HOME HELP FEEDBACK SUBSCRIPTIONS ARCHIVE SEARCH TABLE OF CONTENTS		QUICK SEARCH:   [advanced] Author: Keyword(s): Year:  Vol:  Page:

This Article Full Text Full Text (PDF) Alert me when this article is cited Alert me if a correction is posted Citation Map Services Similar articles in this journal Similar articles in PubMed Alert me to new issues of the journal Download to citation manager Citing Articles Citing Articles via HighWire Citing Articles via Google Scholar Google Scholar Articles by Montalbano, A. Articles by Feeney, A. J. Search for Related Content PubMed PubMed Citation Articles by Montalbano, A. Articles by Feeney, A. J.

V(D)J Recombination Frequencies Can Be Profoundly Affected by Changes in the Spacer Sequence¹

Alina Montalbano^2,*, Kisani M. Ogwaro^2,*, Alan Tang^2,*, Adam G. W. Matthews, Mani Larijani, Marjorie A. Oettinger and Ann J. Feeney^3,*

^* Department of Immunology, The Scripps Research Institute, La Jolla, CA 92037; and Department of Molecular Biology, Massachusetts General Hospital, and Department of Genetics, Harvard Medical School, Boston, MA 02114

Each V, D, and J gene segment is flanked by a recombination signal sequence (RSS), composed of a conserved heptamer and nonamer separated by a 12- or 23-bp spacer. Variations from consensus in the heptamer or nonamer at specific positions can dramatically affect recombination frequency, but until recently, it had been generally held that only the length of the spacer, but not its sequence, affects the efficacy of V(D)J recombination. In this study, we show several examples in which the spacer sequence can significantly affect recombination frequencies. We show that the difference in spacer sequence alone of two V_HS107 genes affects recombination frequency in recombination substrates to a similar extent as the bias observed in vivo. We show that individual positions in the spacer can affect recombination frequency, and those positions can often be predicted by their frequency in a database of RSS. Importantly, we further show that a spacer sequence that has an infrequently observed nucleotide at each position is essentially unable to support recombination in an extrachromosmal substrate assay, despite being flanked by a consensus heptamer and nonamer. This infrequent spacer sequence RSS shows only a 2-fold reduction of binding of RAG proteins, but the in vitro cleavage of this RSS is 9-fold reduced compared with a good RSS. These data demonstrate that the spacer sequence should be considered to play an important role in the recombination efficacy of an RSS, and that the effect of the spacer occurs primarily subsequent to RAG binding.

This article has been cited by other articles:

				M. Larijani and A. Martin Single-Stranded DNA Structure and Positional Context of the Target Cytidine Determine the Enzymatic Efficiency of AID Mol. Cell. Biol., December 1, 2007; 27(23): 8038 - 8048. [Abstract] [Full Text] [PDF]

				N. S. Rahman, L. J. Godderz, S. J. Stray, J. D. Capra, and K. K. Rodgers DNA Cleavage of a Cryptic Recombination Signal Sequence by RAG1 and RAG2: IMPLICATIONS FOR PARTIAL VH GENE REPLACEMENT J. Biol. Chem., May 5, 2006; 281(18): 12370 - 12380. [Abstract] [Full Text] [PDF]

				C. M. Johnston, A. L. Wood, D. J. Bolland, and A. E. Corcoran Complete Sequence Assembly and Characterization of the C57BL/6 Mouse Ig Heavy Chain V Region J. Immunol., April 1, 2006; 176(7): 4221 - 4234. [Abstract] [Full Text] [PDF]

				C. R. Espinoza and A. J. Feeney The Extent of Histone Acetylation Correlates with the Differential Rearrangement Frequency of Individual VH Genes in Pro-B Cells J. Immunol., November 15, 2005; 175(10): 6668 - 6675. [Abstract] [Full Text] [PDF]

				S. R. Talukder, D. D. Dudley, F. W. Alt, Y. Takahama, and Y. Akamatsu Increased frequency of aberrant V(D)J recombination products in core RAG-expressing mice Nucleic Acids Res., August 24, 2004; 32(15): 4539 - 4549. [Abstract] [Full Text] [PDF]