• Rbm38 is essential for bone marrow RBC production and erythroid heme biosynthesis.

  • Rbm38 deficiency disrupts the splicing, stability, and translation of Fech, resulting in an EPP–like disorder in mice.

Abstract

RNA splicing and processing are critical for erythropoiesis, because dysregulation of RNA splicing ultimately disrupts protein synthesis. The RNA-binding protein Rbm38 is highly expressed during terminal erythropoiesis. Although in vitro studies have implicated Rbm38 as a key regulator of erythroid differentiation, the landscape of RNA splicing regulated by Rbm38 and its role in terminal erythropoiesis in vivo have not been fully elucidated. Here, we generated whole-body and conditional knockout mouse models for Rbm38 and found that mature red blood cell (RBC) production was impaired in the bone marrow of Rbm38-deficient mice. Rbm38–/– RBCs exhibited reduced hemoglobin content and increased susceptibility to oxidative stress–induced hemolysis. These mutant mice also developed microcytic hypochromic anemia, along with dysregulated iron homeostasis. Additionally, they exhibited decreased mitochondrial heme biosynthesis and accumulation of free protoporphyrin IX (PPIX) in erythrocytes and feces, resembling human erythropoietic protoporphyria (EPP). Mechanistically, Rbm38 regulates the incorporation of ferrous iron (Fe2+) into PPIX to form heme by modulating alternative splicing, messenger RNA decay, and translation of the porphyrin metabolic enzyme gene Ferrochelatase (Fech). Importantly, enforced expression of Fech largely restored erythroid differentiation defects and ameliorated anemia in Rbm38–/– transplants. We further demonstrated that genetic variants in the human RBM38 gene locus influence PPIX levels in erythrocytes from healthy cohorts. Our findings demonstrate that Rbm38 governs terminal erythropoiesis by orchestrating RNA splicing, stability, and translation during heme biosynthesis.

1.
Corley
M
,
Burns
MC
,
Yeo
GW
.
How RNA-binding proteins interact with RNA: molecules and mechanisms
.
Mol Cell
.
2020
;
78
(
1
):
9
-
29
.
2.
Van Nostrand
EL
,
Freese
P
,
Pratt
GA
, et al
.
A large-scale binding and functional map of human RNA-binding proteins
.
Nature
.
2020
;
583
(
7818
):
711
-
719
.
3.
Zou
C
,
Wan
Y
,
He
L
, et al
.
RBM38 in cancer: role and mechanism
.
Cell Mol Life Sci
.
2021
;
78
(
1
):
117
-
128
.
4.
Wang
F
,
Song
W
,
Zhao
H
, et al
.
The RNA-binding protein QKI5 regulates primary miR-124-1 processing via a distal RNA motif during erythropoiesis
.
Cell Res
.
2017
;
27
(
3
):
416
-
439
.
5.
van Zalen
S
,
Jeschke
GR
,
Hexner
EO
,
Russell
JE
.
AUF-1 and YB-1 are critical determinants of beta-globin mRNA expression in erythroid cells
.
Blood
.
2012
;
119
(
4
):
1045
-
1053
.
6.
Naarmann-de Vries
IS
,
Senatore
R
,
Moritz
B
, et al
.
Methylated HNRNPK acts on RPS19 to regulate ALOX15 synthesis in erythropoiesis
.
Nucleic Acids Res
.
2021
;
49
(
6
):
3507
-
3523
.
7.
Ma
Y
,
Liu
S
,
Gao
J
, et al
.
Genome-wide analysis of pseudogenes reveals HBBP1's human-specific essentiality in erythropoiesis and implication in beta-thalassemia
.
Dev Cell
.
2021
;
56
(
4
):
478
-
493.e11
.
8.
Bondu
S
,
Alary
AS
,
Lefèvre
C
, et al
.
A variant erythroferrone disrupts iron homeostasis in SF3B1-mutated myelodysplastic syndrome
.
Sci Transl Med
.
2019
;
11
(
500
):
eaav5467
.
9.
Heinicke
LA
,
Nabet
B
,
Shen
S
, et al
.
The RNA binding protein RBM38 (RNPC1) regulates splicing during late erythroid differentiation
.
PLoS One
.
2013
;
8
(
10
):
e78031
.
10.
Ulirsch
JC
,
Nandakumar
SK
,
Wang
L
, et al
.
Systematic functional dissection of common genetic variation affecting red blood cell traits
.
Cell
.
2016
;
165
(
6
):
1530
-
1545
.
11.
Qi
Q
,
Cheng
L
,
Tang
X
, et al
.
Dynamic CTCF binding directly mediates interactions among cis-regulatory elements essential for hematopoiesis
.
Blood
.
2021
;
137
(
10
):
1327
-
1339
.
12.
