Phenotypic Mutation 'Huang_river' (pdf version)
AlleleHuang_river
Mutation Type missense
Chromosome10
Coordinate21,028,516 bp (GRCm39)
Base Change A ⇒ G (forward strand)
Gene Myb
Gene Name myeloblastosis oncogene
Synonym(s) c-myb
Chromosomal Location 21,000,834-21,036,883 bp (-) (GRCm39)
MGI Phenotype FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene encodes a protein with three HTH DNA-binding domains that functions as a transcription regulator. This protein plays an essential role in the regulation of hematopoiesis. This gene may be aberrently expressed or rearranged or undergo translocation in leukemias and lymphomas, and is considered to be an oncogene. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jan 2016]
PHENOTYPE: Mice homozygous for deficient alleles of this gene display severe hematopoietic abnormalities. Red and white blood cells and platelets are all affected. [provided by MGI curators]
Accession Number

NCBI RefSeq: NM_001198914 (variant 1), NM_010848 (variant 2); MGI:97249

MappedYes 
Limits of the Critical Region 21124930 - 21160984 bp
Amino Acid Change Serine changed to Proline
Institutional SourceBeutler Lab
Gene Model predicted gene model for protein(s): [ENSMUSP00000020158] [ENSMUSP00000139699]
AlphaFold P06876
PDB Structure CRYSTAL STRUCTURE OF C-MYB R1 [X-RAY DIFFRACTION]
CRYSTAL STRUCTURE OF C-MYB R2R3 [X-RAY DIFFRACTION]
CRYSTAL STRUCTURE OF C-MYB R2 [X-RAY DIFFRACTION]
CRYSTAL STRUCTURE OF C-MYB R2 V103L MUTANT [X-RAY DIFFRACTION]
CRYSTAL STRUCTURE OF TERNARY PROTEIN-DNA COMPLEX1 [X-RAY DIFFRACTION]
CRYSTAL STRUCTURE OF TERNARY PROTEIN-DNA COMPLEX2 [X-RAY DIFFRACTION]
STRUCTURE OF MYB TRANSFORMING PROTEIN, NMR, MINIMIZED AVERAGE STRUCTURE [SOLUTION NMR]
STRUCTURE OF MYB TRANSFORMING PROTEIN, NMR, 20 STRUCTURES [SOLUTION NMR]
MOUSE C-MYB DNA-BINDING DOMAIN REPEAT 1 [SOLUTION NMR]
MOUSE C-MYB DNA-BINDING DOMAIN REPEAT 1 [SOLUTION NMR]
>> 8 additional structures at PDB <<
SMART Domains Protein: ENSMUSP00000020158
Gene: ENSMUSG00000019982
AA Change: S116P

DomainStartEndE-ValueType
low complexity region 7 27 N/A INTRINSIC
SANT 39 88 9.52e-20 SMART
SANT 91 140 2.04e-19 SMART
SANT 143 191 1.75e-18 SMART
low complexity region 227 239 N/A INTRINSIC
Pfam:LMSTEN 267 313 4e-29 PFAM
Pfam:Cmyb_C 399 559 1.5e-64 PFAM
Predicted Effect probably damaging

PolyPhen 2 Score 0.998 (Sensitivity: 0.27; Specificity: 0.99)
(Using ENSMUST00000020158)
SMART Domains Protein: ENSMUSP00000139699
Gene: ENSMUSG00000019982
AA Change: S116P

DomainStartEndE-ValueType
low complexity region 7 27 N/A INTRINSIC
SANT 39 88 9.52e-20 SMART
SANT 91 140 2.04e-19 SMART
SANT 143 191 1.75e-18 SMART
low complexity region 227 239 N/A INTRINSIC
Pfam:LMSTEN 266 313 3.6e-32 PFAM
low complexity region 409 421 N/A INTRINSIC
Pfam:Cmyb_C 516 682 8.5e-66 PFAM
Predicted Effect probably damaging

PolyPhen 2 Score 0.995 (Sensitivity: 0.68; Specificity: 0.97)
(Using ENSMUST00000188495)
Meta Mutation Damage Score 0.9162 question?
Is this an essential gene? Essential (E-score: 1.000) question?
Phenotypic Category Autosomal Semidominant
Candidate Explorer Status loading ...
Single pedigree
Linkage Analysis Data
Penetrance  
Alleles Listed at MGI

