(375 Aa) Was Cloned Into the Pym-IRES-Neo Vector and Various Mutations and Deletions of LDB1 Were Created (By Site Directed Mutagenesis) in This Background

Supplementary Material

Supplementary Materials and Methods

Plasmid construction The HA tagged full length LDB1 cDNA (375 aa) was cloned into the pYM-IRES-Neo vector and various mutations and deletions of LDB1 were created (by site directed mutagenesis) in this background. The shRNA target sequence located in the LID coding sequence of Ldb1 cDNA was altered without changing the amino acid coding sequence of LDB1 protein. The shRNA target sequence is underlined and mutated nucleotides are bolded and underlined:

Wild type: cgacgaggacagctttaacaa Mutant: tgatgaagattcattcaataa

The dimerization domain of LDB1 (amino acids 1-200) was deleted and the K365R (AAA to CGA) mutation at 3’ end of Ldb1 cDNA was introduced to stabilize the protein thus created. Deletions in the LDB1 DD included sequences encoding amino acids 31 to 43 (Δ1), 58-62 (Δ2), 86 to 97 (Δ3) or 173 to 192 (Δ4/5). DD-only proteins were created by deletion of LDB1 C- terminal sequences encoding amino acids 201-375. Further details of cloning are available upon request. For the LMO2 fusion (2xLMO2), LMO2 cDNAs were tethered in the sense orientation through a flexible linker (22-aa polypeptide [GT(GGGS)4GGGT]) (Wang et al., 2008).

Co-immunoprecipitation Protein complexes were precipitated with anti-HA agarose (Sigma, A2095) overnight at 4oC. Agarose was washed 3 times with IP100 buffer (Brand et al., 2004). Bound proteins were eluted with HA peptides (Sigma) and analyzed by western blot. For LDB1/FOG1 experiments, the protein complexes were precipitated overnight at 4oC by antibodies against LDB1 or FOG1 and Dynabeads® Protein G (Life Technologies, 10004D), then washed once with IP500 and two times with IP100 and eluted as described (Brand et al., 2004).

RNA-seq library construction, sequencing and computational analysis RNA-seq libraries were constructed for induced MEL WT cells, LDB1 KD cells and LDB1 KD cells expressing either LDB1 FL or LDB1Δ4/5 using TruSeq RNA Sample Prep Kit V2 (Illumina) according to the manufacturers protocol. Three biological replicates of each cell type were sequenced on a HiSeq 2000. Illumina TruSeq adapters from the 51-bp single-end reads were clipped using cutadapt v.1.1 with default parameters (Martin, 2011). Clipped reads were then mapped to the UCSC mm9 assembly with TopHat v1.4.1 (Trapnell et al., 2009) using default parameters with the additional parameter--butterfly-search. The number of uniquely mapped reads for each library ranged from 13 to 55M, with a median of 24M. Reads mapping to repetitive regions defined by the UCSC RepeatMasker track were removed from further analysis. Reads were counted in exons of the Ensembl release 67 GTF for mm9, using HTSeq 0.5.3p9. Differential expression of genes for all pairwise comparisons was assessed with DESeq v1.10.1 (Anders and Huber, 2010).

We defined genes repressed by LDB1 KD as those that, in the DESeq analysis, had an adjusted P value < 0.05 and a log2 fold change < -1 in gene expression between LDB1 KD cells and WT. To define rescued genes, we first used the variance-stabilized transformation (VST) in the DESeq package to obtain comparable scaled counts for all experiments. VST-scaled counts for replicates were averaged to obtain per-treatment values. Then, rescued genes were defined as those LDB1 KD repressed genes with equal or greater expression in LDB1 KD cells expressing LDB1 FL than WT, or, if genes have lower expression in LDB1 KD cells expressing LDB1 FL than WT, whose expression difference between WT and LDB1 FL expressing cells was less than half the expression difference between WT and LDB1 KD cells. More precisely, a gene was defined as rescued if it was an LDB1 KD repressed gene and satisfied the condition:

((WT - LDB1 FL) < 0) OR ((WT - LDB1 FL) < (0.5 * (WT - LDB1 KD)) AND ((WT - LDB1 FL) > 0)), where "WT", "LDB1 FL", and "LDB1 KD" are the averaged, VST- scaled counts for each treatment.