Zhang
J
,
Xu
E
,
Ren
C
, et al
.
Mice deficient in Rbm38, a target of the p53 family, are susceptible to accelerated aging and spontaneous tumors
.
Proc Natl Acad Sci U S A
.
2014
;
111
(
52
):
18637
-
18642
.
13.
Balwani
M
,
Doheny
D
,
Bishop
DF
, et al
.
Loss-of-function ferrochelatase and gain-of-function erythroid-specific 5-aminolevulinate synthase mutations causing erythropoietic protoporphyria and x-linked protoporphyria in North American patients reveal novel mutations and a high prevalence of X-linked protoporphyria
.
Mol Med
.
2013
;
19
(
1
):
26
-
35
.
14.
Corces
MR
,
Buenrostro
JD
,
Wu
B
, et al
.
Lineage-specific and single-cell chromatin accessibility charts human hematopoiesis and leukemia evolution
.
Nat Genet
.
2016
;
48
(
10
):
1193
-
1203
.
15.
Yin
R
,
Chang
J
,
Li
Y
, et al
.
Differential m(6)A RNA landscapes across hematopoiesis reveal a role for IGF2BP2 in preserving hematopoietic stem cell function
.
Cell Stem Cell
.
2022
;
29
(
1
):
149
-
159.e7
.
16.
Downes
DJ
,
Beagrie
RA
,
Gosden
ME
, et al
.
High-resolution targeted 3C interrogation of cis-regulatory element organization at genome-wide scale
.
Nat Commun
.
2021
;
12
(
1
):
531
.
17.
Bozhilov
YK
,
Downes
DJ
,
Telenius
J
, et al
.
A gain-of-function single nucleotide variant creates a new promoter which acts as an orientation-dependent enhancer-blocker
.
Nat Commun
.
2021
;
12
(
1
):
3806
.
18.
Romano
O
,
Petiti
L
,
Felix
T
, et al
.
GATA factor-mediated gene regulation in human erythropoiesis
.
iScience
.
2020
;
23
(
4
):
101018
.
19.
Kingsley
PD
,
Greenfest-Allen
E
,
Frame
JM
, et al
.
Ontogeny of erythroid gene expression
.
Blood
.
2013
;
121
(
6
):
e5
-
e13
.
20.
Oudelaar
AM
,
Beagrie
RA
,
Gosden
M
, et al
.
Dynamics of the 4D genome during in vivo lineage specification and differentiation
.
Nat Commun
.
2020
;
11
(
1
):
2722
.
21.
Cai
W
,
Huang
J
,
Zhu
Q
, et al
.
Enhancer dependence of cell-type-specific gene expression increases with developmental age
.
Proc Natl Acad Sci U S A
.
2020
;
117
(
35
):
21450
-
21458
.
22.
Huang
P
,
Keller
CA
,
Giardine
B
, et al
.
Comparative analysis of three-dimensional chromosomal architecture identifies a novel fetal hemoglobin regulatory element
.
Genes Dev
.
2017
;
31
(
16
):
1704
-
1713
.
23.
Francis
HS
,
Harold
CL
,
Beagrie
RA
, et al
.
Scalable in vitro production of defined mouse erythroblasts
.
PLoS One
.
2022
;
17
(
1
):
e0261950
.
24.
Alvarez-Dominguez
JR
,
Zhang
X
,
Hu
W
.
Widespread and dynamic translational control of red blood cell development
.
Blood
.
2017
;
129
(
5
):
619
-
629
.
25.
Liu
J
,
Zhang
J
,
Ginzburg
Y
, et al
.
Quantitative analysis of murine terminal erythroid differentiation in vivo: novel method to study normal and disordered erythropoiesis
.
Blood
.
2013
;
121
(
8
):
e43
-
e49
.
26.
Mei
Y
,
Zhao
B
,
Basiorka
AA
, et al
.
Age-related inflammatory bone marrow microenvironment induces ineffective erythropoiesis mimicking del(5q) MDS
.
Leukemia
.
2018
;
32
(
4
):
1023
-
1033
.
27.
Mei
Y
,
Zhao
B
,
Yang
J
, et al
.
Ineffective erythropoiesis caused by binucleated late-stage erythroblasts in mDia2 hematopoietic specific knockout mice
.
Haematologica
.
2016
;
101
(
1
):
e1
-
e5
.
28.
Mei
Y
,
Ren
K
,
Liu
Y
, et al
.
Bone marrow-confined IL-6 signaling mediates the progression of myelodysplastic syndromes to acute myeloid leukemia
.
J Clin Invest
.
2022
;
132
(
17
):
e152673
.
29.
Li
Z
,
Su
M
,
Xie
X
, et al
.
mDia formins form hetero-oligomers and cooperatively maintain murine hematopoiesis
.
