The research team, led by investigators at Harbin Medical University and Northeast Agricultural University, used two complementary models of cell fate change: the reprogramming of mouse embryonic fibroblasts into induced pluripotent stem cells and the differentiation of embryonic stem cells into neuroectoderm. In both systems, disrupting SEC with KL-2, a peptidomimetic compound that selectively interferes with the interaction between the SEC scaffold protein AFF4 and the P-TEFb subunit Cyclin T1, dramatically impaired the transition. Crucially, the compound had no effect on the survival or proliferation of fibroblasts or stem cells under steady-state conditions, indicating that SEC is dispensable for maintaining a cell’s existing identity but indispensable for building a new one.

Timing proved to be everything. When the researchers inhibited SEC during the early days of reprogramming, the efficiency of induced pluripotent stem cell colony formation collapsed, and cells remained trapped in a mesenchymal state, never acquiring the epithelial morphology that marks successful reprogramming. RNA sequencing at day four revealed that more than half of the differentially expressed genes were downregulated, including core reprogramming factors such as Klf4 and Myc, along with cell cycle genes like Orc1 and pluripotency-associated genes such as Sall1. The downstream consequences were severe: cells accumulated in the G0/G1 phase, spindle structures became multipolar and abnormal, and karyotype analysis showed widespread chromosome number abnormalities in daughter cells.

To understand how SEC controls these genes, the team turned to the biophysics of transcription. After RNA polymerase II initiates transcription, it typically pauses 20 to 100 nucleotides downstream of the transcription start site, awaiting a release signal before productive elongation begins. Using published RNA polymerase II ChIP-seq datasets, the researchers quantified pause dynamics with two complementary metrics: the Traveling Ratio, which compares promoter-proximal to gene-body polymerase occupancy, and a two-dimensional Traveling Matrix method that simultaneously maps changes at both regions. Their analysis showed that early-activated genes like Klf4 and Myc carry pre-established paused polymerase even before reprogramming begins, and that reprogramming triggers their rapid release. In contrast, Oct4 and Sox2 lack pre-paused polymerase and instead acquire pause and release in a coupled, sequential manner during the mid-late stage.

CUT&Tag experiments confirmed that early SEC inhibition caused polymerase to pile up at the promoters of Klf4 and Myc while depleting from their gene bodies, a signature of failed pause release. ChIP-qPCR further showed reduced Ser2 phosphorylation of the polymerase C-terminal domain, the hallmark of productive elongation, and elevated pause indices at both loci. Ethynyl uridine incorporation assays demonstrated a global collapse in nascent RNA synthesis after SEC disruption, while overexpression of the SEC component ELL boosted it. The picture that emerged is one in which SEC acts as the trigger for the first transcriptional wave of reprogramming by liberating polymerase that was already parked at the most critical genes.

The most striking discovery, however, lay beyond the canonical mechanism. SEC is classically understood to promote pause release through P-TEFb-mediated phosphorylation of the polymerase C-terminal domain and the pause factors DSIF and NELF. But the researchers noticed that more than 40 percent of SEC target transcripts carry N6-methyladenosine, or m6A, the most abundant internal modification on eukaryotic messenger RNA. In Drosophila, m6A had already been shown to promote pause release, but whether the same held true in mammals was unknown. When the team inhibited SEC early in reprogramming, global m6A levels dropped sharply, as measured by RNA dot blot, ELISA, and the antibody-independent GLORI-seq method, which converts unmodified adenosines to inosines for single-nucleotide quantification. More than 23,000 m6A sites showed decreased modification, and the classic DRACH motif was enriched among the affected peaks, confirming their identity as bona fide m6A marks.

