Octamer transcription factors 1 and 2 each bind to two different functional elements in the immunoglobulin heavy-chain promoter

1989 ◽  
Vol 9 (2) ◽  
pp. 747-756
Author(s):  
L Poellinger ◽  
R G Roeder
Keyword(s):  
Transcription Factors ◽  
Heavy Chain ◽  
Protein Interactions ◽  
Transcription Initiation ◽  
Immunoglobulin Heavy Chain ◽  
Sequence Motifs ◽  
Cell Type Specificity ◽  
Conserved Sequence ◽  
Octamer Motif ◽  
Sequence Elements

Immunoglobulin heavy-chain genes contain two conserved sequence elements 5' to the site of transcription initiation: the octamer ATGCAAAT and the heptamer CTCATGA. Both of these elements are required for normal cell-specific promoter function. The present study demonstrates that both the ubiquitous and lymphoid-cell-specific octamer transcription factors (OTF-1 and OTF-2, respectively) interact specifically with each of the two conserved sequence elements, forming either homo- or heterodimeric complexes. This was surprising, since the heptamer and octamer sequence motifs bear no obvious similarity to each other. Binding of either factor to the octamer element occurred independently. However, OTF interaction with the heptamer sequence appeared to require the presence of an intact octamer motif and occurred with a spacing of either 2 or 14 base pairs between the two elements, suggesting coordinate binding resulting from protein-protein interactions. The degeneracy in sequences recognized by the OTFs may be important in widening the range over which gene expression can be modulated and in establishing cell type specificity.

scholarly journals Octamer transcription factors 1 and 2 each bind to two different functional elements in the immunoglobulin heavy-chain promoter.

1989 ◽  
Vol 9 (2) ◽  
pp. 747-756 ◽  
Author(s):  
L Poellinger ◽  
R G Roeder
Keyword(s):  
Transcription Factors ◽  
Heavy Chain ◽  
Protein Interactions ◽  
Transcription Initiation ◽  
Immunoglobulin Heavy Chain ◽  
Sequence Motifs ◽  
Cell Type Specificity ◽  
Conserved Sequence ◽  
Octamer Motif ◽  
Sequence Elements

Immunoglobulin heavy-chain genes contain two conserved sequence elements 5' to the site of transcription initiation: the octamer ATGCAAAT and the heptamer CTCATGA. Both of these elements are required for normal cell-specific promoter function. The present study demonstrates that both the ubiquitous and lymphoid-cell-specific octamer transcription factors (OTF-1 and OTF-2, respectively) interact specifically with each of the two conserved sequence elements, forming either homo- or heterodimeric complexes. This was surprising, since the heptamer and octamer sequence motifs bear no obvious similarity to each other. Binding of either factor to the octamer element occurred independently. However, OTF interaction with the heptamer sequence appeared to require the presence of an intact octamer motif and occurred with a spacing of either 2 or 14 base pairs between the two elements, suggesting coordinate binding resulting from protein-protein interactions. The degeneracy in sequences recognized by the OTFs may be important in widening the range over which gene expression can be modulated and in establishing cell type specificity.

scholarly journals Octamer transcription factors bind to two different sequence motifs of the immunoglobulin heavy chain promoter.

1989 ◽  
Vol 8 (7) ◽  
pp. 2001-2008 ◽  
Author(s):  
I. Kemler ◽  
E. Schreiber ◽  
M. M. Müller ◽  
P. Matthias ◽  
W. Schaffner
Keyword(s):  
Transcription Factors ◽  
Heavy Chain ◽  
Immunoglobulin Heavy Chain ◽  
Sequence Motifs

scholarly journals Olfactory expression of trace amine-associated receptors requires cooperative cis-acting enhancers

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Ami Shah ◽  
Madison Ratkowski ◽  
Alessandro Rosa ◽  
Paul Feinstein ◽  
Thomas Bozza
Keyword(s):  
Gene Expression ◽  
Large Family ◽  
Sequence Motifs ◽  
Specific Expression ◽  
Cis Acting ◽  
Conserved Sequence ◽  
Trace Amine ◽  
Sequence Elements ◽  
Cell Type Specific Expression ◽  
Cell Type Specific