PLoS Genet
.
2023
;
19
(
12
):
e1011084
.
30.
Li
W
,
Wang
Y
,
Zhao
H
, et al
.
Identification and transcriptome analysis of erythroblastic island macrophages
.
Blood
.
2019
;
134
(
5
):
480
-
491
.
31.
Schwartz
AJ
,
Das
NK
,
Ramakrishnan
SK
, et al
.
Hepatic hepcidin/intestinal HIF-2alpha axis maintains iron absorption during iron deficiency and overload
.
J Clin Invest
.
2019
;
129
(
1
):
336
-
348
.
32.
Shah
DI
,
Takahashi-Makise
N
,
Cooney
JD
, et al
.
Mitochondrial Atpif1 regulates haem synthesis in developing erythroblasts
.
Nature
.
2012
;
491
(
7425
):
608
-
612
.
33.
Yien
YY
,
Perfetto
M
.
Regulation of heme synthesis by mitochondrial homeostasis proteins
.
Front Cell Dev Biol
.
2022
;
10
:
895521
.
34.
Liu
G
,
Sil
D
,
Maio
N
, et al
.
Heme biosynthesis depends on previously unrecognized acquisition of iron-sulfur cofactors in human amino-levulinic acid dehydratase
.
Nat Commun
.
2020
;
11
(
1
):
6310
.
35.
Nguyen
AT
,
Prado
MA
,
Schmidt
PJ
, et al
.
UBE2O remodels the proteome during terminal erythroid differentiation
.
Science
.
2017
;
357
(
6350
):
eaan0218
.
36.
Bailey
HJ
,
Bezerra
GA
,
Marcero
JR
, et al
.
Human aminolevulinate synthase structure reveals a eukaryotic-specific autoinhibitory loop regulating substrate binding and product release
.
Nat Commun
.
2020
;
11
(
1
):
2813
.
37.
Guernsey
DL
,
Jiang
H
,
Campagna
DR
, et al
.
Mutations in mitochondrial carrier family gene SLC25A38 cause nonsyndromic autosomal recessive congenital sideroblastic anemia
.
Nat Genet
.
2009
;
41
(
6
):
651
-
653
.
38.
Bayeva
M
,
Khechaduri
A
,
Wu
R
, et al
.
ATP-binding cassette B10 regulates early steps of heme synthesis
.
Circ Res
.
2013
;
113
(
3
):
279
-
287
.
39.
Beilschmidt
LK
,
Ollagnier de Choudens
S
,
Fournier
M
, et al
.
ISCA1 is essential for mitochondrial Fe(4)S(4) biogenesis in vivo
.
Nat Commun
.
2017
;
8
:
15124
.
40.
Lill
R
,
Hoffmann
B
,
Molik
S
, et al
.
The role of mitochondria in cellular iron-sulfur protein biogenesis and iron metabolism
.
Biochim Biophys Acta
.
2012
;
1823
(
9
):
1491
-
1508
.
41.
Zhang
P
,
Park
HJ
,
Zhang
J
, et al
.
Translation of the intrinsically disordered protein alpha-synuclein is inhibited by a small molecule targeting its structured mRNA
.
Proc Natl Acad Sci U S A
.
2020
;
117
(
3
):
1457
-
1467
.
42.
Deacon
AC
,
Elder
GH
.
ACP Best Practice No 165: front line tests for the investigation of suspected porphyria
.
J Clin Pathol
.
2001
;
54
(
7
):
500
-
507
.
43.
Lennon
ÁM
,
Brune
L
,
Techert
S
,
Buchalla
W
.
Fluorescence spectroscopy shows porphyrins produced by cultured oral bacteria differ depending on composition of growth media
.
Caries Res
.
2023
;
57
(
1
):
74
-
86
.
44.
van der Harst
P
,
Zhang
W
,
Mateo Leach
I
, et al
.
Seventy-five genetic loci influencing the human red blood cell
.
Nature
.
2012
;
492
(
7429
):
369
-
375
.
45.
Choudhuri
A
,
Trompouki
E
,
Abraham
BJ
, et al
.
Common variants in signaling transcription-factor-binding sites drive phenotypic variability in red blood cell traits
.
Nat Genet
.
2020
;
52
(
12
):
1333
-
1345
.
46.
Traxler
EA
,
Thom
CS
,
Yao
Y
,
Paralkar
V
,
Weiss
MJ
.
Nonspecific inhibition of erythropoiesis by short hairpin RNAs
.
Blood
.
2018
;
131
(
24
):
2733
-
2736
.
47.
Zhao
B
,
Keerthivasan
G
,
Mei
Y
, et al
.
Targeted shRNA screening identified critical roles of pleckstrin-2 in erythropoiesis
.
Haematologica
.