Using metabolic labeling with 4-thiouridine to isolate newly transcribed RNA, the researchers showed that SEC regulates m6A deposition co-transcriptionally. The single-base SELECT assay revealed that SEC inhibition significantly reduced m6A at specific sites in nascent Klf4 and Myc transcripts, including the promoter-proximal A701 site and gene-body A855 site of Klf4, while leaving non-m6A control sites untouched. Molecular docking predicted a close interaction between the SEC component ELL and the m6A methyltransferase METTL3, and this was validated by co-immunoprecipitation and immunofluorescence co-localization. ChIP-qPCR demonstrated that METTL3 and ELL co-occupy the promoters of Klf4 and Myc, and that SEC inhibition evicts both from these loci without changing total METTL3 protein levels. More than half of the transcripts losing m6A after SEC inhibition overlapped with those affected by METTL3 knockout, pointing to a shared regulatory pathway.

Functional experiments sealed the argument. Inhibiting METTL3 with the selective inhibitor STM2457 during the early stage of reprogramming reproduced the effects of SEC disruption: Klf4 and Myc expression fell, polymerase accumulated at their promoters, Ser2 phosphorylation declined, and reprogramming efficiency collapsed. Intriguingly, the study also uncovered a stage-specific duality: while early METTL3 inhibition was catastrophic for reprogramming, inhibition during the mid-late stage actually enhanced colony formation, suggesting that m6A plays opposing roles at different phases of the process. This may explain why previous studies have reported conflicting results about METTL3’s role in pluripotency. Most decisively, combined inhibition of SEC and METTL3 produced no additional increase in polymerase pausing beyond either treatment alone, and METTL3 overexpression could not rescue pause release when SEC was disrupted — evidence that the two operate in a single pathway, with SEC providing the scaffold that recruits METTL3 to specific loci.

The team then asked whether the same logic governs normal development. During retinoic acid-induced differentiation of embryonic stem cells, SEC inhibition selectively impaired the neuroectoderm lineage while leaving mesoderm and endoderm differentiation largely intact. Neural genes such as Nes and Tubb3 showed increased promoter-proximal pausing and reduced Ser2 phosphorylation upon SEC disruption, and global m6A levels again declined. STM2457 treatment similarly blocked neural marker acquisition, and reanalysis of published NET-seq data from METTL3 knockout cells revealed stalled nascent transcripts at the promoters of Nes and Tubb3. The authors propose that the functional divergence between SEC and the related elongation factor BRD4, which is known to drive mesendoderm specification, may act as a molecular determinant of lineage choice.

The implications extend well beyond the culture dish. Because SEC is dispensable for cell survival under steady-state conditions but essential whenever a cell must adopt a new identity, the findings suggest it may be a common driver of cell fate transitions throughout life, including embryonic development, tissue regeneration, and the initiation and progression of diseases such as cancer. The discovery that a transcription elongation complex doubles as a scaffold for RNA methylation adds a new layer to the growing intersection between the epitranscriptome and the transcriptional machinery, and hints that m6A deposited through the SEC-METTL3 pathway may act on R-loops to resolve paused polymerase. If confirmed, targeting this pathway could open new therapeutic avenues for conditions in which cell identity goes awry, from tumorigenesis to infertility.

Subject of Research: Role of the Super Elongation Complex and METTL3-mediated m6A modification in regulating RNA polymerase II pause release during cell identity transitions

Article Title: SEC Mediates m6A Deposition and Transcription Pause Release to Drive Cell Identity Transition

Article References: Zhang, Z., Xu, J., Wu, Y., Qu, Y., Hu, X., Sun, Y., Wu, Y., Liu, Z., Wang, J., & Lei, L. (2026). SEC Mediates m 6 A Deposition and Transcription Pause Release to Drive Cell Identity Transition. Advanced Science, Article e78131. https://doi.org/10.1002/advs.78131

Image Credits: AI Generated

DOI: 10.1002/advs.78131

Keywords: Super Elongation Complex, m6A, METTL3, RNA polymerase II, transcription pause release, iPSC reprogramming, embryonic stem cells, neuroectoderm differentiation, Klf4, Myc, cell fate transition, epitranscriptomics

