BEND2 (protein)
BEND2 is a protein that in humans is encoded by the BEND2 gene. It is also found in other vertebrates, including mammals, birds, and reptiles. The expression of BEND2 in Homo sapiens is regulated and occurs at high levels in the skeletal muscle tissue of the male testis and in the bone marrow. The presence of the BEN domains in the BEND2 protein indicates that this protein may be involved in chromatin modification and regulation.
Gene
Common aliases
BEND2 stands for BEN domain containing 2 and is also known as CXorf20.Locus and size
The locus for BEND2 is on the minus strand of the X chromosome at Xp22.13. The gene is approximately 58 kilobases in length.mRNA
Alternative splicing
BEND2 contains 14 exons which undergo alternative splicing to create five transcript variants that vary from 4,720 base pairs to 2,144 bp in the mature mRNA. The longest and most complete transcript of the gene, variant 1, encodes isoform 1 of the BEND2 protein.5' and 3'UTR
The untranslated regions flanking the coding sequence of BEND2 at the 5' and 3' end of the mature mRNA molecule contain sites for RNA-binding proteins, including RBMX, pum2, and EIF4B as well as microRNA binding sites. The 5'UTR also contains an upstream in-frame stop codon and the 3'UTR contains a polyadenylation signal sequence.Protein (Isoform 1)
Molecular weight and internal composition
The predicted molecular weight is 87.9 kDal.The predicted isoelectric point is pH 5.07.
The internal composition is enriched for serine residues.
Isoforms
Corresponding to the five alternative transcripts of BEND2, the protein encoded by this gene is found in two isoforms as well as three predicted structures. These isoforms range from 813 to 645 amino acids in length. Isoform 1 is 799 amino acids in length.Subcellular location
The presence of nuclear localization signals within the amino acid sequence or primary structure of the BEND2 protein leads to a prediction of subcellular localization in the nucleus. The pat7 signal and a nuclear bipartite signal are both found near the N-terminus of the protein.Structure
The secondary structure for BEND2 is unclear, in particular at the N-terminus, which is poorly conserved between orthologs. The C-terminus contains two BEN domains, which are predicted to form a series of alpha helices.Post-translational modifications
Based on its primary structure, BEND2 is predicted to undergo N-terminus acetylation, glycation of several lysine residues, SUMOlation, a SUMO interaction at the N-terminus, S-palmitoylation, and extensive phosphorylation.Interacting Proteins
BEND2 is found to interact with the following proteins through experimental yeast two-hybrid screens or pull down assays.| Experiment type | Protein | Protein Function | Associated diseases |
| Two-hybrid screen | Ataxin 1 | Chromatin-binding factor; RNA metabolism | Spinocerebellar ataxia 1/spinocerebellar degeneration |
| Two-hybrid screen | Splicing factor 3A subunit 2 | Activation of U2 snRNP; microtubule-binding protein | |
| Two-hybrid screen | LIM Homeobox 2 | Transcriptional regulator for cell differentiation; sequence-specific DNA binding | Schizencephaly |
| Two-hybrid screen | Proline Rich 20D | Unknown function | |
| Pull down assay | Amyolid precursor protein | Cell surface receptor in neurons; cleaved to form transcriptional activators | Cerebral amyloid angiopathy; Alzheimer's disease |
BEN Domains (protein feature)
BEND2 has two BEN domains at its C-terminus. BEN domains are found in a diverse array of proteins and are predicted to be important for chromatin remodeling as well as for the recruitment of chromatin-modifying factors utilized during the process of transcriptional regulation of gene expression. BEN domains are predicted to form four alpha helices that allow this domain to interact with its DNA target.showed that the Drosophila melanogaster Insensitive gene and corresponding protein has no domains of known chemical function yet it contains a single BEN domain. They illustrated the activity of the Insv protein in transcriptional regulation of genes and obtained a crystal structure of two Insv BEN domains interacting with their DNA target site.
