the human brain
- James R. Tollervey,
- Zhen Wang,
- Tibor Hortobágyi,
- Joshua T. Witten,
- Kathi Zarnack,
- Melis Kayikci,
- Tyson A. Clark,
- Anthony C. Schweitzer,
- Gregor Rot,
- Tomaž Curk,
- Blaž Zupan,
- Boris Rogelj,
- Christopher E. Shaw,
- and Jernej Ule
Genome Res. October 2011 21: 1572-1582; Published in Advance August 16, 2011, doi:10.1101/gr.122226.111
...of neuronal progenitor cells to mature neurons (Boutz et al. 2007a; Makeyev et al. 2007). This is of particular interest due to a recent finding that expression of microRNAs and their target mRNAs links development and aging in human and macaque brain (Somel et al. 2010). We also detected decreased levels...
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Research: Human-specific features of spatial gene expression and regulation in eight brain regions
- Chuan Xu,
- Qian Li,
- Olga Efimova,
- Liu He,
- Shoji Tatsumoto,
- Vita Stepanova,
- Takao Oishi,
- Toshifumi Udono,
- Katsushi Yamaguchi,
- Shuji Shigenobu,
- Akiyoshi Kakita,
- Hiroyuki Nawa,
- Philipp Khaitovich,
- and Yasuhiro Go
Genome Res. August 2018 28: 1097-1110; Published in Advance June 13, 2018, doi:10.1101/gr.231357.117
...) and Qubit Fluorometer (Thermo Fisher Scientific), respectively, and the RNA Integrity Numbers (RIN) were determined using Bioanalyzer RNA 6000 Nano Kit (Agilent).RNA-sequencingSequencing libraries were prepared using the NEBNext mRNA Library Prep Kit for nondirectional libraries and the NEBNext Ultra...
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Research: Birth and expression evolution of mammalian microRNA genes
- Julien Meunier,
- Frédéric Lemoine,
- Magali Soumillon,
- Angélica Liechti,
- Manuela Weier,
- Katerina Guschanski,
- Haiyang Hu,
- Philipp Khaitovich,
- and Henrik Kaessmann
Genome Res. January 2013 23: 34-45; Published in Advance October 3, 2012, doi:10.1101/gr.140269.112
...Birth and expression evolution of mammalian microRNA genes Julien Meunier 1 , 2 , 7 , Frédéric Lemoine 1 , 4 , Magali Soumillon 1 , 2 , 5 , 6 , Angélica Liechti 1 , Manuela Weier 1 , Katerina Guschanski 1 , 2...
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Research: Impact of microRNA regulation on variation in human gene expression
- Jian Lu and
- Andrew G. Clark
Genome Res. July 2012 22: 1243-1254; Published in Advance March 28, 2012, doi:10.1101/gr.132514.111
...Population Samples used in HapMap? Platform for mRNA Probes expressed Platform for miRNA Wang et al. 2009 I Lymphoblastoid 90 European-American males No human-6 V2 BeadChip 14,172 Illumina microRNA chip Idaghdour et al. 2010 II Leukocyte 194 Arab and Amazighs people No HumanHT-12 BeadChip 22,300 N/A Stranger...
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Research: RBFOX and PTBP1 proteins regulate the alternative splicing of micro-exons in human brain transcripts
- Yang I. Li,
- Luis Sanchez-Pulido,
- Wilfried Haerty,
- and Chris P. Ponting
Genome Res. January 2015 25: 1-13; Published in Advance December 18, 2014, doi:10.1101/gr.181990.114
...into short exonic sequences separated by longer intronic stretches that are removed during mRNA maturation. Although alternative splicing of exons allows multiple protein isoforms to be produced from the same gene, many isoforms appear to lack functional roles, owing to their low evolutionary conservation...
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Methods: Many novel mammalian microRNA candidates identified by extensive cloning and RAKE analysis
- Eugene Berezikov,
- Geert van Tetering,
- Mark Verheul,
- Jose van de Belt,
- Linda van Laake,
- Joost Vos,
- Robert Verloop,
- Marc van de Wetering,
- Victor Guryev,
- Shuji Takada,
- Anton Jan van Zonneveld,
- Hiroyuki Mano,
- Ronald Plasterk,
- and Edwin Cuppen
Genome Res. October 2006 16: 1289-1298; Published in Advance September 5, 2006, doi:10.1101/gr.5159906
....B. , Bartel, D.P. ( 2003 ) Vertebrate microRNA genes . Science 299 , 1540 . ↵ Lim, L.P. , Lau, N.C. , Garrett-Engele, P. , Grimson, A. , Schelter, J.M. , Castle, J. , Bartel, D.P. , Linsley, P.S. , Johnson, J.M. ( 2005 ) Microarray analysis shows that some microRNAs downregulate large numbers of target mRNAs...
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Research: Germline and somatic imprinting in the nonhuman primate highlights species differences in oocyte methylation
- Clara Y. Cheong,
- Keefe Chng,
- Shilen Ng,
- Siew Boom Chew,
- Louiza Chan,
- and Anne C. Ferguson-Smith
Genome Res. May 2015 25: 611-623; Published in Advance April 10, 2015, doi:10.1101/gr.183301.114
...variant 1 (hereafter abbreviated as INPP5F_v1 and INPP5F_v2, respectively) has also been reported in human fetal spinal cord, brain, heart, and tongue (Wood et al. 2007b). Likewise, in macaques, INPP5F_v1 shows no evidence of imprinted expression, while INPP5F_v2 is monoallelically expressed in all...
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Research: Extension of cortical synaptic development distinguishes humans from chimpanzees and macaques
- Xiling Liu,
- Mehmet Somel,
- Lin Tang,
- Zheng Yan,
- Xi Jiang,
- Song Guo,
- Yuan Yuan,
- Liu He,
- Anna Oleksiak,
- Yan Zhang,
- Na Li,
- Yuhui Hu,
- Wei Chen,
- Zilong Qiu,
- Svante Pääbo,
- and Philipp Khaitovich
Genome Res. April 2012 22: 611-622; Published in Advance February 2, 2012, doi:10.1101/gr.127324.111
...; Supplemental Table S6). To test the validity of these results and the reproducibility of the module expression profiles, we measured mRNA expression in the PFC and CBC in human, chimpanzee, and rhesus macaque newborns and adults (data set 1) and in the PFC of 14 humans, 14 chimpanzees, and 15 rhesus macaques...
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