AbstractOlfactory sensory neurons express a large family of odorant receptors (ORs) and a small family of trace amine-associated receptors (TAARs). While both families are subject to so-called singular expression (expression of one allele of one gene), the mechanisms underlying TAAR gene choice remain obscure. Here, we report the identification of two conserved sequence elements in the mouse TAAR cluster (T-elements) that are required for TAAR gene expression. We observed that cell-type-specific expression of a TAAR-derived transgene required either T-element. Moreover, deleting either element reduced or abolished expression of a subset of TAAR genes, while deleting both elements abolished olfactory expression of all TAARs in cis with the mutation. The T-elements exhibit several features of known OR enhancers but also contain highly conserved, unique sequence motifs. Our data demonstrate that TAAR gene expression requires two cooperative cis-acting enhancers and suggest that ORs and TAARs share similar mechanisms of singular expression.

scholarly journals Sequence conservation, domain architectures, and phylogenetic distribution of the HD-GYP type c-di-GMP phosphodiesterases

2021 ◽  
Author(s):  
Michael Y. Galperin ◽  
Shan-Ho Chou
Keyword(s):  
Protein Interactions ◽  
Regulatory Protein ◽  
Second Messenger ◽  
Distribution Patterns ◽  
Distribution Functions ◽  
Amino Acid Residues ◽  
Sequence Motifs ◽  
Protein Protein Interactions ◽  
Conserved Sequence ◽  
Common Domain

The HD-GYP domain, named after two of its conserved sequence motifs, was first described in 1999 as a specialized version of the widespread HD phosphohydrolase domain that had additional highly conserved amino acid residues. Domain associations of HD-GYP indicated its involvement in bacterial signal transduction and distribution patterns of this domain suggested that it could serve as a hydrolase of the bacterial second messenger c-di-GMP, in addition to or instead of the EAL domain. Subsequent studies confirmed the ability of various HD-GYP domains to hydrolyze c-di-GMP to linear pGpG and/or GMP. Certain HD-GYP-containing proteins hydrolyze another second messenger, cGAMP, and some HD-GYP domains participate in regulatory protein-protein interactions. The recently solved structures of HD-GYP domains from four distinct organisms clarified the mechanisms of c-di-GMP binding and metal-assisted hydrolysis. However, the HD-GYP domain is poorly represented in public domain databases, which causes certain confusion about its phylogenic distribution, functions, and domain architectures. Here, we present a refined sequence model for the HD-GYP domain and describe the roles of its most conserved residues in metal and/or substrate binding. We also calculate the numbers of HD-GYPs encoded in various genomes and list the most common domain combinations involving HD-GYP, such as the RpfG (REC-HD-GYP), Bd1817 (DUF3391-HD-GYP), and PmGH (GAF-HD-GYP) protein families. We also provide the descriptions of six HD-GYP-associated domains, including four novel integral membrane sensor domains. This work is expected to stimulate studies of diverse HD-GYP-containing proteins, their N-terminal sensor domains, and the signals to which they respond.

scholarly journals The immunoglobulin heavy chain locus contains another B-cell-specific 3' enhancer close to the alpha constant region.

1993 ◽  
Vol 13 (3) ◽  
pp. 1547-1553 ◽  
Author(s):  
P Matthias ◽  
D Baltimore
Keyword(s):  
Transcription Factors ◽  
B Cell ◽  
Heavy Chain ◽  
Variable Region ◽  
Immunoglobulin Heavy Chain ◽  
Immunoglobulin Genes ◽  
Constant Region ◽  
Transcriptional Enhancer ◽  
Additional Control ◽  
Complex Regulation

The transcription of immunoglobulin genes is controlled by variable region promoters and by enhancers, both of which are lymphoid specific. Because immunoglobulin genes are subject to an extremely complex regulation, we anticipated that there might be additional control elements for these genes. We therefore sought additional enhancers and demonstrate here that there is indeed another weak transcriptional enhancer just 3' to the mouse alpha constant region. This novel immunoglobulin enhancer is lymphoid specific and at two positions can bind members of the Oct family of transcription factors.