Next, of the genes that were rescued by LDB1 FL, we defined a gene to be 4/5-dependent if it was repressed in LDB1 KD cells expressing LDB1Δ4/5 compared to LDB1 KD cells expressing

LDB1 FL (that is, log2 fold change < -1 and adjusted P value < 0.05). Otherwise, it was defined as 4/5-independent. Since the transcribed sequence for LDB1 differs between LDB1 delta 4/5 and LDB1 FL, we removed LDB1 from consideration in the downstream RNA-seq rescue and 4/5-dependence analysis. Finally, genes were defined to be LDB1 bound if there was an LDB1 peak in induced MEL cells within 1kb of the start position of the gene, inside gene body or within 1 kb of the end position of the gene ((Soler et al., 2010); BED file downloaded from the PSU genome browser, http://main.genome-browser.bx.psu.edu). The OMIM database was downloaded from a URL provided by omim.org (September 2013). A combination of Ensembl's BioMart (mapping human HGNC to orthologous mouse Ensembl IDs) and the "mousecorr" field in the OMIM database were used to identify human homologs of mouse genes. An OMIM entry was considered orthologous in mouse if one of these methods successfully mapped the HGNC human gene symbol to a mouse Ensembl gene.

Primers ChIP primers Alas2 + 2kb Fw AGGGCAGGACTTTGCCTCTAATCT Alas2 + 2kb Rev AGATGTCCCAGTTCCTGCAGGTTT GypA Fw GTCCTCGCAGTTATGCAGAC GypA Rev GGCCTCTATCCGTTGACACA α-globin HS26 Fw TGACCATAGTCAACAGCAGGT α-globin HS26 Rev GCTCGTTCAAGCATCTCCAT A730036l17Rik Fw TCAAAACTCTGCCTCCTCCC A730036l17Rik Rev GATAGGTGAAAAGGCGCCAG Kctd14 Fw CTTAGAGTTCCTCAGGGGCG Kctd14 Rev GGGTACACAACGCTGTCTTG Ubash3a Fw TTTTCTTCACAGCCTCAGCC Ubash3a Rev CCATGTCTTCCTGCTTGCTG CD24a Fw AACAAAGGAAACTTGGGCCG CD24a Rev CTCTGGCACAGCTAGGGTTT Treml1 Fw TGTCAGCCTCGATGGATAGC Treml1 Rev GCTGGGCAGTAGTAGGTTCT Ypel3 Fw CAGCCCTTTCTCTCCTTCCA Ypel3 Rev TCCCAGCCGTTGTCTTTGAT qRT-PCR primers α-globin Fw GCTGAAGCCCTGGAAAGGAT α-globin Rev GGCTTACATCAAAGTGAGGAAAGT Alas2 Fw CCATCTTAAGGCAACCAAGGC

Alas2 Rev ACAGCATGAAAGGACAATGGC GypA Fw ATTCATGTCTCAACTTATCACA GypA Rev CCAATGTGTGGTGAGACAGGCT A730036l17Rik Fw GCATTCAGGACTTGCTCTGG A730036l17Rik Rev GTCCTCACACTTGGCTTGTG Kctd14 Fw ATGCCACAGATCTTCGGTGA Kctd14 Rev AGGACCTCCAGGTTTTCTCTG Ubash3a Fw GCCAGTAAAGACGCTGACAC Ubash3a Rev ACCTCTTCCTGGAAAGCTCG CD24a Fw AGTAACGCTACCACCAGAGG CD24a Rev GTTTCCTGGCCTGAGTCTCT Treml1 Fw GATCCACCATCAAGCGAACC Treml1 Rev TCCTGGGAAGACAACTGTGG Ypel3 Fw CATGTGGCTTCAGCCTGG Ypel3 Rev GTACAGGAGCTGGGTCCTTC Neo Fw TCGACGTTGTCACTGAAGCG Neo Rev GGATACTTTCTCGGCAGGAGC Ldb1’UTR Fw GGGGTACTCATGTGGATGCCTGT Ldb1 3’UTR Rev ACCCAGAACCTGGGGTAAGAACG Hprt Fw TGACACTGGTAAAACAATGCAAACT Hprt Rev AACAAAGTCTGGCCTGTATCCAA All other primers have been described (Song et al., 2007; Handoko et al., 2011).