All Mutations and Alleles(23) : Chemically induced (ENU)(4) Chemically induced (other)(1) Gene trapped(3) Targeted(13) Transgenic(2)

Lab Alleles
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL00654:Myb APN 10 21017725 missense probably damaging 0.99
IGL00707:Myb APN 10 21024283 missense probably damaging 1.00
IGL00796:Myb APN 10 21017698 missense probably benign 0.00
IGL01012:Myb APN 10 21022159 missense probably benign 0.03
IGL01082:Myb APN 10 21028843 missense probably damaging 1.00
IGL01365:Myb APN 10 21028401 missense probably benign 0.31
IGL01906:Myb APN 10 21028533 missense probably damaging 1.00
IGL02560:Myb APN 10 21028347 missense probably damaging 1.00
PIT4495001:Myb UTSW 10 21028521 missense probably damaging 0.98
R0385:Myb UTSW 10 21030611 missense possibly damaging 0.73
R0442:Myb UTSW 10 21002095 missense probably benign 0.05
R0759:Myb UTSW 10 21020927 missense probably benign 0.01
R0882:Myb UTSW 10 21032259 missense possibly damaging 0.75
R0920:Myb UTSW 10 21002133 missense possibly damaging 0.80
R1401:Myb UTSW 10 21028844 missense probably damaging 1.00
R1651:Myb UTSW 10 21002097 missense probably damaging 1.00
R1752:Myb UTSW 10 21032336 missense possibly damaging 0.89
R1879:Myb UTSW 10 21017876 missense probably benign 0.24
R1971:Myb UTSW 10 21016555 missense probably benign 0.00
R4355:Myb UTSW 10 21028516 missense probably damaging 1.00
R4611:Myb UTSW 10 21021223 missense probably damaging 1.00
R4650:Myb UTSW 10 21028840 missense probably damaging 1.00
R4888:Myb UTSW 10 21002137 missense probably benign 0.01
R5121:Myb UTSW 10 21002137 missense probably benign 0.01
R5922:Myb UTSW 10 21028826 missense probably damaging 1.00
R5955:Myb UTSW 10 21028398 missense probably damaging 1.00
R6116:Myb UTSW 10 21030653 missense probably damaging 1.00
R6150:Myb UTSW 10 21017668 missense probably damaging 1.00
R6207:Myb UTSW 10 21021221 missense probably benign
R6656:Myb UTSW 10 21028844 missense probably damaging 1.00
R6801:Myb UTSW 10 21020865 splice site probably null
R6824:Myb UTSW 10 21021019 missense probably benign 0.00
R6884:Myb UTSW 10 21028431 missense probably damaging 1.00
R6977:Myb UTSW 10 21028551 missense probably damaging 0.96
R7562:Myb UTSW 10 21017653 splice site probably null
R7651:Myb UTSW 10 21032273 missense probably damaging 1.00
R7747:Myb UTSW 10 21032324 missense possibly damaging 0.89
R8346:Myb UTSW 10 21002136 missense probably benign 0.00
R8683:Myb UTSW 10 21026405 missense possibly damaging 0.53
R8829:Myb UTSW 10 21021130 missense probably damaging 0.96
R9227:Myb UTSW 10 21030612 missense probably benign 0.03
R9228:Myb UTSW 10 21030612 missense probably benign 0.03
R9240:Myb UTSW 10 21016500 missense probably damaging 1.00
R9304:Myb UTSW 10 21028516 missense probably damaging 1.00
R9408:Myb UTSW 10 21026275 missense probably benign 0.21
R9517:Myb UTSW 10 21030612 missense probably benign 0.03
R9576:Myb UTSW 10 21030612 missense probably benign 0.03
R9577:Myb UTSW 10 21030612 missense probably benign 0.03
R9610:Myb UTSW 10 21030627 nonsense probably null
Mode of Inheritance Autosomal Semidominant
Local Stock gDNA
Repository
Last Updated 2019-09-04 9:43 PM by Diantha La Vine
Record Created 2016-04-11 4:57 PM by Xue Zhong
Record Posted 2018-09-07
Phenotypic Description
Figure 1. Huang_river mice exhibit decreased frequencies of peripheral B1a cells. Flow cytometric analysis of peripheral blood was utilized to determine B1a cell frequency. Normalized data are shown. Abbreviations: WT, wild-type; REF, homozygous reference mice; HET, heterozygous variant mice; VAR, homozygous variant mice. Mean (μ) and standard deviation (σ) are indicated.
Figure 2. Huang_river mice exhibit increased frequencies of peripheral NK cells. Flow cytometric analysis of peripheral blood was utilized to determine NK cell frequency. Normalized data are shown. Abbreviations: WT, wild-type; REF, homozygous reference mice; HET, heterozygous variant mice; VAR, homozygous variant mice. Mean (μ) and standard deviation (σ) are indicated.

