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Updated: Feb 22, 2026

A Novel Microdissection Approach to Recovering Mycobacterium tuberculosis Specific Transcripts from Formalin Fixed Paraffin Embedded Lung Granulomas

A Novel Microdissection Approach to Recovering Mycobacterium tuberculosis Specific Transcripts from Formalin Fixed Paraffin Embedded Lung Granulomas

Published on: June 5, 2014

Genómica libre de células revela principios regulatorios fundamentales del ciclo de transcripción de Mycobacterium

Ruby Froom¹, Michael B Wolfe², Kelly N Eckartt³

¹Laboratory of Molecular Pathogenesis, The Rockefeller University, New York, NY 10065, USA; Laboratory of Host-Pathogen Biology, The Rockefeller University, New York, NY 10065, USA.

|February 20, 2026

Abstract:

Tiers of gene regulation govern cellular life. The intrinsic activities of RNA polymerase (RNAP) constitute a primary tier, while direct modulation by accessory transcription factors (TFs) constitutes a secondary tier. Cellular signaling cascades and feedback loops generate tertiary and higher-order tiers. Dissecting gene regulation requires distinguishing direct TF targets at the genome scale from indirect network effects. A major obstacle is the lack of tools to interrogate transcription machineries from difficult-to-culture microbes-such as pathogens, commensals, and environmental species-at the genome scale. Here, we introduce cell-free genomics (CFG), an empirical approach that identifies the direct targets of RNAP and TFs and systematizes their transcriptional effects. We demonstrate the efficacy of CFG by characterizing global and essential transcription initiation (CRP and holo-WhiB1) and elongation-termination factors (NusA and NusG) from the deadly pathogen, Mycobacterium tuberculosis. CFG expands our understanding of transcription principles and is broadly extensible to other perturbations and diverse species.

Palabras clave:

Mycobacterium tuberculosis ARN polimerasa genómica libre de células transcripción a escala genómica factores de transcripción regulación de la transcripción

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