A research team led by Javier M. Di Noia at the Institut de Recherches Cliniques de Montréal, working with colleagues including François Robert and Nicole J. Francis, set out to find what distinguishes the handful of genomic regions that AID actually mutates from the thousands it merely visits. Their search converged on two proteins with a storied history in cancer biology: MLLT1, also known as ENL, and its close relative MLLT3, also known as AF9. Both are components of the super elongation complex, a molecular machine that helps RNA polymerase II push through genes during transcription. Crucially, both proteins carry YEATS domains, which are so-called histone readers, modules that recognize and bind specific chemical tags on histone proteins, the spools around which DNA is wound. This ability to read chromatin marks positions MLLT1 and MLLT3 at active, acetylated regions of the genome, including enhancers and super-enhancers.

The team’s first and most striking finding came from removing these proteins. When they deleted both MLLT1 and MLLT3 from mouse B cells, every AID-dependent mutagenic process ground to a halt. Class-switch recombination, the process that lets antibodies change their effector function, was abolished. Somatic hypermutation, which introduces point mutations into antibody variable regions to sharpen their binding, disappeared entirely. In functional terms, the double-knockout cells looked as if AID itself had been deleted, even though the enzyme was still present and expressed at normal levels. Single knockouts produced partial defects, revealing that the two proteins act redundantly, with MLLT1 playing the dominant role in mice. The effect was not limited to engineered cell lines: conditional knockout mice lacking MLLT1 or MLLT3 in their B cells showed impaired antibody class switching, and chemical inhibitors targeting the YEATS domains of both proteins suppressed immunoglobulin diversification in both mouse and human B cells.

A critical clue came from mapping where MLLT1 and MLLT3 sit in the genome. Using chromatin immunoprecipitation sequencing with spike-in normalization, the researchers found that the genomic regions that AID mutates, in both mouse and human B cells, are precisely marked by unusually high occupancy of both proteins, a signature the authors denote MLLT1/MLLT3-high. This was not a loose correlation. When the team ranked genes by MLLT1 or MLLT3 signal and stratified them at an inflection point separating high from moderate occupancy, AID targets clustered overwhelmingly in the high-occupancy group. The pattern held across B cell lines, primary mouse B cells, and human lymphoma cell lines, and it extended to the super-enhancers that aberrant somatic hypermutation frequently strikes in diffuse large B cell lymphoma. The most frequently mutated loci in a catalogue of 610 lymphoma cases correlated with MLLT1 and MLLT3 enrichment, linking the mechanism directly to human disease.

One obvious explanation for the loss of AID activity in the knockout cells would be that MLLT1 and MLLT3 are simply needed to transcribe the target genes, and without them the antibody loci fall silent. The researchers tested this rigorously and found it was not the case. Transcriptional changes after deleting both readers were modest. Measurements of nascent transcription by TT-seq, along with analyses of RNA polymerase II pausing and elongation indices, showed that the antibody germline transcripts and AID’s own expression were largely preserved. The dramatic collapse in mutagenesis could not be accounted for by changes in how much or how fast the relevant genes were being transcribed. Whatever MLLT1 and MLLT3 were doing for AID, it was something beyond their canonical role in transcriptional elongation.

The mechanistic picture that emerged is one of local concentration rather than global recruitment. The researchers showed that MLLT1 and MLLT3 are dispensable for tethering AID to chromatin in general; even without them, AID still associates broadly with the genome. What the readers provide is local enrichment: they concentrate AID specifically in the regions just downstream of promoters, within roughly two kilobases of the transcription start site, which is exactly the window in which somatic hypermutation operates. Both proteins physically bind to AID, and chromatin immunoprecipitation of tagged AID revealed that its signal at target regions drops sharply in cells lacking both readers. In other words, AID can touch the genome anywhere, but only where MLLT1 and MLLT3 pile up does it reach the concentrations needed to inflict mutations.