2014
;
99
(
7
):
1157
-
1167
.
48.
Zhao
B
,
Mei
Y
,
Cao
L
, et al
.
Loss of pleckstrin-2 reverts lethality and vascular occlusions in JAK2V617F-positive myeloproliferative neoplasms
.
J Clin Invest
.
2018
;
128
(
1
):
125
-
140
.
49.
Thom
CS
,
Traxler
EA
,
Khandros
E
, et al
.
Trim58 degrades dynein and regulates terminal erythropoiesis
.
Dev Cell
.
2014
;
30
(
6
):
688
-
700
.
50.
Lee
E
,
Choi
HS
,
Hwang
JH
,
Hoh
JK
,
Cho
YH
,
Baek
EJ
.
The RNA in reticulocytes is not just debris: it is necessary for the final stages of erythrocyte formation
.
Blood Cells Mol Dis
.
2014
;
53
(
1-2
):
1
-
10
.
51.
Skulski
M
,
Bartoszewski
R
,
Majkowski
M
, et al
.
Efficient method for isolation of reticulocyte RNA from healthy individuals and hemolytic anaemia patients
.
J Cell Mol Med
.
2019
;
23
(
1
):
487
-
496
.
52.
Jain
V
,
Yang
WH
,
Wu
J
,
Roback
JD
,
Gregory
SG
,
Chi
JT
.
Single cell RNA-seq analysis of human red cells
.
Front Physiol
.
2022
;
13
:
828700
.
53.
Lyu
J
,
Gu
Z
,
Zhang
Y
, et al
.
A glutamine metabolic switch supports erythropoiesis
.
Science
.
2024
;
386
(
6723
):
eadh9215
.
54.
Qi
D
,
Geng
Y
,
Cardenas
J
, et al
.
Transcriptomic analyses of patient peripheral blood with hemoglobin depletion reveal glioblastoma biomarkers
.
NPJ Genom Med
.
2023
;
8
(
1
):
2
.
55.
Hatta
S
,
Fujiwara
T
,
Yamamoto
T
, et al
.
A defined culture method enabling the establishment of ring sideroblasts from induced pluripotent cells of X-linked sideroblastic anemia
.
Haematologica
.
2018
;
103
(
5
):
e188
-
e191
.
56.
Barman-Aksözen
J
,
Halloy
F
,
Iyer
PS
, et al
.
Delta-aminolevulinic acid synthase 2 expression in combination with iron as modifiers of disease severity in erythropoietic protoporphyria
.
Mol Genet Metab
.
2019
;
128
(
3
):
304
-
308
.
57.
Ricci
A
,
Di Betto
G
,
Bergamini
E
,
Buzzetti
E
,
Corradini
E
,
Ventura
P
.
Iron metabolism in the disorders of heme biosynthesis
.
Metabolites
.
2022
;
12
(
9
):
819
.
58.
Dandekar
T
,
Stripecke
R
,
Gray
NK
, et al
.
Identification of a novel iron-responsive element in murine and human erythroid delta-aminolevulinic acid synthase mRNA
.
EMBO J
.
1991
;
10
(
7
):
1903
-
1909
.
59.
Medlock
AE
,
Shiferaw
MT
,
Marcero
JR
, et al
.
Identification of the mitochondrial heme metabolism complex
.
PLoS One
.
2015
;
10
(
8
):
e0135896
.
60.
Tutois
S
,
Montagutelli
X
,
Da Silva
V
, et al
.
Erythropoietic protoporphyria in the house mouse. A recessive inherited ferrochelatase deficiency with anemia, photosensitivity, and liver disease
.
J Clin Invest
.
1991
;
88
(
5
):
1730
-
1736
.
61.
Lyoumi
S
,
Abitbol
M
,
Andrieu
V
, et al
.
Increased plasma transferrin, altered body iron distribution, and microcytic hypochromic anemia in ferrochelatase-deficient mice
.
Blood
.
2007
;
109
(
2
):
811
-
818
.
62.
Magness
ST
,
Maeda
N
,
Brenner
DA
.
An exon 10 deletion in the mouse ferrochelatase gene has a dominant-negative effect and causes mild protoporphyria
.
Blood
.
2002
;
100
(
4
):
1470
-
1477
.
63.
Barman-Aksözen
J
,
C Wiek
P
,
Bansode
VB
, et al
.
Modeling the ferrochelatase c.315-48C modifier mutation for erythropoietic protoporphyria (EPP) in mice
.
Dis Model Mech
.
2017
;
10
(
3
):
225
-
233
.
64.
Gouya
L
,
Puy
H
,
Robreau
AM
, et al
.
The penetrance of dominant erythropoietic protoporphyria is modulated by expression of wildtype FECH
.
Nat Genet
.
2002
;
30
(
1
):
27
-
28
.
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