Antibodies

Antibodies used for western blots were against HA (Roche, 11867423001), Tubulin (Sigma, T5168), LDB1 (Santa Cruz Biotechnology, sc-11198), TAL1 (Santa Cruz Biotechnology, sc- 12984), FOG1 (Santa Cruz Biotechnology, sc-9361), ETO2 (Santa Cruz Biotechnology, sc- 9739), GATA1 (Santa Cruz Biotechnology, sc-265), LMO2 (R&D, AF2726) and appropriate HRP-fused secondary antibodies from Santa Cruz Biotechnology or Goat TrueBlot®: Anti-Goat IgG HRP (Rockland Immunochemicals, 18-8814-33).

Antibodies from Santa Cruz Biotechnology were used in ChIP for GATA1 (sc-1233), BRG1 (sc- 10768), Pol II (sc-899), FOG1 (Santa Cruz Biotechnology,sc-9361), MTA2 (sc-9474), HDAC1 (sc-7872), CBP (sc-369) and LAMB1 (sc-6217). Other antibodies were against AcH3 (Millipore, 06-599), H3 (Abcam, ab1791), and HA (Millipore, 05-904).

For immuno-staining antibody against LAMB1 (Santa Cruz Biotechnology, sc-6216) and secondary anti-Goat DyLight 594 (Jackson ImmunoResearch, 805-515-180) were been used.

Supplementary References

Anders S, Huber W. 2010. Differential expression analysis for sequence count data. Genome. Biol. 11: R106.

Brand M, Ranish JA, Kummer NT, Hamilton J, Igarashi K, Francastel C, Chi TH, Crabtree GR, Aebersold R, Groudine M. 2004. Dynamic changes in transcription factor complexes during erythroid differentiation revealed by quantitative proteomics. Nat. Struct. Mol Biol. 11: 73-80.

Handoko L, Xu H, Li G, Ngan CY, Chew E, Schnapp M, Lee CW, Ye C, Ping JL, Mulawadi F et al. 2011. CTCF-mediated functional chromatin interactome in pluripotent cells. Nat Genet 43: 630-638.

Martin M. 2011. Cutadapt removes adaptor sequences from high-throughput sequencing reads. EMBnet. journal 17: 10-12.

Soler E, Andrieu-Soler C, de Boer E., Bryne JC, Thongjuea S, Stadhouders R, Palstra RJ, Stevens M, Kockx C, van IW et al. 2010. The genome-wide dynamics of the binding of Ldb1 complexes during erythroid differentiation. Genes Dev 24: 277-289.

Song S-H, Hou C, Dean A. 2007. A positive role for NLI/Ldb1 in long-range -globin locus control region function. Mol. Cell 28: 810-822.

Trapnell C, Pachter L, Salzberg SL. 2009. TopHat: discovering splice junctions with RNA-Seq. Bioinformatics. 25: 1105-1111.

Wang J, Levasseur DN, Orkin SH. 2008. Requirement of Nanog dimerization for stem cell self-renewal and pluripotency. Proc. Natl. Acad. Sci U. S. A. 105: 6326-6331.