The most conceptually adventurous part of the study concerns how MLLT1 achieves this concentration. Beyond its structured YEATS domain, MLLT1 carries a large intrinsically disordered region, a floppy protein segment that lacks a fixed three-dimensional shape. Such regions are hallmarks of proteins that drive phase separation, the process by which certain molecules coalesce into droplet-like condensates, concentrating specific partners much like oil droplets form in water. The team purified MLLT1 and MLLT3 proteins and showed in vitro that MLLT1 forms droplets that are sensitive to the aliphatic alcohol 1,6-hexanediol and to high salt, treatments that disrupt many condensates. When they incubated these droplets with extracts from cells expressing fluorescently tagged AID, AID preferentially partitioned into the MLLT1 condensates. Live-cell imaging and partition-coefficient measurements in cells reinforced the same conclusion: AID is drawn into MLLT1-rich condensates, and this depends on AID’s own interaction surface, since a point mutation in AID, R174E, reduced its partitioning and altered its protein-proximity network as measured by BioID proximity labeling.

The functional tests were decisive. Swapping the intrinsically disordered regions between MLLT1 and MLLT3 showed that MLLT1’s disordered region is what gives it its dominant role in promoting condensates that concentrate AID in mice. Most strikingly, when the researchers artificially fused AID directly to MLLT1 or to MLLT3, forcing the enzyme into proximity with the readers regardless of natural interactions, class-switch recombination and mutagenesis were restored in cells lacking both endogenous proteins. This rescue experiment demonstrates that spatial confinement with MLLT1 or MLLT3 is not merely correlated with AID activity but is sufficient to license it, arguing that the local concentration of AID is the rate-limiting ingredient for mutagenesis at any given locus.

The implications ripple outward in several directions. For basic immunology, the work solves a long-standing puzzle by proposing a licensing model: transcription opens the door, but MLLT1/MLLT3-high chromatin determines which rooms AID is allowed to enter and vandalize. For cancer biology, it offers a mechanistic explanation for why lymphomas repeatedly acquire aberrant mutations at super-enhancers, which are precisely the structures richest in super elongation complex components and their histone-reading modules. Intriguingly, MLLT1 and MLLT3 are themselves established oncogenic players, most famously as fusion partners of MLL in acute leukemia, and small-molecule chemical probes against their YEATS domains already exist. The study raises the possibility that such inhibitors, which suppressed antibody diversification in the current experiments, could in principle modulate AID’s off-target mutagenesis in disease contexts. At the same time, the findings suggest a caution: any therapy that disrupts these condensates might impair the antibody diversification that vaccines and immune memory depend on. What began as a question about a single mutagenic enzyme has ended up connecting antibody immunity, transcriptional condensates, and lymphoma genetics into one coherent physical model, and it is likely to keep both immunologists and cancer biologists busy for years to come.

Subject of Research: Mechanism of locus-specific targeting of the mutagenic enzyme AID by the histone readers MLLT1 and MLLT3 in B cells

Article Title: Histone readers MLLT1 and MLLT3 concentrate AID to confer locus specificity

Article References: Seija, N., Gannon, S., Häfner, K. A., Gemeinhardt, T. M., Ridani, J., Alvarez, D., Provencher, M., Subramani, P. G., Poitras, C., Piskor, E.-M., Möröy, T., Vonniessen, N., Mazer, B., Navarrette, M. A., Francis, N. J., Robert, F., & Di Noia, J. M. (2026). Histone readers MLLT1 and MLLT3 concentrate AID to confer locus specificity. Nature. https://doi.org/10.1038/s41586-026-11087-1

Image Credits: AI Generated

DOI: 10.1038/s41586-026-11087-1

Keywords: AID, MLLT1, MLLT3, somatic hypermutation, class-switch recombination, histone readers, super elongation complex, phase separation, condensates, B cell lymphoma, immunoglobulin genes, chromatin