Follicular lymphoma with a novel t(14;18) breakpoint involving the immunoglobulin heavy chain switch mu region indicates an origin from germinal center B cells

Blood ◽  
2002 ◽  
Vol 99 (2) ◽  
pp. 716-718 ◽  
Author(s):  
James A. L. Fenton ◽  
Jan-Willem Vaandrager ◽  
Wilhelmina M. Aarts ◽  
Richard J. Bende ◽  
Karel Heering ◽  
...  
Keyword(s):  
Sequence Analysis ◽  
Follicular Lymphoma ◽  
Heavy Chain ◽  
Germinal Center ◽  
Transcription Initiation ◽  
Immunoglobulin Heavy Chain ◽  
Initiation Site ◽  
Cell Stage ◽  
Class Switch ◽  
Germinal Center B Cell

Abstract With the use of DNA-fiber fluorescent in situ hybridization, a BCL2 protein positive follicular lymphoma with a novel BCL2 breakpoint involving the immunoglobulin heavy chain (IGH) switch mu (Sμ) region instead of the JH orDH gene segments was identified. Sequence analysis showed that the genomic breakpoint is localized between the Sμ region of the IGH complex and the first intron of BCL2. Reverse-transcriptase polymerase chain reaction showed expression of a unique hybrid IGH-BCL2 transcript involving the transcription initiation site Iμ. Sequence analysis of the VH region of the functional nontranslocatedIGH allele showed multiple shared somatic mutations but also a high intraclonal variation (53 differences in 15 clones), compatible with the lymphoma cells staying in or re-entering the germinal center. This is the first example of a t(14;18) translocation that results from an illegitimate IGH class-switch recombination during the germinal center B-cell stage.

scholarly journals Evolutionary divergence of motifs in B-class MADS-box proteins of seed plants

2021 ◽  
Vol 28 (1) ◽  
Author(s):  
Gangxu Shen ◽  
Yong Jia ◽  
Wei-Lung Wang
Keyword(s):  
Transcription Factors ◽  
Functional Divergence ◽  
Acid Sites ◽  
Evolutionary Divergence ◽  
Alternative Mechanism ◽  
Sequence Motifs ◽  
Mads Box ◽  
Mads Box Genes ◽  
Systematic Analysis ◽  
Conserved Sequence

Abstract Background MADS-box transcription factors function as homo- or heterodimers and regulate many aspects of plant development; moreover, MADS-box genes have undergone extensive duplication and divergence. For example, the morphological diversity of floral organs is closely related to the functional divergence of the MADS-box gene family. B-class genes (such as Arabidopsis thaliana APETALA3 [AP3] and PISTILLATA [PI]) belong to a subgroup of MADS-box genes. Here, we collected 97 MADS-box B protein sequences from 21 seed plant species and examined their motifs to better understand the functional evolution of B proteins. Results We used the MEME tool to identify conserved sequence motifs in these B proteins; unique motif arrangements and sequences were identified in these B proteins. The keratin-like domains of Malus domestica and Populus trichocarpa B proteins differed from those in other angiosperms, suggesting that a novel regulatory network might have evolved in these species. The MADS domains of Nelumbo nucifera, Glycine max, and Amborella trichopoda B-proteins contained motif 9; in contrast, those of other plants contained motif 1. Protein modelling analyses revealed that MADS domains with motif 9 may lack amino acid sites required for DNA-binding. These results suggested that the three species might share an alternative mechanism controlling floral development. Conclusions Amborella trichopoda has B proteins with either motif 1 or motif 9 MADS domains, suggesting that these two types of MADS domains evolved from the ancestral domain into two groups, those with motif 9 (N. nucifera and G. max), and those with motif 1. Moreover, our results suggest that the homodimer/heterodimer intermediate transition structure first appeared in A. trichopoda. Therefore, our systematic analysis of the motifs in B proteins sheds light on the evolution of these important transcription factors.

Sign in / Sign up

Export Citation Format

Share Document