Supplementary Figure Legends Figure S1. LDB1 FL fully rescues β-globin expression in induced LDB1 KD MEL cells. (A) Diagram of LDB1 FL cDNA expressed in induced LDB1 KD MEL cells. Colored rectangles: purple, HA tag; green, DD domain; orange, nuclear localization signal (NLS); yellow, LID. (B) Western blot of protein extracts from three induced LDB1 FL-expressing LDB1 KD MEL cell lines with LDB1 or HA antibodies. α-tubulin served as loading control. (C) β-globin and

endogenous LDB1 gene expression in three induced LDB1 FL-expressing LDB1 KD MEL cell lines. Induced cells containing an empty vector (Empty) served as a control. Expression in induced WT MEL cells was set to 1. Error bars indicate SEM, N=3 biological replicates.

Figure S2. K365R mutation stabilizes LDB1ΔDD. (A) Western blotting of protein extracts from LDB1 KD MEL cells expressing LDB1 FL and LDB1ΔDD with antibodies against HA. α- tubulin served as loading control. (B) Expression level of transgenic RNA measured by real-time PCR with primers to neo-resistant gene. Expression level in LDB1 FL was set to 1. Error bars indicate SEM, N=3. (C) Western blotting of protein extracts from LDB1 KD MEL cells expressing LDB1ΔDD incubated at 30o C overnight or treated with 26S proteasome inhibitor MG132 with antibodies against HA. α-tubulin served as loading control. (D) Western blotting of protein extracts from LDB1 KD MEL cells expressing LDB1 FL, LDB1 FL K365R, LDB1ΔDD and LDB1ΔDD K365R with antibodies against HA. α-tubulin served as loading control.

Figure S3. Heterologous dimerizing or physical tethering of LMO2 fails to rescue activation of β-globin gene expression. (A) Expression level of the β-globin gene in induced MEL LDB1 KD cell lines expressing LDB1 FL, LMO-Lex, 2xLMO2 or GATA1-DD. (B) Locus-wide crosslinking frequencies analyzed by 3C-qPCR using the LCR HS2 as the anchor fragment (red vertical bar). Relative crosslinking frequencies observed in induced LDB1 KD MEL cell lines expressing LDB1 FL, LMO-DD, LMO-Lex, 2xLMO2 or GATA1-DD or containing an empty expression vector are shown. The X-axis shows the genomic coordinates of the interacting fragments and globin gene locations in the locus. Yellow triangles mark BglII restriction sites. Error bars in both panels indicate SEM, N=3 biological replicates.

Figure S4. Conserved and structural elements in DD domain of LDB1. Alignment of amino acid sequences of LDB1 homologs from M. musculus, D.melanogaster and C.elegans. Yellow color marks coincidence in all sequences, blue – in two, green - conserved substitutions. Cylinders mark potential helical regions.

Figure S5. Inducible deletion of endogenous LDB1 in E14.5 fetal liver cells. (A) Experimental strategy of endogenous Ldb1 deletion and overexpression of transgenic versions of

LDB1. (B) Ldb1 deletion in E14.5 Ldbfl/fl fetal liver cells with and without Mx1CreDNA was analyzed by PCR of genomic DNA for the presence of the Mx1Cre, Ldb1 deleted allele (Ldb1Δ) and floxed allele (Ldb1fl) before and after IFN-β treatment. (C) Expression level of Ldb1 and β- globin genes in Mx1Cre Ldb1fl/fl and control Ldb1fl/fl E14.5 fetal liver cells after 3 days of IFN-β treatment. Expression level in control cells was set to 1. Error bars indicate SEM, N=3 biological replicates.

Figure S6. DD4/5 region is not required for LDB1 dimerization. (A) Diagram of cDNAs of DD and deleted versions without the LDB1 C-terminal LID that were expressed in wild type MEL cells. Designations are the same as Figure 2A. (B) Western blots of protein extracts from representative wild type MEL cells expressing the indicated proteins. α-tubulin served as loading control. (C) Immunoprecipitation (IP) was performed with an antibody to the HA tag using nuclear extracts from induced WT MEL cells expressing the DD (left panel). IP material was analyzed by western blot with antibodies to LDB1, LMO2 and TAL1. The DD interacted with endogenous LDB1 and through this interaction with LDB1 complex members LMO2 and TAL1. Antibodies to the HA tag and ETO2 served as positive and negative controls. IP and western blotting for cells expressing DDΔ1 or DDΔ4/5 were performed in the same way (right panels). (D) β-globin expression in induced MEL cells expressing DD, DDΔ1 or DDΔ4/5 compared to induced WT MEL cells (set to 1). Error bars indicate SEM, N=3 biological replicates.