The Huang_river phenotype was identified among N-ethyl-N-nitrosourea (ENU)-mutagenized G3 mice of the pedigree R4355, some of which showed a reduced frequency of B1a cells (Figure 1) with a concomitant increase in the frequency of NK cells (Figure 2) in the peripheral blood.

Nature of Mutation
Figure 3. Linkage mapping of increased frequency of peripheral blood NK cells using an additive model of inheritance. Manhattan plot shows -log10 P values (Y-axis) plotted against the chromosome positions of 58 mutations (X-axis) identified in the G1 male of pedigree R4355. Normalized phenotype data are shown for single locus linkage analysis without consideration of G2 dam identity. Horizontal pink and red lines represent thresholds of P = 0.05, and the threshold for P = 0.05 after applying Bonferroni correction, respectively.
Figure 4. CRISPR-Myb mice exhibit increased frequencies of peripheral NK cells. Flow cytometric analysis of peripheral blood was utilized to determine NK cell frequency. Normalized data are shown. Abbreviations: WT, wild-type; REF, homozygous reference mice; HET, heterozygous variant mice; VAR, homozygous variant mice. Mean (μ) and standard deviation (σ) are indicated.

Whole exome HiSeq sequencing of the G1 grandsire identified 58 mutations. All of the above phenotypes were linked by continuous variable mapping to a mutation in Myb: a T to C transition at base pair 21,152,617 (v38) on chromosome 10, or base pair 8,368 in the GenBank genomic region NC_000076 encoding Myb. The strongest association was found with an additive model of inheritance to the NK cell frequency phenotype, wherein four variant homozygotes and 24 heterozygous mice departed phenotypically from 12 homozygous reference mice with a P value of 6.033 x 10-11 (Figure 3).  

The mutation corresponds to residue 612 in the mRNA sequence NM_010848 within exon 5 of 15 total exons.

597 GGTCCGAAGCGTTGGTCTGTTATTGCCAAGCAC

111 -G--P--K--R--W--S--V--I--A--K--H-

The mutated nucleotide is indicated in red.  The mutation results in a serine (S) to proline (P) substitution at position 116 (S116P) in the MYB protein, and is strongly predicted by PolyPhen-2 to be damaging (score = 0.998).

The causative mutation in Myb was confirmed by CRISPR-mediated replacement of the MybHuang_river allele (Figure 4 (FACS NK cells; P = 2.469 x 10-7) and Table 1).

Table 1. CRISPR results

Screen

CRISPR P-value

FACS NK cells

2.469 x 10-7

FACS B1a cells

8.895 x 10-4

Illustration of Mutations in
Gene & Protein
Protein Prediction
Figure 5. Domain organization of the c-Myb protein. The Huang_river mutation results in a serine to proline substitution at position 116 of the protein. Abbreviations: HTH, helix-turn-helix; DBD, DNA-binding domain; TAD, transactivation domain; NRD, negative regulatory domain

Myb encodes c-Myb, a member of the Myb transcription factor superfamily. Similar to other members of the Myb family (i.e., A-Myb and B-Myb in vertebrates), c-Myb has an N-terminal DNA-binding domain (DBD; alternatively, SANT [Swi3, Ada2, N-Cor, and TFIIIB]-like domain) with three HTH (helix-turn-helix) repeats and a nuclear localization signal, a central transactivation domain (TAD), and a C-terminal negative regulatory domain (NRD) involved in transcriptional repression (Figure 5). 

The HTH motifs are imperfect repeats of approximately 50 amino acids. The HTH motifs have a conserved tryptophan spaced between 18/19 amino acids that participates in forming a hydrophobic core [PDB:1MBK; (1;2)]. The HTH repeats, namely HTH2 and HTH3, specifically bind to the DNA sequence 5’-pYAACG/TG-3’ (3-5). HTH1 is not required for DNA binding, but does mediate the interaction of c-Myb with its associated proteins (6).

