The DNA Sequence, Annotation and Analysis of Human Chromosome 3 Accepted for publication in Nature, 03/2006 ( Finished Chr 3 sequence GenBank accession #: NC_000003 )   Corresponding authors: Steven Scherer (sscherer@bcm.tmc.edu) Human Genome Sequencing Center, Baylor College of Medicine Huanming Yang (yanghm@genomics.org.cn) Beijing Genomics Institute, Chinese Academy of Sciences, Beijing 101300, China Complete author and affiliation list
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Abstract Figure List Supplemental Figures Supplemental Tables Abstract: After the completion of a draft human genome sequence1, the International Human Genome Sequencing Consortium has proceeded to finish, annotate and describe each of the 24 chromosomes comprising the human genome. Here we describe the sequencing and analysis of human chromosome 3, one of the largest human chromosomes. Chromosome 3 comprises just four contigs, one of which currently represents the longest contiguous stretch of finished DNA sequence known so far. The chromosome is remarkable in having the lowest rate of segmental duplication in the genome. It also contains a chemokine receptor gene cluster as well as numerous loci involved in multiple human cancers such as the gene encoding FHIT, which contains the most common constitutive fragile site in the genome, FRA3B. Using genomic sequence from chimpanzee and rhesus macaque, we were able to characterize the breakpoints defining a large pericentric inversion that occurred some time after the split of Homininae from Ponginae, and propose an evolutionary history of the inversion.

Figure List:

Figure 1:	Correlation of syntenic breakpoints with general chromosome landscape features.
Figure 2:	Human chromosome 3 pericentric inversion breakpoints.

Supplemental Figures:

Supp. Figure 1:	Genetic map marker order correspondence with sequence position.
Supp. Figure 2:	Comparison of Physical and Genetic Map Distance.
Supp. Figure 3:	Ancient duplications mapped between chromosomes 3 and 17.
Supp. Figure 4:	Alignment of segmental duplication at human chromosome 3 inversion breakpoint to chromosome 11.
Supp. Figure 5:	Percentage of chromosome 3 total cancer and case breakpoints versus chromosome band position.

Supplemental Tables:

Supp. Table 1:	Calculation of chromosome 3 euchromatic sequence gap sizes.
Supp. Table 2:	Predicted ncRNA candidates on human chromosome 3.
Supp. Table 3:	Comprehensive predicted ncRNA candidates on human chromosome 3
Supp. Table 4:	Inversion breakpoint region coordinates in human (NCBI Build 35), chimpanzee (UCSC panTro1) and Rhesus macaque (HGSC Mmul_0.1).
Supp. Table 5:	Repeat and GC composition as percentages of 10 kbp windows spanning the Rhesus breakpoints and the orthologous human sequence.
Supp. Table 6:	The most referenced chromosome 3 disease phenotypes and associated genes.
Supp. Table 7:	The most referenced chromosome 3 disease phenotypes and causitive genes sorted by function.

Complete Author & Affiliation List:

Donna M. Muzny¹, Steven E. Scherer¹, Rajinder Kaul², Jing Wang³, Jun Yu³, Ralf Sudbrak⁴,⁵, Christian J. Buhay¹, Rui Chen¹, Andrew Cree¹, Yan Ding¹, Shannon Dugan-Rocha¹, Rachel Gill¹, Preethi Gunaratne¹, R. Alan Harris¹, Alicia C. Hawes¹, Judith Hernandez¹, Anne V. Hodgson¹, Jennifer Hume¹, Andrew Jackson¹, Ziad Mohid Khan¹, Christie Kovar-Smith¹, Lora R. Lewis¹, Ryan J. Lozado¹, Michael L. Metzker¹, Aleksandar Milosavljevic¹, George R. Miner¹, Margaret B. Morgan¹, Lynne V. Nazareth¹, Graham Scott¹, Erica Sodergren¹, Xing-Zhi Song¹, David Steffen¹, Sharon Wei¹, David A. Wheeler¹, Mathew W. Wright⁶, Kim C. Worley¹, Ye Yuan¹, Zhengdong Zhang¹, Charles Q. Adams¹, M. Ali Ansari-Lari¹, Mulu Ayele¹, Mary J. Brown¹, Guan Chen¹, Zhijian Chen¹, James Clendenning², Kerstin P. Clerc-Blankenburg¹, Runsheng Chen³, Zhu Chen³, Clay Davis¹, Oliver Delgado¹, Huyen H. Dinh¹, Wei Dong³, Heather Draper¹, Stephen Ernst², Gang Fu³, Manuel L. Gonzalez-Garay¹, Dawn K. Garcia⁷, Will Gillett², Jun Gu³, Bailin Hao³, Eric Haugen², Paul Havlak¹, Xin He⁷, Steffen Hennig⁸, Songnian Hu³, Wei Huang³, Laronda R. Jackson¹, Leni S. Jacob¹, Susan H. Kelly¹, Michael Kube⁴, Ruth Levy², Zhangwan Li¹, Bin Liu³, Jing Liu¹, Wen Liu¹, Jing Lu¹, Manjula Maheshwari¹, Bao-Viet Nguyen¹, Geoffrey O. Okwuonu¹, Anthony Palmeiri², Shiran Pasternak¹, Lesette M. Perez¹, Karen A. Phelps², Farah J. H. Plopper¹, Boqin Qiang³, Christopher Raymond², Ruben Rodriguez⁷, Channakhone Saenphimmachak², Jireh Santibanez¹, Hua Shen¹, Yan Shen³, Sandhya Subramanian², Paul E. Tabor¹, Daniel Verduzco¹, Lenee Waldron¹, Jian Wang³, Jun Wang³, Qiaoyan Wang¹, Gabrielle A. Williams¹, Gane K.-S. Wong³, Zhijian Yao³, JingKun Zhang¹, Xiuqing Zhang³, Guoping Zhao³, Jianling Zhou¹, Yang Zhou², David Nelson¹, Hans Lehrach⁴, Richard Reinhardt⁴, Susan L. Naylor⁷, Huanming Yang³, Maynard Olson², George Weinstock¹ & Richard A. Gibbs¹

Affiliations:

1. Human Genome Sequencing Center, Baylor College of Medicine, 1 Baylor Plaza, Houston, Texas 77030, USA
2. Department of Medicine, Division of Medical Genetics, University of Washington Genome Center, Fluke Hall on Mason Rd, Box 352145 Seattle, Washington 98195, USA
3. Beijing Genomics Institute, Chinese Academy of Sciences, Beijing 101300, China; James D. Watson Institute of Genome Sciences, Zhejiang University, Hangzhou 310008, China; Chinese National Human Genome Center at Shanghai (CHGC), Shanghai 201203, China; and Chinese National Human Genome Center, Beijing (CHGB), Beijing 100176, China
4. Max Planck Institute for Molecular Genetics, 14195 Berlin-Dahlem, Germany
5. Institute for Clinical Molecular Biology, Christian-Albrechts University, 24105 Kiel, Germany
6. HUGO Gene Nomenclature Committee, The Galton Laboratory, Department of Biology, University College London, Wolfson House, 4 Stephenson Way, London NW1 2HE, UK
7. University of Texas Health Science Center at San Antonio, 7703 Floyd Curl Drive, San Antonio, Texas 78229, USA
8. RZPD German Resource Center for Genome Research, 14059 Berlin, Germany.