Figure S7. Association of LAMB1 with the β-globin locus. ChIP was performed with a LAMB1 antibody and chromatin from uninduced LDB1 KD MEL cells expressing LDB1 FL and induced LDB1 KD MEL cells expressing LDB1 FL, LDB1Δ4/5 or LMO-DD. LAD served as positive control and Trem151a served as a negative control (Handoko et al., 2011). Error bars indicate SEM, N=3 biological replicates. Values are compared to the value for uninduced LDB1 KD cells expressing LDB1 FL and * indicates P<0.05 by Student’s t-test.

Figure S8. Failure to recruit BRG1 affects DNase I sensitivity. Nuclei from induced LDB1 KD MEL cells expressing LDB1 FL, LDB1Δ4/5, LMO-DD or containing an empty expression vector were digested with increasing amounts of DNase I (from left to right: 15, 30, 45 U). DNase I sensitivity was normalized by signal from coding region of actB gene. Values are

7 compared to the value for LDB1 FL and * indicates P<0.05 by Student’s t-test. (A) HS2 region DNase I sensitivity. (B) β-globin promoter DNAseI sensitivity. Error bars in both panels indicate SEM, N=3 biological replicates.

Figure S9. RNA-seq analysis of genes directly regulated by LDB1 in induced MEL cells. (A) Strategy to identify genes that are directly regulated by LDB1 and sensitive to the presence of the 4/5 region in the DD of LDB1. Bar plots show representative expression profiles of genes in each class (see Supplementary Materials and Methods for details). The solid horizontal line in the second panel indicates one-half the expression difference between WT and Ldb1 KD. (B) Effect of knocking down Ldb1 on the 94 LDB1-occupied 4/5 dependent genes and 148 LDB1- occupied 4/5 independent genes. Genes are ranked by log2 fold change in Ldb1 KD vs WT, and erythroid genes are highlighted in red.

Figure S10. UCSC genome browser screenshots of selected LDB1-dependent genes. RNA- seq signal (top) and induced MEL cells ChIP-seq signal and peaks (bottom) over representative genes that are 4/5-independent (A), 4/5-dependent (B) and 4/5-dependent with LDB1 only peak (C). Each RNA-seq track represents combined coverage for all replicates, divided by the number of million reads in the merged library (tags per million, TPM). Induced MEL cells ChIP-seq data (Soler et al., 2010), were downloaded from the PSU genome browser ( http://main.genome- browser.bx.psu.edu). As described at http://main.genome-browser.bx.psu.edu/cgi- bin/hgTrackUi?g=grosveldTfbs&db=mm9, ChIP-seq signal is in read depth, and peaks were called with MACS. Bottom point equals zero.

Figure S11. OMIM database analysis. (A) Strategy to identify disease-associated human homologs of mouse LDB1-activated and occupied genes. (B) Enrichment of disease-associated genes among LDB1 4/5-dependent, LDB1 4/5-independent and all other human genes with mouse homologues. The number of genes in each group was compared with the group of all human genes using a Fisher’s exact test and the P values are shown. (C) Blood related diseases among LDB1 4/5-dependent and LB1 4/5-independent disease-associated genes.