The NRD contains a leucine zipper-like motif, FAETL domain, TPTPF motif, and an EVES motif. The leucine zipper is predicted to mediate dimer formation (7). The FAETL domain is required for the function of v-Myb (an oncogene found in two avian retroviruses that induce leukemia) (8). The FAETL domain is highly conserved, but the function in mouse and/or humans is unknown. The function of the TPTPF domain is also unknown. The EVES motif is highly conserved in vertebrate c-Myb. The EVES motif contains a phosphorylation site that negatively regulates c-Myb function. The EVES motif mediates interaction with the transcriptional coactivator p100 as well as interactions with the c-Myb N-terminus as a method of intramolecular regulation (9).

c-Myb can interact with 50 proteins, many of which function as either coactivators (e.g., FLASH, p100, Menin, Mi-2α, Mybbp1a, and CBP/p300) or corepressors (e.g., N-Cor, mSin-3a, TIF-1β, and C-Ski) [(10); reviewed in (11)]. c-Myb also interacts with cyclin D1 and D2 (12). Interaction between the c-Myb TAD, CBP (CREB-binding protein), and p300 promotes transactivation in hematopoietic cells. A LxxLL motif within the TAD mediates the interaction with p300. For a full list of interacting proteins see BioGRID.

c-Myb undergoes several posttranslational modifications, including serine and threonine phosphorylation (9;13-18), lysine acetylation (19), SUMOylation (18;20;21), and ubiquitination (22). The c-Myb posttranslational modifications putatively alter protein-protein interactions to positively or negatively regulate c-Myb function.

Humans have two major c-Myb isoforms: p89-Myb (89 kD; isoform 1) and p72-Myb (72 kD; isoform 2) (23); p72-Myb is the canonical c-Myb isoform. p89-Myb is the product of alternative splicing, having an extra spliced exon 9B that encodes 121 amino acids. The function of p89-Myb is unknown, but it is not required for hematopoietic development (24). There are at least 29 MYB minor transcript isoforms in human CD34+ progenitor and Jurkat-T cells; the functions of these minor isoforms are unknown (25).

The Huang_river mutation results in a serine (S) to proline (P) substitution at position 116 (S116P) in the c-Myb protein; amino acid 116 is within the second HTH repeat.

Expression/Localization

c-Myb is highly expressed in immature, proliferating epithelial, endothelial and hematopoietic cells and is downregulated as cells become more differentiated. c-Myb localizes to the nucleus.

Background
Figure 6. The effects of c-Myb deficiency on hematopoiesis. (+) Indicates an increase in cell population after loss of c-Myb; (-) indicates a decrease in cell population.

c-Myb is a transcription regulator that functions in hematopoiesis and erythropoiesis (Figure 6) (26).  c-Myb is a stem cell regulator in hematopoietic stem cells (27), neurons (28), colonic crypts (29), and vascular smooth muscle cells (30). c-Myb has over 80 validated target genes [Table 1; reviewed in (31)]. Most c-Myb target genes are positively regulated by c-Myb, but some are repressed by c-Myb.

Table 1. Select c-Myb target genes

Target gene

Details

References

Cell proliferation

Myc

Oncogene; iPS cell transformation transcription factor

(32;33)

Kit

Proto-oncogene; see the record for pretty2

(34)

Ccnb1 (cyclin B1) and Ccne1 (cyclin E1)

Cell cycle factors at the G2/M transition in the cell cycle

(35;36)

Cell differentiation

Myadm (myeloid-associated differentiation marker

Myeloid differentiation

(37)

Klf4 (Kruppel-like factor 4)

Transcription factor; skin development

(36)

Pf4 (platelet factor 4)

Chemokine; inhibits hematopoiesis, angiogenesis, and T cell function

Nanog

Transcription factor required for embryonic stem cell proliferation, renewal, and acquisition of pluripotency

Elane (neutrophil elastase 2)

Serine protease; see the record for Ruo

(38;39)

Gata3 (GATA binding protein 3)

Transcription factor that promotes helper T cell development and blocks development of cytotoxic T cells

(40)

Bcl2

Apoptosis regulator in T cell development

(41;42)