Expression
Tissue expression pattern
The expression of the BEND2 gene is regulated and it is therefore not ubiquitously expressed in the human body. High expression occurs in the testis and in the bone marrow. The NCBI EST profile for this gene shows expression only in the testis and in the muscle.Transcriptional regulation of expression
The promoter regulating expression of BEND2 is 1255 base pairs in length and is located directly upstream of the BEND2 gene. It regulates transcription of all five transcriptional variants of BEND2. Genomatix's MatInspector program predicted 418 transcription factor binding sites within the BEND2 promoter, including for SRY, neurogenin, interferon regulatory factor-3, Ikaros2, and TCF/LEF-1.Homology
Paralogs
The BEND2 protein has no known paralogs within the human genome.BEN-domain containing gene family
The BEND2 gene belongs to a family of human genes known as . This includes BANP, BEND3, BEND4, BEND5, BEND6, BEND7, NACC1, and NACC2. The loci for these genes are spread throughout the human genome. Each of these genes contains between one and four BEN domains. Except for at these motifs, the genes of the BEN family do not have similar sequences.Orthologs
The BEND2 gene is conserved across evolutionary time as it has 114 known orthologs in a wide range of vertebrate species including mammals, birds, crocodilia, and amphibians. The BEND2 protein has 42 known orthologs. The C-terminus of the protein, the location of its BEN domains, is highly conserved; however, the N-terminus is not well conserved, even within the order of Primates.| Genus/species | Common name | Order | Date of divergence from H. sapiens | Accession number | Sequence length | Whole sequence identity | C-terminus identity |
| Homo sapiens | Human | Primates | 0 | NP_699177.2 | 799 | 1.000 | 1.000 |
| Pongo abelii | Orangutan | Primates | 15.76 | -- | 784 | 0.921 | 0.854 |
| Macaca nemestrina | Southern pig-tailed macaque | Primates | 29.44 | XP_011733709.1 | 823 | 0.694 | 0.828 |
| Vicugna pacos | Alpaca | Artiodactyla | 96 | XP_015106214.1 | 740 | 0.433 | 0.512 |
| Ceratotherium simum simum | White rhinoceros | Perissodactyla | 96 | XP_014646569.1 | 864 | 0.412 | 0.527 |
| Loxodonta africana | African bush elephant | Proboscidea | 105 | XP_010594135.1 | 829 | 0.382 | 0.489 |
| Canis lupus familiaris | Dog | Carnivora | 96 | XP_013967473.1 | 900 | 0.362 | 0.445 |
| Ailuropoda melanoleuca | Giant panada | Carnivora | 96 | XP_019665441.1 | 852 | 0.353 | 0.460 |
| Rhinolophus sinicus | Chinese horseshoe bat | Chiroptera | 96 | XP_019610944.1 | 808 | 0.345 | 0.459 |
| Dasypus novemcinctus | Nine-banded armadillo | Cingulata | 105 | XP_012377569.1 | 886 | 0.342 | 0.500 |
| Trichechus manatus latirostris | Manatee | Sirenia | 105 | XP_012412857.1 | 950 | 0.335 | 0.475 |
| Chrysochloris asiatica | Cape golden mole | Afrosoricida | 105 | XP_006835746.1 | 683 | 0.330 | 0.443 |
| Oryctolagus cuniculus | European rabbit | Lagomorpha | 90 | XP_017205124.1 | 811 | 0.305 | 0.438 |
| Monodelphis domestica | Gray short-tailed opossum | Didelphimorphia | 159 | XP_007500895.1 | 728 | 0.303 | 0.443 |
| Ornithorhynchus anatinus | Platypus | Monotremata | 177 | XP_007668655.1 | 715 | 0.302 | 0.429 |
| Gavialis gangeticus | Fish-eating crocodile | Crocodilia | 312 | XP_019380828.1 | 697 | 0.309 | 0.458 |
| Chelonia mydas | Green sea turtle | Testudines | 312 | XP_007070584.1 | 749 | 0.297 | 0.453 |
| Apteryx australis mantelli | North Island brown kiwi | Apterygiformes | 312 | XP_013807123.1 | 647 | 0.295 | 0.444 |
| Columba livia | Rock dove | Columbiformes | 312 | XP_005509980.1 | 668 | 0.287 | 0.442 |
| Pygoscelis adeliae | Adelie penguin | Sphenisciformes | 312 | XP_009323754.1 | 657 | 0.282 | 0.458 |
| Nanorana parkeri | Tibet frog | Anura | 352 | XP_018417228.1 | 586 | 0.260 | 0.376 |
Function
BEND2 is predicted to be a DNA-binding protein due to the presence of BEN domains at its C-terminus, a hypothesis supported by its localization to the nucleus, the transcription factors found in its promoter region, and the nature of the proteins it interacts with. Though the precise function of the BEND2 protein is not yet well understood by the scientific community, BEN domains have been found to be important regulators of transcription.Clinical significance
The diseases that have been linked to BEND2 are related to the central nervous system though expression of the gene is not highly observed in these tissues.- BEND2 was identified as one of the genes that causes a central nervous system primitive neuroectodermal tumor when fused with the MN1 gene, which is located on chromosome 22.
- A rare primary central nervous system lymphoma tumor was found to have a high mutation ratio for BEND2; however, the authors do not describe this gene as primarily responsible for the tumor.
- A young girl diagnosed with severe epileptic encephalopathy was found to have a 300-kb deletion in a region that included BEND2, an extremely rare mutation not found in her parents’ genomes.
- An individual with adult autism was identified to have a copy-number variant of unknown significance in a region only containing BEND2.