Krivega_FigS1

A LDB1 FL DD NLS LID

B HA-LDB1 FL αLDB1 αHA αTub

β-globin Endogenous Ldb1 C 1.4 1.2

n 1 o 0.8 0.6

Expressi 0.4 0.2 0 LDB1 FL Krivega_FigS2

A B 1.5 l leve

1 Transgenic αHA mRNA mRNA

0.5 level

αTub Relative 0

C D

αHA αHA αTub

LDB1ΔDD αTub Krivega_FigS3

A 1.4 1.2 1 0.8 expression

0.6

bin 040.4 o gl ‐

 0.2 0

HS2 12 Empty 10 LDB1 FL LMO‐Lex 8 2xLMO2 6 GATA‐DD slinking frequency

cros 4

Relative 0 103659323 103679323 103699323 103719323 Chr 7

βmin βmaj βH1 εy Krivega_FigS4

1 C.elegans D.melanogaster M.musculus 2 3

C.elegans D.melanogaster M.musculus 4 5

C.elegans D.melanogaster M.musculus A Cre Virus Krivega_FigS5 induction infection

Time (h) 0 24 72

B - - ++IFN-β Ldb1fl Ldb1∆ Cre + - + - + - Cre Mx1Cre Ldb1 primers

C 1.2

sion 080.8 fl/fl Ldb1

expres 0.6

fl/fl Mx1CRE Ldb1 0.4

Relative 0.2

0 Ldb1 β-globin Krivega_FigS6

A B 1 2 3 45 DD αΗΑ 2 3 45 DD∆1 1 2 3 DD∆4/5 αTub

D C 1.2 Input Input 1 DD DDΔ1 αLDB1 αLDB1 0.8 αHA

αLMO2 Expression 0.6 Input

αTAL1 bin 0.4 DDΔ4/5 o αETO2 αLDB1 gl 0.2 β‐ αHA αHA 0 WT MEL cells induced DD DDΔ1DDΔ4/5 WT Krivega_FigS7

LAMB1 occupancy

0.35* * 0.3

0.25 LDB1 FL uninduced ment 0.2 LDB1 FL induced

0.15 LDB1 ∆4/5 induced

Enrich LMO-DD induced 0.1 * * 0.05

0 LADTrem151a HS2 β Krivega_FigS8

ABHS2 β promoter 2 8 y

6 1.5 Empty Empty * sensitivit * * * 4 Ldb1LDB1 FLFL 1 * * * Ldb1LDB1 FLFL * * * Ldb1LDB1 ΔΔ4/54 Ldb1LDB1 ΔΔ4/54 DNase I

DNaseI sensitivity 2 0.5 LMO‐DD ive LMO‐DD tive t

0 Rela 0 Rela 15U 30U 45U 15U 30U 45U Krivega_FigS9

Slamf1 A730036I17Rik 2010016I18Rik Gm15623 A B Cnnm1 Spock2 Csf2rb2 ENSMUSG00000085092 Rnf43 ENSMUSG00000086809 1521 genes Gm9320 Adamts13 Btn1a1 F630028O10Rik ENSMUSG00000090473 Ankrd61 repressed by LDB1 KD Otop2 Ptprn Col4a2 4930417G10Rik Fat3 Msrb3 4930565N06Rik 6030468B19Rik Treml1 Gm15024 Hbb-b1 Slc25a35 Slc4a1 Ubash3a A930005I04Rik Gm16253 Rbp1 6530409C15Rik BC049352 Sox6 WT Poln Snx32 Pcx Kctd14 Add2 Kcnd1 AY036118 Grm5

LDB1KD Rgs10 Ermap Ltbp2 2410066E13Rik Csf2rb Hecw1 Gypa Pfn4 Ppox Ssx2ip Siglec1 Hist1h1e Dapk2 Bbs7 Rab3il1 Tspan33 Il1r1 Trove2 Cd200r1 Acvr2a 496 genes Kctd11 Gm9766 Aqp9 Zfc3h1 LDB1-occupied, 4/5 dependent Arhgdib Rsbn1 LDB1-occupied, 4/5 independent rescued by LDB1 FL Adam33 L1cam Alas2 Tbc1d15 Hbb-b2 ENSMUSG00000065265 Tnik Pbx3 Rab40b Ypel2 Emilin2 Mblac2 or Scd1 Per1 Cpeb4 Yod1 Atf6 ENSMUSG00000085462 Spef1 Zfp110