Car1 (carbonic anhydrase 1)

Enzyme that mediates differentiation of mouse erythroleukemia cells

(43)

H2afz (H2A histone Z)

Histone component

(44)

Ptcra (pre-T cell antigen receptor alpha)

TCR subunit

(38;41)

Rag2 (recombination activating gene 2)

Factor in V(D)J recombination; see the record for snowcock

(41;45;46)

Cd4

TCR co-receptor; see the record for thoth

(47)

Tcrd (TCR delta chain)

TCR subunit

(48;49)

Tcrg (TCR gamma chain)

TCR subunit

(50)

c-Myb is an oncogene. Aberrant c-Myb expression, MYB gene rearrangements, or MYB translocations have been detected in some leukemias and lymphomas [(51;52); reviewed in (11)]. High expression levels of MYB have also been found in pancreatic, colon, and breast tumors [(53;54); reviewed in (55)].

Myb-deficient (Myb-/-) mice exhibited embryonic lethality between days E14 and E15 due to failure to develop mature blood cells (56-58). Myb-/- mice exhibit reduced body sizes, anemia, and reduced thymocyte numbers as well as abnormal erythropoiesis, B cell differentiation, and T cell differentiation (57-59). Heterozygous Myb (Myb+/-) mice exhibited reduced B1 B cells in the spleen and peritoneal cavity and pre-B cells in the bone marrow due to arrested B cell differentiation at the pro- to pre-B cell transition (60). Homozygous mice expressing a ENU-induced mutant Myb allele (Mybboo/boo; E308G) exhibited abnormal erythropoiesis and hematopoiesis (61). The spleen in the Mybboo/boo mice was enlarged, the number of neutrophils decreased, and they exhibited reduced B cell lymphoiesis (61). Homozygous mice expressing a second ENU-induced mutant Myb allele (MybM303V/M303V; M303V) exhibited reduced splenocyte and thymocyte numbers (i.e., B220+ B cells, CD4+ T cells, and CD8+ T cells), block at the pro- to pre-B cell transition, arrested T cell differentiation, anemia, reduced numbers of eosinophils (27).

Putative Mechanism

c-Myb functions in the differentiation of lymphocytes from precursor stem cells. Loss of c-Myb expression blocks early T cell development (62). In T cell development, c-Myb promotes the development of helper T cells and blocks cytotoxic T cell development (40). c-Myb is also essential for B cell development (63). Loss of c-Myb expression results in a block in the transition from the pro-B cell stage to the pre-B cell stage putatively due to defects in IL-7 signaling. The phenotype of the Huang_river mice indicates loss of c-Myb-related function.

Primers PCR Primer
Huang_river_pcr_F: TTGTTGCCCAAGTCTTACCG
Huang_river_pcr_R: GGTTTCTCACCCCAAGGAAG

Sequencing Primer
Huang_river_seq_F: AAGTCTTACCGTCCGGGCAG
Huang_river_seq_R: CAGGAAGTAAAGGGCTGGCTCC
Genotyping

PCR program

1) 94°C 2:00
2) 94°C 0:30
3) 55°C 0:30
4) 72°C 1:00
5) repeat steps (2-4) 40x
6) 72°C 10:00
7) 4°C hold


The following sequence of 420 nucleotides is amplified (chromosome 10, - strand):


1   ggtttctcac cccaaggaag caatttaaat cttcaaacag gaagtaaagg gctggctcct
61  gcatgtccag tggatgaaag cagattattt caagatctga agatcttgta acattgaggc
121 ttgatgacgc tgactctttc cgtaacatta aaacacagat tatttttctg ttcatctgaa
181 ggtcatagag cttgtccaga aatatggtcc gaagcgttgg tctgttattg ccaagcactt
241 aaaagggaga attggaaagc agtgtcggga gaggtggcac aaccatttga atccagaagt
301 taagaaaacc tcctggacag aagaggagga cagaatcatt taccaggcac acaagcgtct
361 ggggaacaga tgggcagaga tcgcaaagct gctgcccgga cggtaagact tgggcaacaa 


Primer binding sites are underlined and the sequencing primers are highlighted; the mutated nucleotide is shown in red.

References
Science Writers Anne Murray
Illustrators Diantha La Vine
AuthorsMing Zeng, Xue Zhong, and Bruce Beutler