ARID Genomic sequences

Minimum number of tobacco ARID genes: 8

Count of tobacco ARID sequences: 11

Pfam accession: PF01388 ARID

SHOULD possess PF01388 ARID domain and COULD   possess HMG_box Myb_DNA-binding domains

This domain is known as ARID for AT-Rich Interaction Domain, and also known as the BRIGHT domain.

Members of the recently discovered ARID (AT-rich interaction domain) family of DNA-binding proteins are found in fungi and invertebrate and vertebrate metazoans. ARID-encoding genes are involved in a variety of biological processes including embryonic development, cell lineage gene regulation and cell cycle control. Although the specific roles of this domain and of ARID-containing proteins in transcriptional regulation are yet to be elucidated, they include both positive and negative transcriptional regulation and a likely involvement in the modification of chromatin structure. The basic structure of the ARID domain domain appears to be a series of six alpha-helices separated by beta-strands, loops, or turns, but the structured region may extend to an additional helix at either or both ends of the basic six. Based on primary sequence homology, they can be partitioned into three structural classes: Minimal ARID proteins that consist of a core domain formed by six alpha helices; ARID proteins that supplement the core domain with an N-terminal alpha-helix; and Extended-ARID proteins, which contain the core domain and additional alpha-helices at their N- and C-termini.

The human SWI-SNF complex protein p270 is an ARID family member with non-sequence-specific DNA binding activity. The ARID consensus and other structural features are common to both p270 and yeast SWI1, suggesting that p270 is a human counterpart of SWI1. The approximately 100-residue ARID sequence is present in a series of proteins strongly implicated in the regulation of cell growth, development, and tissue-specific gene expression. Although about a dozen ARID proteins can be identified from database searches, to date, only Bright (a regulator of B-cell-specific gene expression), dead ringer (a Drosophila melanogaster gene product required for normal development), and MRF-2 (which represses expression from the cytomegalovirus enhancer) have been analyzed directly in regard to their DNA binding properties. Each binds preferentially to AT-rich sites. In contrast, p270 shows no sequence preference in its DNA binding activity, thereby demonstrating that AT-rich binding is not an intrinsic property of ARID domains and that ARID family proteins may be involved in a wider range of DNA interactions.

Members of the recently discovered ARID (AT-rich interaction domain) family of DNA-binding proteins are found in fungi and invertebrate and vertebrate metazoans. ARID-encoding genes are involved in a variety of biological processes including embryonic development, cell lineage gene regulation and cell cycle control. Although the specific roles of this domain and of ARID-containing proteins in transcriptional regulation are yet to be elucidated, they include both positive and negative transcriptional regulation and a likely involvement in the modification of chromatin structure (Kortschak et al., 2000).

The ARID (A-T Rich Interaction Domain) is a helix-turn-helix motif-based DNA-binding domain, conserved in all eukaryotes and diagnostic of a family that includes 15 distinct human proteins with important roles in development, tissue-specific gene expression and proliferation control. Most ARID family members have not been characterized with respect to their DNA-binding behavior, but it is already apparent that not all ARIDs conform to the pattern of binding AT-rich sequences (Patsialou et al., 2005).



Papers

Kortschak, RD; Tucker, PW; Saint, R. ARID proteins come in from the desert. Trends Biochem. Sci. 2000. 25(6):294-9 PMID: 10838570

Patsialou, A; Wilsker, D; Moran, E. DNA-binding properties of ARID family proteins. Nucleic Acids Res. 2005. 33(1):66-80 PMID: 15640446

Wilsker, D; Patsialou, A; Dallas, PB; Moran, E. ARID proteins: a diverse family of DNA binding proteins implicated in the control of cell growth, differentiation, and development. Cell Growth Differ. 2002. 13(3):95-106 PMID: 11959810

Wilsker, D; Probst, L; Wain, HM; Maltais, L; Tucker, PW; Moran, E. Nomenclature of the ARID family of DNA-binding proteins. Genomics 2005. 86(2):242-51 PMID: 15922553



Number of contigs: 8

Number of singlets: 4

Number of N terminal – 3

Number of C terminal – 3

Number of full – 5

Total minimum number – 8






Search sequences and info


Transcription factor sequences
Locus
Description
NCBI
ARID_1 [comment=C terminal] ET042001
ET042000
ARID_2 [comment=full] ET045401
ET050718
ARID_3 [comment=N terminal] ET050482
ET045955
ARID_4 [comment=full] ET044998
ET043103
ET050346
ARID_5 [comment=C terminal] ET047239
ET049123
ET047231
ET045903
ARID_6 [comment=full] ET051727
ET047298
ET046310
ET050591
ET042039
ARID_7 [comment=full] ET050034
ET044994
ET051017
ET051018
ET047347
ARID_8 [comment=full] ET049597
ARID_9 [comment=C terminal] ET044995
ARID_10 [comment=N terminal] ET043049
ARID_11 [comment=N terminal] ET043129


Tobacco published genes related to transcription factor family ARID
Family Genbank ID Name
Authors of this site:

Paul J Rushton
Marta T. Bokowiec
Xianfeng (Jeff) Chen
Thomas (Tom) W Laudeman
Jennifer F. Brannock
Michael P. Timko

Contact:

pr8y@virginia.edu