WT WT Itga2b Mst1 Gadd45a Tspo2 A630001G21Rik Clcn5 Sdk2 Megf9 LDB1FL LDB1FL LDB1KD LDB1KD Alox5 C1galt1 Atp1b1 Gm15726 Thsd4 2900056M20Rik Fam3a Gpcpd1 Mxi1 Rabgap1l Rgs18 Fam123b Fgd6 Fbxl2 Ehd3 Itga4 Jhdm1d Dok3 Mybpc3 Tet2 Scube2 Rel 349 genes 147 genes D930015E06Rik Bcl2l13 Lrrc29 Ppp1r15b Pfkfb4 Ttc14 4/5-independent 4/5-dependent Gm10658 Xk ENSMUSG00000090409 Znrf2 Tmod1 Spopl Cd24a Lrig2 Rab20 Pgm2l1 Rabgef1 Ccdc15 Ypel3 Dnaja4 Apobec2 Cux1 AA986860 Nr4a2 Lims1 Abca5

WT WT Ncoa4 Rbm3 Atp2b4 Kdm6a Stx11 A930001N09Rik Dennd2d Tyk2

LDB1FL LDB1FL Clk3 Taf1d LDB1KD LDB1KD

LDB1Δ4/5 LDB1Δ4/5 Ppp6r2 Zfp516 Rhag Fam188a Capn2 Slc35a3 Rph3al Mospd1 Ppp1cb Rnf123 Plcb2 Zfp329 Dgka Cachd1 Fam46c Fam63b Arhgef3 Ufl1 Apc2 Nhlrc4 148 genes 93 genes Dnm2 Kifc2 Dusp10 Adcy7 Epb4.2 Bcl2 Capn5 Trio occupied by LDB1 occupied by LDB1 Htr2a Atg4c Klhl7 Nek7 Pkn2 Syt14 Tfdp2 Tgfbr1 4933431E20Rik Mpp5 Serinc3 Slc16a6 Ppp3ca Frs2 Unkl Rngtt Ppp1r12b Eps15 Ccdc167 Kif5b Vamp4 Btnl10 Pou2f1 Rint1 Dbt Bach1 Dpy19l1 Cdc25b Vopp1 Nr1d2 Wdr13 AW549877 Fgfr1op2 1300018J18Rik Abcg2 Pdlim5 Phf21b Pitpnc1 Golim4 Gab2 Zbtb41 Zranb2 Chd9 Dennd2c Lpin2 C8g 4632404H12Rik Eif4a2 Hps5 Ap3s1 Nlrp6 Plag1 1700037H04Rik Tnfaip8 Ern1 Gng12 Klhl24 -5-6-7 -1-2-3-4 Log2 fold change (KD / WT) Krivega_FigS10

2 kb A chr7:104599207-104608879 Kctd14 Kctd14 0.35 Kctd14 WT 0.35 LDB1 KD 0.35 LDB1 FL

RNA-seq(TPM) 0.35 LDB1Δ4/5 56 LDB1 56 GATA1 (depth)

ChIP-seq 56 TAL1 RepMask

5 kb B chr8:83016644-83036057 40 Gypa WT 40 LDB1 KD 40 LDB1 FL

RNA-seq(TPM) 40 LDB1Δ4/5 126 LDB1 126 GATA1 (depth)

ChIP-seq 126 TAL1 RepMask

2 kb C chr17:48498362-48507191 Treml1 Treml1 Treml1 Treml1 Treml1 0.25 WT 0.25 LDB1 KD 0.25 LDB1 FL

RNA-seq(TPM) 0.25 LDB1Δ4/5 48 LDB1 48 GATA1 (depth)

ChIP-seq 48 TAL1 RepMask Krivega_FigS11

p=.001

A B 35

30 LDB1-activated and occupied p=.93 4/5‐dependent mouse gene 25 4/5‐independent ated genes i 20 Human homolog all 15

Disease association 10 (OMIM base) 5 of disease assoc of disease % 0

Human disease-associated homologs from OMIM C 4/5-dependent 4/5-independent disease related genes disease related genes

blood related diseases

others